Datasets:

lanesket

/

r-asts

like 0

[](){expression}<LSEP>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){opts_chunk}<LEND>[](symbol){set}<LEND>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){#>}<LSEP>[argument 4; litteral](str){100%}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dispositionEffect}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dplyr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){tidyr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){lubridate}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){skimr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){ggplot2}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){ggridges}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){gghalves}<LEND>[assign](){<-}<LSEP>[](symbol){trx}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DEanalysis}<LSEP>[](symbol){transactions}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){trx}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){skimr}<LSEP>[](symbol){skim}<LEND>[](symbol){trx}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){trx}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){trx}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){mutate}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){lubridate}<LSEP>[](symbol){year}<LEND>[](symbol){datetime}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){count}<LEND>[](symbol){investor}<LSEP>[](symbol){year}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){arrange}<LEND>[](symbol){year}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tidyr}<LSEP>[](symbol){pivot_wider}<LEND>[](symbol){year}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){left_join}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){count}<LEND>[](symbol){trx}<LSEP>[](symbol){investor}<LEND>[argument 1; litteral](str){investor}<LEND>[assign](){<-}<LSEP>[](symbol){mkt}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DEanalysis}<LSEP>[](symbol){marketprices}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){mkt}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){skimr}<LSEP>[](symbol){skim}<LEND>[](symbol){mkt}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){mkt}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){mutate}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){lubridate}<LSEP>[](symbol){year}<LEND>[](symbol){datetime}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){count}<LEND>[](symbol){asset}<LSEP>[](symbol){year}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){arrange}<LEND>[](symbol){year}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tidyr}<LSEP>[](symbol){pivot_wider}<LEND>[](symbol){year}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){head}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[assign](){<-}<LSEP>[](symbol){trx_QZ621}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){filter}<LEND>[](symbol){trx}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){investor}<LSEP>[argument 1; litteral](str){QZ621}<LEND>[assign](){<-}<LSEP>[](symbol){mkt_QZ621}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){filter}<LEND>[](symbol){mkt}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){asset}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){asset}<LEND>[assign](){<-}<LSEP>[](symbol){p_res}<LEND>[call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){p_res}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){skimr}<LSEP>[](symbol){skim}<LEND>[](symbol){p_res}<LEND>[assign](){<-}<LSEP>[](symbol){de}<LEND>[call](){}<LSEP>[](symbol){disposition_compute}<LSEP>[](symbol){p_res}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){de}<LEND>[call](){}<LSEP>[](symbol){disposition_compute}<LSEP>[](symbol){p_res}<LSEP>[](symbol){mean}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){de_stat}<LEND>[call](){}<LSEP>[](symbol){disposition_summary}<LSEP>[](symbol){p_res}<LEND>[](symbol){de_stat}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LSEP>[argument 2; litteral](str){none}<LEND>[argument 1; call](){}<LSEP>[](symbol){head}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LSEP>[argument 2; litteral](str){count}<LEND>[argument 1; call](){}<LSEP>[](symbol){head}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LSEP>[argument 2; litteral](str){total}<LEND>[argument 1; call](){}<LSEP>[](symbol){head}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LSEP>[argument 2; litteral](str){value}<LEND>[argument 1; call](){}<LSEP>[](symbol){head}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LSEP>[argument 2; litteral](str){duration}<LEND>[argument 1; call](){}<LSEP>[](symbol){head}<LEND>[assign](){<-}<LSEP>[](symbol){p_res_all}<LEND>[call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){trx_QZ621}<LSEP>[](symbol){mkt_QZ621}<LSEP>[argument 2; litteral](str){all}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){skimr}<LSEP>[](symbol){skim}<LEND>[](symbol){p_res_all}<LEND>[call](){}<LSEP>[](symbol){disposition_compute}<LSEP>[](symbol){p_res_all}<LSEP>[](symbol){mean}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){trx_list}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){trx}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){group_by}<LEND>[](symbol){investor}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){group_split}<LEND>[call](){}<LSEP>[](symbol){load}<LSEP>[argument 0; litteral](str){figures/p_res_full.RData}<LEND>[assign](){<-}<LSEP>[](symbol){de}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){map}<LEND>[](symbol){p_res_full}<LSEP>[](symbol){disposition_compute}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_rows}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){skimr}<LSEP>[](symbol){skim}<LEND>[](symbol){de}<LEND>[assign](){<-}<LSEP>[](symbol){de_mean}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){map}<LEND>[](symbol){p_res_full}<LSEP>[](symbol){disposition_compute}<LSEP>[](symbol){mean}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_rows}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){arrange}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){desc}<LEND>[](symbol){DE_count}<LEND>[](symbol){de_mean}<LEND>[assign](){<-}<LSEP>[](symbol){de_stat}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){map}<LEND>[](symbol){p_res_full}<LSEP>[](symbol){disposition_summary}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_rows}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){de_stat}<LSEP>[argument 1; litteral](real){7.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){de}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){DE_count}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_histogram}<LEND>[argument 0; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){..density..}<LEND>[argument 1; litteral](str){darkblue}<LSEP>[argument 2; litteral](str){yellow}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_density}<LEND>[argument 0; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){..density..}<LEND>[argument 1; litteral](str){darkblue}<LSEP>[argument 2; litteral](str){yellow}<LSEP>[argument 3; litteral](real){0.400000}<LEND>[argument 1; call](){}<LSEP>[](symbol){scale_x_continuous}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme}<LEND>[argument 0; call](){}<LSEP>[](symbol){element_rect}<LSEP>[argument 0; litteral](str){grey92}<LEND>[argument 1; call](){}<LSEP>[](symbol){element_rect}<LSEP>[argument 0; litteral](str){grey85}<LSEP>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){element_text}<LSEP>[argument 0; litteral](real){20.000000}<LEND>[argument 3; litteral](str){none}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[argument 0; litteral](str){Disposition Effect Distribution}<LSEP>[argument 1; litteral](str){Disposition Effect}<LSEP>[argument 2; litteral](str){Frequency}<LEND>[assign](){<-}<LSEP>[](symbol){de_stat}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){de_stat}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){filter}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){stat}<LSEP>[argument 1; litteral](str){StDev}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){mutate}<LEND>[argument 0; call](){}<LSEP>[](symbol){factor}<LSEP>[](symbol){stat}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Min}<LSEP>[argument 1; litteral](str){Q1}<LSEP>[argument 2; litteral](str){Median}<LSEP>[argument 3; litteral](str){Mean}<LSEP>[argument 4; litteral](str){Q3}<LSEP>[argument 5; litteral](str){Max}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){de_stat}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){DE_count}<LSEP>[](symbol){stat}<LSEP>[](symbol){stat}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_density_ridges}<LEND>[argument 1; call](){}<LSEP>[](symbol){scale_fill_viridis_d}<LEND>[argument 1; call](){}<LSEP>[](symbol){scale_x_continuous}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme}<LEND>[argument 0; call](){}<LSEP>[](symbol){element_rect}<LSEP>[argument 0; litteral](str){grey92}<LEND>[argument 1; call](){}<LSEP>[](symbol){element_rect}<LSEP>[argument 0; litteral](str){grey85}<LSEP>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){element_text}<LSEP>[argument 0; litteral](real){20.000000}<LEND>[argument 3; litteral](str){none}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[argument 0; litteral](str){Disposition Effect Statistics'...}<LSEP>[argument 1; litteral](str){Disposition Effect}<LSEP>[argument 2; litteral](str){}<LEND>[assign](){<-}<LSEP>[](symbol){top5_assets}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){trx}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){count}<LEND>[](symbol){asset}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){arrange}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){desc}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){slice}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){pull}<LEND>[](symbol){asset}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){filter}<LEND>[](symbol){de}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){asset}<LSEP>[](symbol){top5_assets}<LEND>[argument 1; call](){}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){asset}<LSEP>[](symbol){DE_count}<LSEP>[](symbol){asset}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_half_boxplot}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](real){0.800000}<LSEP>[argument 2; litteral](real){0.020000}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_half_violin}<LSEP>[argument 0; litteral](str){r}<LSEP>[argument 1; litteral](real){0.020000}<LSEP>[argument 2; litteral](real){0.800000}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_jitter}<LSEP>[argument 0; litteral](str){grey40}<LEND>[argument 1; call](){}<LSEP>[](symbol){scale_fill_viridis_d}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme}<LEND>[argument 0; call](){}<LSEP>[](symbol){element_rect}<LSEP>[argument 0; litteral](str){grey92}<LEND>[argument 1; call](){}<LSEP>[](symbol){element_rect}<LSEP>[argument 0; litteral](str){grey85}<LSEP>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){element_text}<LSEP>[argument 0; litteral](real){20.000000}<LEND>[argument 3; litteral](str){none}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[argument 0; litteral](str){Volatility & Disposition Effect}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){Disposition Effect}

[](){expression}<LSEP>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){opts_chunk}<LEND>[](symbol){set}<LEND>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){#>}<LSEP>[argument 4; litteral](str){100%}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dispositionEffect}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dplyr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){foreach}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){parallel}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){doParallel}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){future}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){furrr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){bench}<LEND>[assign](){<-}<LSEP>[](symbol){portfolio_compute_parallel}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){portfolio_transactions}<LSEP>[](symbol){market_prices}<LSEP>[](symbol){plan}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){investors_id}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){map_chr}<LEND>[](symbol){portfolio_transactions}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){pluck}<LEND>[](symbol){.}<LSEP>[argument 1; litteral](str){investor}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){portfolio_compute_safe}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){safely}<LEND>[](symbol){portfolio_compute}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){plan}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ncores}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){future}<LSEP>[](symbol){availableCores}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ncores}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){new_plan}<LSEP>[litteral](str){multisession}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){new_plan}<LSEP>[litteral](str){sequential}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){new_plan}<LSEP>[](symbol){plan}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){old_plan}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){future}<LSEP>[](symbol){plan}<LEND>[](symbol){new_plan}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){furrr}<LSEP>[](symbol){future_map}<LEND>[](symbol){portfolio_transactions}<LSEP>[](symbol){portfolio_compute_safe}<LSEP>[](symbol){market_prices}<LSEP>[](symbol){...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){transpose}<LEND>[](symbol){res}<LEND>[](symbol){result}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[](symbol){investors_id}<LEND>[statement 7; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){future}<LSEP>[](symbol){plan}<LEND>[](symbol){old_plan}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){trx}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DEanalysis}<LSEP>[](symbol){transactions}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){group_by}<LEND>[](symbol){investor}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){group_split}<LEND>[assign](){<-}<LSEP>[](symbol){mkt}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DEanalysis}<LSEP>[](symbol){marketprices}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){include_graphics}<LEND>[argument 0; litteral](str){figures/de-parallel-bench1.PNG}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){include_graphics}<LEND>[argument 0; litteral](str){figures/de-parallel-bench2.PNG}<LEND>[](symbol){version}

[](){expression}<LSEP>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){opts_chunk}<LEND>[](symbol){set}<LEND>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){#>}<LSEP>[argument 4; litteral](str){100%}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dispositionEffect}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){investor}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){marketprices}<LEND>[assign](){<-}<LSEP>[](symbol){portfolio_results}<LEND>[call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){investor}<LSEP>[](symbol){marketprices}<LSEP>[argument 2; litteral](str){count}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){select}<LEND>[](symbol){portfolio_results}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){datetime}<LEND>[call](){}<LSEP>[](symbol){disposition_effect}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){RG_count}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){PG_count}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){RL_count}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){PL_count}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){disposition_effect}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){RG_count}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){PG_count}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){RL_count}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){PL_count}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){asset_de}<LEND>[call](){}<LSEP>[](symbol){disposition_compute}<LSEP>[](symbol){portfolio_results}<LEND>[](symbol){asset_de}<LEND>[assign](){<-}<LSEP>[](symbol){investor_de}<LEND>[call](){}<LSEP>[](symbol){disposition_compute}<LSEP>[](symbol){portfolio_results}<LSEP>[](symbol){mean}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[](symbol){investor_de}<LEND>[call](){}<LSEP>[](symbol){disposition_summary}<LSEP>[](symbol){portfolio_results}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){ggplot2}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){asset_de}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){aes}<LEND>[](symbol){asset}<LSEP>[](symbol){DE_count}<LSEP>[](symbol){asset}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){geom_col}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){scale_fill_viridis_d}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){labs}<LEND>[argument 0; litteral](str){Disposition Effect results of ...}<LSEP>[argument 1; litteral](str){Method Count}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}

[](){expression}<LSEP>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){opts_chunk}<LEND>[](symbol){set}<LEND>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){#>}<LSEP>[argument 4; litteral](str){100%}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dispositionEffect}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){dplyr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){tidyr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){purrr}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){ggplot2}<LEND>[assign](){<-}<LSEP>[](symbol){portfolio_results_ts}<LEND>[call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){investor}<LSEP>[](symbol){marketprices}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){portfolio}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results_ts}<LSEP>[](symbol){portfolio}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){select}<LEND>[](symbol){portfolio}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){datetime}<LEND>[assign](){<-}<LSEP>[](symbol){timeseries}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results_ts}<LSEP>[](symbol){timeseries}<LEND>[call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){timeseries}<LEND>[call](){}<LSEP>[](symbol){disposition_summary_ts}<LSEP>[](symbol){timeseries}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){timeseries}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tidyr}<LSEP>[](symbol){pivot_longer}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){starts_with}<LEND>[argument 0; litteral](str){DE}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){aes}<LEND>[](symbol){datetime}<LSEP>[](symbol){value}<LSEP>[](symbol){name}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){geom_line}<LEND>[argument 0; litteral](real){1.500000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){scale_colour_viridis_d}<LEND>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){labs}<LEND>[argument 0; litteral](str){Time Series Disposition Effect...}<LSEP>[argument 1; litteral](str){Method Count}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){theme}<LEND>[argument 0; litteral](str){bottom}<LEND>[assign](){<-}<LSEP>[](symbol){portfolio_results_ts_assets}<LEND>[call](){}<LSEP>[](symbol){portfolio_compute}<LSEP>[](symbol){investor}<LSEP>[](symbol){marketprices}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ACO}<LSEP>[argument 1; litteral](str){LSUG}<LEND>[assign](){<-}<LSEP>[](symbol){timeseries_assets}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){portfolio_results_ts_assets}<LSEP>[](symbol){timeseries}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){timeseries_assets}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){head}<LSEP>[](symbol){timeseries_assets}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){7.000000}<LSEP>[argument 1; litteral](real){8.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){disposition_summary_ts}<LSEP>[](symbol){timeseries_assets}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){disposition_summary_ts}<LSEP>[](symbol){timeseries_assets}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){7.000000}<LSEP>[argument 1; litteral](real){8.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){timeseries_assets}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tidyr}<LSEP>[](symbol){pivot_longer}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){contains}<LEND>[argument 0; litteral](str){DE}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){aes}<LEND>[](symbol){datetime}<LSEP>[](symbol){value}<LSEP>[](symbol){name}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){geom_line}<LEND>[argument 0; litteral](real){1.500000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){scale_colour_viridis_d}<LEND>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){facet_wrap}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){name}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){labs}<LEND>[argument 0; litteral](str){Assets Time Series Disposition...}<LSEP>[argument 1; litteral](str){Method Count}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){theme}<LEND>[argument 0; litteral](str){bottom}<LEND>[call](){}<LSEP>[](symbol){load}<LSEP>[argument 0; litteral](str){figures/ts_res.RData}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){purrr}<LSEP>[](symbol){map}<LEND>[](symbol){timeseries_10_investors}<LSEP>[](symbol){disposition_summary_ts}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_rows}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){filter}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stat}<LSEP>[argument 1; litteral](str){Mean}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){arrange}<LEND>[argument 0; call](){}<LSEP>[](symbol){desc}<LSEP>[](symbol){DETs_count}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){timeseries_10_investors}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_rows}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tidyr}<LSEP>[](symbol){pivot_longer}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){contains}<LEND>[argument 0; litteral](str){DE}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){aes}<LEND>[](symbol){datetime}<LSEP>[](symbol){value}<LSEP>[](symbol){investor}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){geom_line}<LEND>[argument 0; litteral](real){0.750000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){scale_colour_viridis_d}<LEND>[argument 0; litteral](real){0.900000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){facet_wrap}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){name}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){labs}<LEND>[argument 0; litteral](str){10 Investors Time Series Dispo...}<LSEP>[argument 1; litteral](str){Method Count}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){theme}<LEND>[argument 0; litteral](str){bottom}

[](){expression}<LSEP>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[argument 0; litteral](str){spelling}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){spelling}<LSEP>[](symbol){spell_check_test}<LEND>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){testthat}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[call](){}<LSEP>[](symbol){test_check}<LSEP>[argument 0; litteral](str){paleotree}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){contradiction distance tests w...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){C}<LSEP>[argument 1; litteral](str){D}<LEND>[argument 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){C}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){B}<LSEP>[argument 1; litteral](str){C}<LEND>[argument 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){D}<LEND>[argument 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){B}<LSEP>[argument 1; litteral](str){D}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){expected}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){TRUE}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[statement 3; call](){}<LSEP>[](symbol){expect_identical}<LSEP>[](symbol){test}<LSEP>[](symbol){expected}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LSEP>[argument 2; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LSEP>[argument 2; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){C}<LSEP>[argument 1; litteral](str){D}<LEND>[argument 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LSEP>[argument 2; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){C}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LSEP>[argument 2; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){B}<LSEP>[argument 1; litteral](str){C}<LEND>[argument 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LSEP>[argument 2; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){D}<LEND>[argument 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){testContradiction}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){A}<LSEP>[argument 1; litteral](str){B}<LSEP>[argument 2; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){B}<LSEP>[argument 1; litteral](str){D}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){expected}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){TRUE}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[statement 6; call](){}<LSEP>[](symbol){expect_identical}<LSEP>[](symbol){test}<LSEP>[](symbol){expected}<LEND>[statement 7; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){treeA}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){rtree}<LEND>[argument 0; litteral](real){30.000000}<LSEP>[argument 1; litteral](NULL){NULL}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){treeB}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){rtree}<LEND>[argument 0; litteral](real){30.000000}<LSEP>[argument 1; litteral](NULL){NULL}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){treeC}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){stree}<LEND>[argument 0; litteral](real){30.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){treeContradiction}<LSEP>[](symbol){treeA}<LSEP>[](symbol){treeC}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){treeContradiction}<LSEP>[](symbol){treeB}<LSEP>[](symbol){treeC}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){treeContradiction}<LSEP>[](symbol){treeA}<LSEP>[](symbol){treeA}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){expect_true}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){test}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord doesn't produc...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){saved_seed}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](integer){10403}<LSEP>[argument 1; litteral](integer){571}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1853698735}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1617683795}<LEND>[argument 4; litteral](integer){1433983323}<LSEP>[argument 5; litteral](integer){1602013699}<LEND>[argument 6; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2139602443}<LEND>[argument 7; litteral](integer){828740635}<LSEP>[argument 8; litteral](integer){810136674}<LEND>[argument 9; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){222442686}<LEND>[argument 10; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1062350433}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){279344709}<LEND>[argument 12; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2137247395}<LEND>[argument 13; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){966848151}<LEND>[argument 14; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){488751592}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1706372736}<LEND>[argument 16; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){462208098}<LEND>[argument 17; litteral](integer){2108738791}<LSEP>[argument 18; litteral](integer){1854509369}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1307471181}<LEND>[argument 20; litteral](integer){1824146925}<LSEP>[argument 21; litteral](integer){1513717001}<LSEP>[argument 22; litteral](integer){275256421}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1846634309}<LEND>[argument 24; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){833859483}<LEND>[argument 25; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){734561029}<LEND>[argument 26; litteral](integer){1042021435}<LSEP>[argument 27; litteral](integer){809711929}<LSEP>[argument 28; litteral](integer){419243244}<LEND>[argument 29; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){802286761}<LEND>[argument 30; litteral](integer){1497007147}<LSEP>[argument 31; litteral](integer){81557787}<LEND>[argument 32; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){660252751}<LEND>[argument 33; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){97986758}<LEND>[argument 34; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1448549103}<LEND>[argument 35; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1958553833}<LEND>[argument 36; litteral](integer){2138156950}<LSEP>[argument 37; litteral](integer){1516137314}<LEND>[argument 38; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1055500571}<LEND>[argument 39; litteral](integer){1731328840}<LEND>[argument 40; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){224850824}<LEND>[argument 41; litteral](integer){578689076}<LSEP>[argument 42; litteral](integer){75625678}<LEND>[argument 43; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1737530033}<LEND>[argument 44; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1970920588}<LEND>[argument 45; litteral](integer){655890861}<LSEP>[argument 46; litteral](integer){1915360703}<LEND>[argument 47; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2005923087}<LEND>[argument 48; litteral](integer){465893075}<LEND>[argument 49; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){987497959}<LEND>[argument 50; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1961535427}<LEND>[argument 51; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1630816780}<LEND>[argument 52; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2054701103}<LEND>[argument 53; litteral](integer){1923176537}<LEND>[argument 54; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){615338329}<LEND>[argument 55; litteral](integer){903476606}<LSEP>[argument 56; litteral](integer){1020325941}<LEND>[argument 57; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1477321166}<LEND>[argument 58; litteral](integer){1366880540}<LSEP>[argument 59; litteral](integer){461923545}<LSEP>[argument 60; litteral](integer){911670059}<LSEP>[argument 61; litteral](integer){456674787}<LSEP>[argument 62; litteral](integer){1757261593}<LEND>[argument 63; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){214157451}<LEND>[argument 64; litteral](integer){23884317}<LEND>[argument 65; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){61834478}<LEND>[argument 66; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1284939658}<LEND>[argument 67; litteral](integer){60821190}<LSEP>[argument 68; litteral](integer){1290224258}<LSEP>[argument 69; litteral](integer){1637433497}<LSEP>[argument 70; litteral](integer){1829748002}<LEND>[argument 71; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1496828380}<LEND>[argument 72; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1589954927}<LEND>[argument 73; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){431184785}<LEND>[argument 74; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){98000072}<LEND>[argument 75; litteral](integer){1734108228}<LEND>[argument 76; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1060726931}<LEND>[argument 77; litteral](integer){1424209627}<LEND>[argument 78; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){492293930}<LEND>[argument 79; litteral](integer){1827255675}<LEND>[argument 80; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1515697483}<LEND>[argument 81; litteral](integer){1705432642}<LEND>[argument 82; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){654919731}<LEND>[argument 83; litteral](integer){479249862}<LEND>[argument 84; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){642548399}<LEND>[argument 85; litteral](integer){463517046}<LSEP>[argument 86; litteral](integer){1437299327}<LEND>[argument 87; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){661009978}<LEND>[argument 88; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){545419484}<LEND>[argument 89; litteral](integer){1095205387}<LSEP>[argument 90; litteral](integer){1204985906}<LSEP>[argument 91; litteral](integer){60112567}<LSEP>[argument 92; litteral](integer){747657768}<LSEP>[argument 93; litteral](integer){1363495870}<LEND>[argument 94; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){619584692}<LEND>[argument 95; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){669186361}<LEND>[argument 96; litteral](integer){852912097}<LSEP>[argument 97; litteral](integer){665320879}<LEND>[argument 98; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){671271289}<LEND>[argument 99; litteral](integer){1086304910}<LEND>[argument 100; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2071286025}<LEND>[argument 101; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1383204603}<LEND>[argument 102; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2113284666}<LEND>[argument 103; litteral](integer){1775147647}<LEND>[argument 104; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1408585778}<LEND>[argument 105; litteral](integer){2079737639}<LSEP>[argument 106; litteral](integer){615561733}<LSEP>[argument 107; litteral](integer){73689641}<LSEP>[argument 108; litteral](integer){1337836445}<LEND>[argument 109; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){122174301}<LEND>[argument 110; litteral](integer){706428174}<LSEP>[argument 111; litteral](integer){1602647067}<LSEP>[argument 112; litteral](integer){124432173}<LSEP>[argument 113; litteral](integer){1689693158}<LSEP>[argument 114; litteral](integer){29308779}<LEND>[argument 115; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1124538333}<LEND>[argument 116; litteral](integer){298880120}<LEND>[argument 117; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1649708682}<LEND>[argument 118; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){955015679}<LEND>[argument 119; litteral](integer){1315162081}<LEND>[argument 120; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){462518049}<LEND>[argument 121; litteral](integer){2013666168}<LSEP>[argument 122; litteral](integer){696045019}<LSEP>[argument 123; litteral](integer){390286924}<LSEP>[argument 124; litteral](integer){1076310877}<LEND>[argument 125; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1361451743}<LEND>[argument 126; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1665344435}<LEND>[argument 127; litteral](integer){1837707039}<LSEP>[argument 128; litteral](integer){163101988}<LSEP>[argument 129; litteral](integer){1829851039}<LEND>[argument 130; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2066823469}<LEND>[argument 131; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){90204041}<LEND>[argument 132; litteral](integer){1814667675}<LEND>[argument 133; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){457052526}<LEND>[argument 134; litteral](integer){123341287}<LSEP>[argument 135; litteral](integer){463472256}<LEND>[argument 136; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1430167168}<LEND>[argument 137; litteral](integer){301112184}<LSEP>[argument 138; litteral](integer){1723064924}<LEND>[argument 139; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1159489234}<LEND>[argument 140; litteral](integer){1076843039}<LEND>[argument 141; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1132661112}<LEND>[argument 142; litteral](integer){27798743}<LEND>[argument 143; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1975550119}<LEND>[argument 144; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1008435513}<LEND>[argument 145; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1504805619}<LEND>[argument 146; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1676524544}<LEND>[argument 147; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){354669894}<LEND>[argument 148; litteral](integer){1138748432}<LEND>[argument 149; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){561934610}<LEND>[argument 150; litteral](integer){1914366784}<LEND>[argument 151; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1982489914}<LEND>[argument 152; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1357599160}<LEND>[argument 153; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1938070906}<LEND>[argument 154; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1806154290}<LEND>[argument 155; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1094073373}<LEND>[argument 156; litteral](integer){2087859816}<LSEP>[argument 157; litteral](integer){1110103573}<LSEP>[argument 158; litteral](integer){2025907443}<LEND>[argument 159; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){379404128}<LEND>[argument 160; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1174067044}<LEND>[argument 161; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1267612669}<LEND>[argument 162; litteral](integer){1573604445}<LSEP>[argument 163; litteral](integer){1001623553}<LEND>[argument 164; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){135456734}<LEND>[argument 165; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1575261349}<LEND>[argument 166; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1815750733}<LEND>[argument 167; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1018860996}<LEND>[argument 168; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){436036596}<LEND>[argument 169; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2138189894}<LEND>[argument 170; litteral](integer){250540748}<LSEP>[argument 171; litteral](integer){910620079}<LSEP>[argument 172; litteral](integer){297999721}<LEND>[argument 173; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){787324315}<LEND>[argument 174; litteral](integer){607555736}<LEND>[argument 175; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){11846095}<LEND>[argument 176; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1836666190}<LEND>[argument 177; litteral](integer){2000222791}<LEND>[argument 178; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){155347258}<LEND>[argument 179; litteral](integer){88808049}<LSEP>[argument 180; litteral](integer){508040486}<LEND>[argument 181; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){448013317}<LEND>[argument 182; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){211033215}<LEND>[argument 183; litteral](integer){2042103042}<LSEP>[argument 184; litteral](integer){1649670458}<LSEP>[argument 185; litteral](integer){2045553063}<LEND>[argument 186; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){16545087}<LEND>[argument 187; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1668583180}<LEND>[argument 188; litteral](integer){1946719758}<LSEP>[argument 189; litteral](integer){781884963}<LSEP>[argument 190; litteral](integer){696941254}<LSEP>[argument 191; litteral](integer){919544888}<LSEP>[argument 192; litteral](integer){1471648712}<LSEP>[argument 193; litteral](integer){549978839}<LSEP>[argument 194; litteral](integer){1889953923}<LSEP>[argument 195; litteral](integer){1640331206}<LEND>[argument 196; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1764565144}<LEND>[argument 197; litteral](integer){277868371}<LSEP>[argument 198; litteral](integer){1655843748}<LEND>[argument 199; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1949612026}<LEND>[argument 200; litteral](integer){1993309602}<LEND>[argument 201; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1700497328}<LEND>[argument 202; litteral](integer){846105420}<LEND>[argument 203; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){709770589}<LEND>[argument 204; litteral](integer){1802532037}<LEND>[argument 205; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1608245964}<LEND>[argument 206; litteral](integer){474706330}<LEND>[argument 207; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1589153638}<LEND>[argument 208; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){698466802}<LEND>[argument 209; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1990683508}<LEND>[argument 210; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1648915059}<LEND>[argument 211; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){518663001}<LEND>[argument 212; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1056118794}<LEND>[argument 213; litteral](integer){424234687}<LSEP>[argument 214; litteral](integer){856322830}<LEND>[argument 215; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1258942958}<LEND>[argument 216; litteral](integer){869424139}<LEND>[argument 217; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){445077723}<LEND>[argument 218; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){973033739}<LEND>[argument 219; litteral](integer){1276005716}<LEND>[argument 220; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){247957612}<LEND>[argument 221; litteral](integer){1239547611}<LSEP>[argument 222; litteral](integer){1574788792}<LEND>[argument 223; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){854735167}<LEND>[argument 224; litteral](integer){1289734935}<LSEP>[argument 225; litteral](integer){852943523}<LSEP>[argument 226; litteral](integer){1296864790}<LEND>[argument 227; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){133808582}<LEND>[argument 228; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){216284195}<LEND>[argument 229; litteral](integer){879457686}<LEND>[argument 230; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1377906328}<LEND>[argument 231; litteral](integer){1597715383}<LEND>[argument 232; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1765177183}<LEND>[argument 233; litteral](integer){482511652}<LEND>[argument 234; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1211171858}<LEND>[argument 235; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1672126265}<LEND>[argument 236; litteral](integer){533761940}<LEND>[argument 237; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){736680301}<LEND>[argument 238; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1584136012}<LEND>[argument 239; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2058234427}<LEND>[argument 240; litteral](integer){1122491067}<LEND>[argument 241; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1312521127}<LEND>[argument 242; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1322337215}<LEND>[argument 243; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){797826844}<LEND>[argument 244; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){36248282}<LEND>[argument 245; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){432167968}<LEND>[argument 246; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1542279032}<LEND>[argument 247; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2078621936}<LEND>[argument 248; litteral](integer){1483903132}<LEND>[argument 249; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2146889202}<LEND>[argument 250; litteral](integer){231610347}<LSEP>[argument 251; litteral](integer){2141070295}<LSEP>[argument 252; litteral](integer){1129857719}<LEND>[argument 253; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1062243101}<LEND>[argument 254; litteral](integer){1500707757}<LEND>[argument 255; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2086555059}<LEND>[argument 256; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){492347650}<LEND>[argument 257; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1756441812}<LEND>[argument 258; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){799029007}<LEND>[argument 259; litteral](integer){643260017}<LSEP>[argument 260; litteral](integer){1081037763}<LEND>[argument 261; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){995194269}<LEND>[argument 262; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){744808703}<LEND>[argument 263; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){300509415}<LEND>[argument 264; litteral](integer){805434156}<LSEP>[argument 265; litteral](integer){1417125810}<LSEP>[argument 266; litteral](integer){1688950459}<LEND>[argument 267; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){647830294}<LEND>[argument 268; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){318983034}<LEND>[argument 269; litteral](integer){1472091132}<LSEP>[argument 270; litteral](integer){1284145290}<LSEP>[argument 271; litteral](integer){438409963}<LSEP>[argument 272; litteral](integer){1039086804}<LEND>[argument 273; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1329068550}<LEND>[argument 274; litteral](integer){1475391745}<LSEP>[argument 275; litteral](integer){743261523}<LSEP>[argument 276; litteral](integer){1844477472}<LEND>[argument 277; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){948242021}<LEND>[argument 278; litteral](integer){2051359923}<LSEP>[argument 279; litteral](integer){1853483022}<LEND>[argument 280; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){602159388}<LEND>[argument 281; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){200059860}<LEND>[argument 282; litteral](integer){1966119739}<LSEP>[argument 283; litteral](integer){2094190721}<LEND>[argument 284; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1852317829}<LEND>[argument 285; litteral](integer){530993408}<LEND>[argument 286; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1476986008}<LEND>[argument 287; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){847875145}<LEND>[argument 288; litteral](integer){909813623}<LEND>[argument 289; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1439558460}<LEND>[argument 290; litteral](integer){1411827320}<LSEP>[argument 291; litteral](integer){349167711}<LSEP>[argument 292; litteral](integer){172282929}<LSEP>[argument 293; litteral](integer){1644103834}<LEND>[argument 294; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){590876338}<LEND>[argument 295; litteral](integer){1223027271}<LEND>[argument 296; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){537116176}<LEND>[argument 297; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1210458223}<LEND>[argument 298; litteral](integer){1908648705}<LSEP>[argument 299; litteral](integer){1394227509}<LEND>[argument 300; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){74821458}<LEND>[argument 301; litteral](integer){2087266771}<LSEP>[argument 302; litteral](integer){47978638}<LSEP>[argument 303; litteral](integer){792460695}<LEND>[argument 304; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1265557208}<LEND>[argument 305; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){80134366}<LEND>[argument 306; litteral](integer){1232891816}<LSEP>[argument 307; litteral](integer){1611714571}<LSEP>[argument 308; litteral](integer){1020846137}<LSEP>[argument 309; litteral](integer){773016345}<LSEP>[argument 310; litteral](integer){1617766307}<LEND>[argument 311; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1235879317}<LEND>[argument 312; litteral](integer){1895391305}<LSEP>[argument 313; litteral](integer){169233468}<LEND>[argument 314; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1258775487}<LEND>[argument 315; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1461443236}<LEND>[argument 316; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1906564258}<LEND>[argument 317; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){933806533}<LEND>[argument 318; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1461390823}<LEND>[argument 319; litteral](integer){1916731630}<LEND>[argument 320; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){731894006}<LEND>[argument 321; litteral](integer){1922128305}<LEND>[argument 322; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1294909155}<LEND>[argument 323; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1490264410}<LEND>[argument 324; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1433634674}<LEND>[argument 325; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){132189123}<LEND>[argument 326; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){633352314}<LEND>[argument 327; litteral](integer){1217080486}<LSEP>[argument 328; litteral](integer){1278041233}<LSEP>[argument 329; litteral](integer){160642529}<LSEP>[argument 330; litteral](integer){2055737957}<LEND>[argument 331; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2035578178}<LEND>[argument 332; litteral](integer){498491404}<LSEP>[argument 333; litteral](integer){1860733850}<LEND>[argument 334; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1545521305}<LEND>[argument 335; litteral](integer){673391474}<LEND>[argument 336; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1944192042}<LEND>[argument 337; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){762553878}<LEND>[argument 338; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1336312142}<LEND>[argument 339; litteral](integer){1232118406}<LSEP>[argument 340; litteral](integer){1955124317}<LEND>[argument 341; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1870118377}<LEND>[argument 342; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1127308999}<LEND>[argument 343; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){172897011}<LEND>[argument 344; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1224248334}<LEND>[argument 345; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1776683384}<LEND>[argument 346; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){922118073}<LEND>[argument 347; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){49032017}<LEND>[argument 348; litteral](integer){1692435451}<LEND>[argument 349; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){857936441}<LEND>[argument 350; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1769584363}<LEND>[argument 351; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1475906502}<LEND>[argument 352; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1496298326}<LEND>[argument 353; litteral](integer){270862639}<LSEP>[argument 354; litteral](integer){940687450}<LEND>[argument 355; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1326161823}<LEND>[argument 356; litteral](integer){2062695569}<LSEP>[argument 357; litteral](integer){436014856}<LEND>[argument 358; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1803713131}<LEND>[argument 359; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){424225252}<LEND>[argument 360; litteral](integer){797426765}<LSEP>[argument 361; litteral](integer){393691671}<LEND>[argument 362; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){673601349}<LEND>[argument 363; litteral](integer){531454110}<LEND>[argument 364; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1225646598}<LEND>[argument 365; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){235716991}<LEND>[argument 366; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1865330947}<LEND>[argument 367; litteral](integer){1263335694}<LEND>[argument 368; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1264999834}<LEND>[argument 369; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){670156227}<LEND>[argument 370; litteral](integer){196235768}<LSEP>[argument 371; litteral](integer){426497556}<LEND>[argument 372; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1369999781}<LEND>[argument 373; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){522140111}<LEND>[argument 374; litteral](integer){1592919051}<LSEP>[argument 375; litteral](integer){1639184800}<LSEP>[argument 376; litteral](integer){1012881521}<LSEP>[argument 377; litteral](integer){1138772221}<LSEP>[argument 378; litteral](integer){424715353}<LSEP>[argument 379; litteral](integer){666399614}<LSEP>[argument 380; litteral](integer){974715248}<LEND>[argument 381; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){712772579}<LEND>[argument 382; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){661399666}<LEND>[argument 383; litteral](integer){2002771233}<LEND>[argument 384; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){425412621}<LEND>[argument 385; litteral](integer){1304477587}<LEND>[argument 386; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1742662538}<LEND>[argument 387; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){869915638}<LEND>[argument 388; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1383823571}<LEND>[argument 389; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){860162588}<LEND>[argument 390; litteral](integer){163863576}<LEND>[argument 391; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1683806652}<LEND>[argument 392; litteral](integer){1091419704}<LEND>[argument 393; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){775859408}<LEND>[argument 394; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){62549785}<LEND>[argument 395; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){162207709}<LEND>[argument 396; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){353924515}<LEND>[argument 397; litteral](integer){620454336}<LEND>[argument 398; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1245118640}<LEND>[argument 399; litteral](integer){1905653577}<LSEP>[argument 400; litteral](integer){636261242}<LEND>[argument 401; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1596437293}<LEND>[argument 402; litteral](integer){16449432}<LEND>[argument 403; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1691767447}<LEND>[argument 404; litteral](integer){1348172727}<LEND>[argument 405; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1384311936}<LEND>[argument 406; litteral](integer){1125393544}<LEND>[argument 407; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2072848942}<LEND>[argument 408; litteral](integer){713008419}<LSEP>[argument 409; litteral](integer){742054253}<LEND>[argument 410; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1476661401}<LEND>[argument 411; litteral](integer){843793876}<LEND>[argument 412; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1284451103}<LEND>[argument 413; litteral](integer){1221778685}<LSEP>[argument 414; litteral](integer){902272468}<LEND>[argument 415; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){218093693}<LEND>[argument 416; litteral](integer){1597593062}<LEND>[argument 417; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1323665945}<LEND>[argument 418; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1641685136}<LEND>[argument 419; litteral](integer){2096268918}<LEND>[argument 420; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1151974505}<LEND>[argument 421; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1966507230}<LEND>[argument 422; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2142822395}<LEND>[argument 423; litteral](integer){1365160752}<LSEP>[argument 424; litteral](integer){1562929423}<LEND>[argument 425; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){971159986}<LEND>[argument 426; litteral](integer){982929974}<LEND>[argument 427; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){943681632}<LEND>[argument 428; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){655961415}<LEND>[argument 429; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1113726106}<LEND>[argument 430; litteral](integer){821777900}<LEND>[argument 431; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1936930352}<LEND>[argument 432; litteral](integer){1658389807}<LEND>[argument 433; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1480587857}<LEND>[argument 434; litteral](integer){1810373062}<LSEP>[argument 435; litteral](integer){1610187420}<LEND>[argument 436; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1061552600}<LEND>[argument 437; litteral](integer){1845170423}<LSEP>[argument 438; litteral](integer){1659752482}<LSEP>[argument 439; litteral](integer){1977364133}<LEND>[argument 440; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2067258745}<LEND>[argument 441; litteral](integer){1988951973}<LEND>[argument 442; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2014122681}<LEND>[argument 443; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1542221550}<LEND>[argument 444; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1160666994}<LEND>[argument 445; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){905249898}<LEND>[argument 446; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1350605932}<LEND>[argument 447; litteral](integer){297765417}<LEND>[argument 448; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){427768077}<LEND>[argument 449; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1468684165}<LEND>[argument 450; litteral](integer){884615840}<LEND>[argument 451; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2061673235}<LEND>[argument 452; litteral](integer){1844719662}<LEND>[argument 453; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1158590253}<LEND>[argument 454; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1572328378}<LEND>[argument 455; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){640196980}<LEND>[argument 456; litteral](integer){919524830}<LEND>[argument 457; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){577017372}<LEND>[argument 458; litteral](integer){1257573538}<LEND>[argument 459; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){556445104}<LEND>[argument 460; litteral](integer){1271285357}<LSEP>[argument 461; litteral](integer){21657835}<LSEP>[argument 462; litteral](integer){1194448631}<LEND>[argument 463; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1270375187}<LEND>[argument 464; litteral](integer){1227184612}<LEND>[argument 465; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){697506}<LEND>[argument 466; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){750946175}<LEND>[argument 467; litteral](integer){936751255}<LSEP>[argument 468; litteral](integer){487023160}<LSEP>[argument 469; litteral](integer){1339140426}<LSEP>[argument 470; litteral](integer){1129432116}<LSEP>[argument 471; litteral](integer){745934588}<LSEP>[argument 472; litteral](integer){827759462}<LSEP>[argument 473; litteral](integer){1487497420}<LEND>[argument 474; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){730778558}<LEND>[argument 475; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1676435491}<LEND>[argument 476; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){808592782}<LEND>[argument 477; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){285203312}<LEND>[argument 478; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){166055190}<LEND>[argument 479; litteral](integer){1501951550}<LSEP>[argument 480; litteral](integer){66472998}<LEND>[argument 481; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){589611882}<LEND>[argument 482; litteral](integer){1998712821}<LEND>[argument 483; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){308880320}<LEND>[argument 484; litteral](integer){1242288438}<LSEP>[argument 485; litteral](integer){2060022343}<LSEP>[argument 486; litteral](integer){998675296}<LEND>[argument 487; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){953336964}<LEND>[argument 488; litteral](integer){1036916920}<LEND>[argument 489; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){290148209}<LEND>[argument 490; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){850088204}<LEND>[argument 491; litteral](integer){1053428966}<LSEP>[argument 492; litteral](integer){424423530}<LSEP>[argument 493; litteral](integer){1220326178}<LSEP>[argument 494; litteral](integer){456053541}<LSEP>[argument 495; litteral](integer){61604734}<LEND>[argument 496; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1953344484}<LEND>[argument 497; litteral](integer){619188727}<LSEP>[argument 498; litteral](integer){440896579}<LEND>[argument 499; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2013706738}<LEND>[argument 500; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2043450736}<LEND>[argument 501; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){84513113}<LEND>[argument 502; litteral](integer){1237269073}<LEND>[argument 503; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){594001374}<LEND>[argument 504; litteral](integer){1018541669}<LSEP>[argument 505; litteral](integer){122526729}<LSEP>[argument 506; litteral](integer){1762858799}<LSEP>[argument 507; litteral](integer){609160311}<LSEP>[argument 508; litteral](integer){141995178}<LSEP>[argument 509; litteral](integer){224443233}<LEND>[argument 510; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1020010147}<LEND>[argument 511; litteral](integer){192517030}<LEND>[argument 512; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2090136902}<LEND>[argument 513; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1491007030}<LEND>[argument 514; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){456193341}<LEND>[argument 515; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1415919708}<LEND>[argument 516; litteral](integer){1073127930}<LEND>[argument 517; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){514912680}<LEND>[argument 518; litteral](integer){1815086148}<LEND>[argument 519; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){12998123}<LEND>[argument 520; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1480420701}<LEND>[argument 521; litteral](integer){387063727}<LSEP>[argument 522; litteral](integer){1636959551}<LEND>[argument 523; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2128380953}<LEND>[argument 524; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){395012474}<LEND>[argument 525; litteral](integer){1840629665}<LSEP>[argument 526; litteral](integer){936331776}<LEND>[argument 527; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){424264728}<LEND>[argument 528; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){181232011}<LEND>[argument 529; litteral](integer){1523099133}<LEND>[argument 530; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1473420234}<LEND>[argument 531; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1722394862}<LEND>[argument 532; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1188569071}<LEND>[argument 533; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1822663880}<LEND>[argument 534; litteral](integer){455731667}<LEND>[argument 535; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1116163407}<LEND>[argument 536; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1184463873}<LEND>[argument 537; litteral](integer){709462160}<LEND>[argument 538; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){102575007}<LEND>[argument 539; litteral](integer){2023507857}<LEND>[argument 540; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1152626809}<LEND>[argument 541; litteral](integer){1507025682}<LEND>[argument 542; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1810804074}<LEND>[argument 543; litteral](integer){754430500}<LSEP>[argument 544; litteral](integer){1253840337}<LEND>[argument 545; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1283465938}<LEND>[argument 546; litteral](integer){1909853053}<LEND>[argument 547; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){517508315}<LEND>[argument 548; litteral](integer){1385022721}<LEND>[argument 549; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){130431013}<LEND>[argument 550; litteral](integer){823102562}<LEND>[argument 551; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){483524280}<LEND>[argument 552; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1176901917}<LEND>[argument 553; litteral](integer){2026469711}<LEND>[argument 554; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){680898713}<LEND>[argument 555; litteral](integer){948804489}<LEND>[argument 556; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){513523886}<LEND>[argument 557; litteral](integer){388724366}<LEND>[argument 558; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1732770673}<LEND>[argument 559; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1824387128}<LEND>[argument 560; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){797827748}<LEND>[argument 561; litteral](integer){1942468467}<LEND>[argument 562; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1305606244}<LEND>[argument 563; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1706830508}<LEND>[argument 564; litteral](integer){1795512931}<LEND>[argument 565; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){934665508}<LEND>[argument 566; litteral](integer){1981531473}<LSEP>[argument 567; litteral](integer){1457743656}<LSEP>[argument 568; litteral](integer){836767629}<LEND>[argument 569; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){123389583}<LEND>[argument 570; litteral](integer){1415885779}<LSEP>[argument 571; litteral](integer){745320262}<LSEP>[argument 572; litteral](integer){599784800}<LEND>[argument 573; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){857165284}<LEND>[argument 574; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1164506705}<LEND>[argument 575; litteral](integer){1234223610}<LSEP>[argument 576; litteral](integer){21605988}<LEND>[argument 577; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){675791210}<LEND>[argument 578; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1216791157}<LEND>[argument 579; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){692101884}<LEND>[argument 580; litteral](integer){660234683}<LSEP>[argument 581; litteral](integer){1803226399}<LEND>[argument 582; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){683833859}<LEND>[argument 583; litteral](integer){35139070}<LEND>[argument 584; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){639158710}<LEND>[argument 585; litteral](integer){13069439}<LEND>[argument 586; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1617037945}<LEND>[argument 587; litteral](integer){1582373318}<LEND>[argument 588; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){567721642}<LEND>[argument 589; litteral](integer){2090187424}<LSEP>[argument 590; litteral](integer){890488569}<LEND>[argument 591; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){978532023}<LEND>[argument 592; litteral](integer){1145450893}<LSEP>[argument 593; litteral](integer){530946503}<LEND>[argument 594; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1357110337}<LEND>[argument 595; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1119543141}<LEND>[argument 596; litteral](integer){1864871195}<LEND>[argument 597; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){212985630}<LEND>[argument 598; litteral](integer){1132921875}<LEND>[argument 599; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){581074538}<LEND>[argument 600; litteral](integer){1040283510}<LSEP>[argument 601; litteral](integer){1232269288}<LSEP>[argument 602; litteral](integer){858962061}<LSEP>[argument 603; litteral](integer){496032078}<LEND>[argument 604; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1700434939}<LEND>[argument 605; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1259189619}<LEND>[argument 606; litteral](integer){2110196018}<LEND>[argument 607; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1015246932}<LEND>[argument 608; litteral](integer){1805885105}<LEND>[argument 609; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1645832437}<LEND>[argument 610; litteral](integer){1000860821}<LEND>[argument 611; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){693011612}<LEND>[argument 612; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){843431922}<LEND>[argument 613; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){242650762}<LEND>[argument 614; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){558676179}<LEND>[argument 615; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1256790071}<LEND>[argument 616; litteral](integer){800396782}<LEND>[argument 617; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1748206454}<LEND>[argument 618; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){555738314}<LEND>[argument 619; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1512478199}<LEND>[argument 620; litteral](integer){1947141636}<LSEP>[argument 621; litteral](integer){1852784704}<LEND>[argument 622; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){6829052}<LEND>[argument 623; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1614695797}<LEND>[argument 624; litteral](integer){1610126043}<LSEP>[argument 625; litteral](integer){1677797671}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){.Random.seed}<LSEP>[](symbol){saved_seed}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.970000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.970000}<LEND>[argument 2; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.970000}<LEND>[argument 3; litteral](real){1.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 8; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){testRes}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LEND>[](symbol){record}<LEND>[statement 5; call](){}<LSEP>[](symbol){expect_true}<LSEP>[](symbol){testRes}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord doesn't produc...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){saved_seed}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](integer){10403}<LSEP>[argument 1; litteral](integer){265}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1894222846}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1933042006}<LEND>[argument 4; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1025502830}<LEND>[argument 5; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){109786859}<LEND>[argument 6; litteral](integer){1221478554}<LEND>[argument 7; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){59892047}<LEND>[argument 8; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){360079513}<LEND>[argument 9; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){583920750}<LEND>[argument 10; litteral](integer){338891203}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1935115524}<LEND>[argument 12; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){633688930}<LEND>[argument 13; litteral](integer){191094328}<LSEP>[argument 14; litteral](integer){2116629319}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1554692779}<LEND>[argument 16; litteral](integer){671635032}<LSEP>[argument 17; litteral](integer){1616298720}<LSEP>[argument 18; litteral](integer){747909975}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1857477573}<LEND>[argument 20; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1721905128}<LEND>[argument 21; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1966599810}<LEND>[argument 22; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){458288604}<LEND>[argument 23; litteral](integer){137723694}<LEND>[argument 24; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){440377403}<LEND>[argument 25; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1939425950}<LEND>[argument 26; litteral](integer){902476805}<LSEP>[argument 27; litteral](integer){790408964}<LSEP>[argument 28; litteral](integer){1602659425}<LEND>[argument 29; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){733101364}<LEND>[argument 30; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){733228360}<LEND>[argument 31; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2027886496}<LEND>[argument 32; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1358793845}<LEND>[argument 33; litteral](integer){2080626873}<LEND>[argument 34; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){100703053}<LEND>[argument 35; litteral](integer){944252198}<LEND>[argument 36; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2093956194}<LEND>[argument 37; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2027713484}<LEND>[argument 38; litteral](integer){1356924611}<LEND>[argument 39; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1187177207}<LEND>[argument 40; litteral](integer){1758828355}<LEND>[argument 41; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){606655471}<LEND>[argument 42; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){454535642}<LEND>[argument 43; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1506092222}<LEND>[argument 44; litteral](integer){679041013}<LEND>[argument 45; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){763194357}<LEND>[argument 46; litteral](integer){758560184}<LSEP>[argument 47; litteral](integer){738323736}<LEND>[argument 48; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1765429573}<LEND>[argument 49; litteral](integer){506550337}<LSEP>[argument 50; litteral](integer){303079099}<LEND>[argument 51; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1230876546}<LEND>[argument 52; litteral](integer){1295138149}<LEND>[argument 53; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1105885258}<LEND>[argument 54; litteral](integer){1196040161}<LSEP>[argument 55; litteral](integer){1170413274}<LSEP>[argument 56; litteral](integer){404825274}<LSEP>[argument 57; litteral](integer){595744542}<LEND>[argument 58; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){847695697}<LEND>[argument 59; litteral](integer){2126907700}<LSEP>[argument 60; litteral](integer){1591716239}<LEND>[argument 61; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){684865548}<LEND>[argument 62; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1235004678}<LEND>[argument 63; litteral](integer){1413962226}<LEND>[argument 64; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){271751711}<LEND>[argument 65; litteral](integer){165126651}<LSEP>[argument 66; litteral](integer){312405022}<LSEP>[argument 67; litteral](integer){60615030}<LSEP>[argument 68; litteral](integer){1229937784}<LSEP>[argument 69; litteral](integer){1511672450}<LSEP>[argument 70; litteral](integer){1468861446}<LEND>[argument 71; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){356273965}<LEND>[argument 72; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1649297319}<LEND>[argument 73; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1694661468}<LEND>[argument 74; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){838441302}<LEND>[argument 75; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){917727042}<LEND>[argument 76; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1943213172}<LEND>[argument 77; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2103049871}<LEND>[argument 78; litteral](integer){1841950735}<LEND>[argument 79; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1394859159}<LEND>[argument 80; litteral](integer){457683985}<LSEP>[argument 81; litteral](integer){665090022}<LSEP>[argument 82; litteral](integer){54389997}<LSEP>[argument 83; litteral](integer){553275031}<LEND>[argument 84; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1469765379}<LEND>[argument 85; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){469346201}<LEND>[argument 86; litteral](integer){714383127}<LEND>[argument 87; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1424970434}<LEND>[argument 88; litteral](integer){1840699287}<LSEP>[argument 89; litteral](integer){392437561}<LEND>[argument 90; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1098254593}<LEND>[argument 91; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){797090633}<LEND>[argument 92; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1792332815}<LEND>[argument 93; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1174883648}<LEND>[argument 94; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){3201984}<LEND>[argument 95; litteral](integer){1852559461}<LSEP>[argument 96; litteral](integer){1536687400}<LSEP>[argument 97; litteral](integer){27854382}<LSEP>[argument 98; litteral](integer){875296809}<LEND>[argument 99; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){662035376}<LEND>[argument 100; litteral](integer){1192198965}<LSEP>[argument 101; litteral](integer){1294474558}<LEND>[argument 102; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1988957560}<LEND>[argument 103; litteral](integer){129449383}<LSEP>[argument 104; litteral](integer){707296415}<LSEP>[argument 105; litteral](integer){28007460}<LSEP>[argument 106; litteral](integer){1183649259}<LEND>[argument 107; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1131063328}<LEND>[argument 108; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){269898345}<LEND>[argument 109; litteral](integer){1861479168}<LSEP>[argument 110; litteral](integer){388860788}<LSEP>[argument 111; litteral](integer){1613081172}<LSEP>[argument 112; litteral](integer){1138238736}<LSEP>[argument 113; litteral](integer){2047005270}<LEND>[argument 114; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2078413210}<LEND>[argument 115; litteral](integer){2025511521}<LSEP>[argument 116; litteral](integer){325802665}<LEND>[argument 117; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1842967785}<LEND>[argument 118; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){798419117}<LEND>[argument 119; litteral](integer){188042860}<LEND>[argument 120; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1814705692}<LEND>[argument 121; litteral](integer){1659615618}<LSEP>[argument 122; litteral](integer){1350586304}<LEND>[argument 123; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1313127794}<LEND>[argument 124; litteral](integer){65202480}<LEND>[argument 125; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1593843941}<LEND>[argument 126; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){904978723}<LEND>[argument 127; litteral](integer){1979268368}<LSEP>[argument 128; litteral](integer){932532199}<LEND>[argument 129; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){337225230}<LEND>[argument 130; litteral](integer){90600732}<LSEP>[argument 131; litteral](integer){159401046}<LEND>[argument 132; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1032048180}<LEND>[argument 133; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){632892775}<LEND>[argument 134; litteral](integer){13543921}<LSEP>[argument 135; litteral](integer){1692578474}<LSEP>[argument 136; litteral](integer){167462303}<LEND>[argument 137; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){246865651}<LEND>[argument 138; litteral](integer){522779771}<LEND>[argument 139; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){996553506}<LEND>[argument 140; litteral](integer){1207589832}<LSEP>[argument 141; litteral](integer){577115772}<LEND>[argument 142; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2044375473}<LEND>[argument 143; litteral](integer){1312177809}<LEND>[argument 144; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2129010739}<LEND>[argument 145; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1355975463}<LEND>[argument 146; litteral](integer){1027687810}<LEND>[argument 147; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1485531717}<LEND>[argument 148; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2100415858}<LEND>[argument 149; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){966373007}<LEND>[argument 150; litteral](integer){999484170}<LSEP>[argument 151; litteral](integer){460509425}<LSEP>[argument 152; litteral](integer){1964376047}<LEND>[argument 153; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1354368904}<LEND>[argument 154; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){234395110}<LEND>[argument 155; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){664717623}<LEND>[argument 156; litteral](integer){2147109960}<LEND>[argument 157; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1968221692}<LEND>[argument 158; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1677520491}<LEND>[argument 159; litteral](integer){129792609}<LSEP>[argument 160; litteral](integer){509654262}<LEND>[argument 161; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1421193626}<LEND>[argument 162; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){279782963}<LEND>[argument 163; litteral](integer){15120314}<LSEP>[argument 164; litteral](integer){1125644024}<LSEP>[argument 165; litteral](integer){2036763253}<LEND>[argument 166; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){447981457}<LEND>[argument 167; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1984274015}<LEND>[argument 168; litteral](integer){71298556}<LEND>[argument 169; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){210209582}<LEND>[argument 170; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2036840306}<LEND>[argument 171; litteral](integer){2007979353}<LEND>[argument 172; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1190316623}<LEND>[argument 173; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){469927145}<LEND>[argument 174; litteral](integer){1629280977}<LEND>[argument 175; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1055303912}<LEND>[argument 176; litteral](integer){1234415967}<LEND>[argument 177; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){587485118}<LEND>[argument 178; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2089269954}<LEND>[argument 179; litteral](integer){286509772}<LSEP>[argument 180; litteral](integer){946522649}<LSEP>[argument 181; litteral](integer){1211190690}<LEND>[argument 182; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){14121361}<LEND>[argument 183; litteral](integer){258907079}<LSEP>[argument 184; litteral](integer){1784863367}<LSEP>[argument 185; litteral](integer){554475819}<LEND>[argument 186; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){554514593}<LEND>[argument 187; litteral](integer){954398875}<LSEP>[argument 188; litteral](integer){673781150}<LEND>[argument 189; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){46512803}<LEND>[argument 190; litteral](integer){774640050}<LSEP>[argument 191; litteral](integer){1708573537}<LEND>[argument 192; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){47339763}<LEND>[argument 193; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2013393611}<LEND>[argument 194; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){999900256}<LEND>[argument 195; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){457200712}<LEND>[argument 196; litteral](integer){1558402571}<LEND>[argument 197; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1407106514}<LEND>[argument 198; litteral](integer){1300781172}<LSEP>[argument 199; litteral](integer){932129338}<LEND>[argument 200; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){941553171}<LEND>[argument 201; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1513433620}<LEND>[argument 202; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){21062085}<LEND>[argument 203; litteral](integer){97749591}<LEND>[argument 204; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1379477749}<LEND>[argument 205; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1468077150}<LEND>[argument 206; litteral](integer){95982036}<LSEP>[argument 207; litteral](integer){1101220499}<LEND>[argument 208; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){502586821}<LEND>[argument 209; litteral](integer){536599039}<LSEP>[argument 210; litteral](integer){1095694083}<LSEP>[argument 211; litteral](integer){1249617249}<LEND>[argument 212; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1720443365}<LEND>[argument 213; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1931911438}<LEND>[argument 214; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){981148786}<LEND>[argument 215; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){992763006}<LEND>[argument 216; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){206132561}<LEND>[argument 217; litteral](integer){1521936283}<LEND>[argument 218; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1652823200}<LEND>[argument 219; litteral](integer){377659524}<LSEP>[argument 220; litteral](integer){724949828}<LSEP>[argument 221; litteral](integer){604415481}<LEND>[argument 222; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){8391854}<LEND>[argument 223; litteral](integer){1964941013}<LSEP>[argument 224; litteral](integer){1495347223}<LEND>[argument 225; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1994892809}<LEND>[argument 226; litteral](integer){470881879}<LSEP>[argument 227; litteral](integer){266007722}<LEND>[argument 228; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1848962333}<LEND>[argument 229; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2046739197}<LEND>[argument 230; litteral](integer){283942407}<LEND>[argument 231; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){803563339}<LEND>[argument 232; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){333999451}<LEND>[argument 233; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){423200686}<LEND>[argument 234; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){548717583}<LEND>[argument 235; litteral](integer){688050236}<LSEP>[argument 236; litteral](integer){731195532}<LEND>[argument 237; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1617231567}<LEND>[argument 238; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){720570633}<LEND>[argument 239; litteral](integer){511131161}<LSEP>[argument 240; litteral](integer){1041348749}<LSEP>[argument 241; litteral](integer){954389980}<LSEP>[argument 242; litteral](integer){529115020}<LEND>[argument 243; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1616795425}<LEND>[argument 244; litteral](integer){1456634933}<LSEP>[argument 245; litteral](integer){360460483}<LEND>[argument 246; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){976729337}<LEND>[argument 247; litteral](integer){1867049220}<LSEP>[argument 248; litteral](integer){611767495}<LSEP>[argument 249; litteral](integer){802211367}<LSEP>[argument 250; litteral](integer){1604830715}<LSEP>[argument 251; litteral](integer){1182753418}<LSEP>[argument 252; litteral](integer){1047551516}<LEND>[argument 253; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){977310009}<LEND>[argument 254; litteral](integer){2144258694}<LSEP>[argument 255; litteral](integer){1498298911}<LSEP>[argument 256; litteral](integer){70959679}<LEND>[argument 257; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1369480719}<LEND>[argument 258; litteral](integer){806573501}<LSEP>[argument 259; litteral](integer){403547392}<LEND>[argument 260; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){195291095}<LEND>[argument 261; litteral](integer){798000418}<LSEP>[argument 262; litteral](integer){2127500694}<LEND>[argument 263; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1849129025}<LEND>[argument 264; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){687303777}<LEND>[argument 265; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1525089479}<LEND>[argument 266; litteral](integer){963593838}<LEND>[argument 267; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){158172092}<LEND>[argument 268; litteral](integer){1635974736}<LSEP>[argument 269; litteral](integer){1521007353}<LEND>[argument 270; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){206583914}<LEND>[argument 271; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){498866465}<LEND>[argument 272; litteral](integer){2055719569}<LEND>[argument 273; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){281672779}<LEND>[argument 274; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){776138912}<LEND>[argument 275; litteral](integer){1380004239}<LEND>[argument 276; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){12670000}<LEND>[argument 277; litteral](integer){270623158}<LEND>[argument 278; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1582392279}<LEND>[argument 279; litteral](integer){645592001}<LEND>[argument 280; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){228728425}<LEND>[argument 281; litteral](integer){2063783501}<LSEP>[argument 282; litteral](integer){2080273936}<LEND>[argument 283; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1987556896}<LEND>[argument 284; litteral](integer){882614370}<LEND>[argument 285; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){61374210}<LEND>[argument 286; litteral](integer){1598242818}<LSEP>[argument 287; litteral](integer){980946572}<LSEP>[argument 288; litteral](integer){1402164002}<LEND>[argument 289; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){445604467}<LEND>[argument 290; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1105176730}<LEND>[argument 291; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1210520032}<LEND>[argument 292; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){123915692}<LEND>[argument 293; litteral](integer){1460384097}<LSEP>[argument 294; litteral](integer){937996104}<LSEP>[argument 295; litteral](integer){1274901112}<LSEP>[argument 296; litteral](integer){685182864}<LSEP>[argument 297; litteral](integer){216007531}<LEND>[argument 298; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1688580657}<LEND>[argument 299; litteral](integer){857895112}<LEND>[argument 300; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1952993872}<LEND>[argument 301; litteral](integer){1499217099}<LSEP>[argument 302; litteral](integer){571656876}<LSEP>[argument 303; litteral](integer){1294862542}<LEND>[argument 304; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1722176048}<LEND>[argument 305; litteral](integer){2018374148}<LEND>[argument 306; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1862438705}<LEND>[argument 307; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1233699590}<LEND>[argument 308; litteral](integer){244698063}<LSEP>[argument 309; litteral](integer){1924312073}<LEND>[argument 310; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1563187722}<LEND>[argument 311; litteral](integer){1726716066}<LSEP>[argument 312; litteral](integer){992879779}<LSEP>[argument 313; litteral](integer){404965833}<LEND>[argument 314; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1960007297}<LEND>[argument 315; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1220769316}<LEND>[argument 316; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1185948758}<LEND>[argument 317; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1498495758}<LEND>[argument 318; litteral](integer){1881545673}<LSEP>[argument 319; litteral](integer){522955932}<LEND>[argument 320; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){865366064}<LEND>[argument 321; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2085420893}<LEND>[argument 322; litteral](integer){18127359}<LSEP>[argument 323; litteral](integer){43138436}<LSEP>[argument 324; litteral](integer){819795107}<LEND>[argument 325; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){244422753}<LEND>[argument 326; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1288075706}<LEND>[argument 327; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){886094963}<LEND>[argument 328; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1297126780}<LEND>[argument 329; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2058220377}<LEND>[argument 330; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){396896852}<LEND>[argument 331; litteral](integer){43446690}<LEND>[argument 332; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1821657650}<LEND>[argument 333; litteral](integer){1531289497}<LEND>[argument 334; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1591850013}<LEND>[argument 335; litteral](integer){150831800}<LSEP>[argument 336; litteral](integer){793565107}<LEND>[argument 337; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){882259681}<LEND>[argument 338; litteral](integer){762444942}<LEND>[argument 339; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){103445203}<LEND>[argument 340; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){175537387}<LEND>[argument 341; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){578957675}<LEND>[argument 342; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1351031238}<LEND>[argument 343; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1022589543}<LEND>[argument 344; litteral](integer){1337840319}<LEND>[argument 345; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){541866608}<LEND>[argument 346; litteral](integer){1989090810}<LEND>[argument 347; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1722102886}<LEND>[argument 348; litteral](integer){1886878736}<LSEP>[argument 349; litteral](integer){1360063345}<LSEP>[argument 350; litteral](integer){1593135967}<LEND>[argument 351; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){467588209}<LEND>[argument 352; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1128453118}<LEND>[argument 353; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1905646124}<LEND>[argument 354; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1520961216}<LEND>[argument 355; litteral](integer){48609795}<LEND>[argument 356; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){857700198}<LEND>[argument 357; litteral](integer){218796654}<LEND>[argument 358; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1318291951}<LEND>[argument 359; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1738945352}<LEND>[argument 360; litteral](integer){1311728022}<LEND>[argument 361; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1533322627}<LEND>[argument 362; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){713857498}<LEND>[argument 363; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1171906773}<LEND>[argument 364; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2075985602}<LEND>[argument 365; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){321165104}<LEND>[argument 366; litteral](integer){1596351694}<LEND>[argument 367; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){871365309}<LEND>[argument 368; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){699691061}<LEND>[argument 369; litteral](integer){1151253950}<LSEP>[argument 370; litteral](integer){438629155}<LSEP>[argument 371; litteral](integer){768729269}<LEND>[argument 372; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){450249120}<LEND>[argument 373; litteral](integer){1237479622}<LEND>[argument 374; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1377066971}<LEND>[argument 375; litteral](integer){1590220252}<LEND>[argument 376; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1687061434}<LEND>[argument 377; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){294506345}<LEND>[argument 378; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){239989571}<LEND>[argument 379; litteral](integer){505223144}<LSEP>[argument 380; litteral](integer){1227858691}<LSEP>[argument 381; litteral](integer){665822658}<LSEP>[argument 382; litteral](integer){1514490062}<LSEP>[argument 383; litteral](integer){423011487}<LSEP>[argument 384; litteral](integer){944652376}<LEND>[argument 385; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){835625330}<LEND>[argument 386; litteral](integer){1176711580}<LSEP>[argument 387; litteral](integer){253591370}<LSEP>[argument 388; litteral](integer){566450670}<LEND>[argument 389; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1306187412}<LEND>[argument 390; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1543751365}<LEND>[argument 391; litteral](integer){1786360920}<LEND>[argument 392; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1522666293}<LEND>[argument 393; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1653504171}<LEND>[argument 394; litteral](integer){339862007}<LEND>[argument 395; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){106544923}<LEND>[argument 396; litteral](integer){704538048}<LSEP>[argument 397; litteral](integer){1444158266}<LEND>[argument 398; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){883518127}<LEND>[argument 399; litteral](integer){1028221995}<LSEP>[argument 400; litteral](integer){194136558}<LEND>[argument 401; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2042150032}<LEND>[argument 402; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){312764949}<LEND>[argument 403; litteral](integer){196771420}<LEND>[argument 404; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1456144739}<LEND>[argument 405; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1955573569}<LEND>[argument 406; litteral](integer){118428340}<LSEP>[argument 407; litteral](integer){1275154082}<LEND>[argument 408; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){808048955}<LEND>[argument 409; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){323931561}<LEND>[argument 410; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1090021379}<LEND>[argument 411; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){636591184}<LEND>[argument 412; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1608385336}<LEND>[argument 413; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){927294454}<LEND>[argument 414; litteral](integer){1625003464}<LEND>[argument 415; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1466232606}<LEND>[argument 416; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1429286560}<LEND>[argument 417; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2144293145}<LEND>[argument 418; litteral](integer){864274577}<LSEP>[argument 419; litteral](integer){305066253}<LSEP>[argument 420; litteral](integer){534550227}<LSEP>[argument 421; litteral](integer){1411403792}<LEND>[argument 422; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){571693490}<LEND>[argument 423; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1689275798}<LEND>[argument 424; litteral](integer){1080320998}<LSEP>[argument 425; litteral](integer){1405114902}<LSEP>[argument 426; litteral](integer){1727996708}<LEND>[argument 427; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1301659212}<LEND>[argument 428; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){607665018}<LEND>[argument 429; litteral](integer){314129719}<LEND>[argument 430; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){602478843}<LEND>[argument 431; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){773921730}<LEND>[argument 432; litteral](integer){1139980041}<LSEP>[argument 433; litteral](integer){715961557}<LSEP>[argument 434; litteral](integer){1830864144}<LSEP>[argument 435; litteral](integer){1525967337}<LEND>[argument 436; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){929643465}<LEND>[argument 437; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1813709190}<LEND>[argument 438; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){929891508}<LEND>[argument 439; litteral](integer){1578676464}<LEND>[argument 440; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1182811762}<LEND>[argument 441; litteral](integer){984922892}<LSEP>[argument 442; litteral](integer){389629469}<LSEP>[argument 443; litteral](integer){1673492755}<LEND>[argument 444; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){462670764}<LEND>[argument 445; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){246277774}<LEND>[argument 446; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){767929486}<LEND>[argument 447; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){802416236}<LEND>[argument 448; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1940884981}<LEND>[argument 449; litteral](integer){640170722}<LEND>[argument 450; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){165993819}<LEND>[argument 451; litteral](integer){1696892218}<LSEP>[argument 452; litteral](integer){1464588922}<LEND>[argument 453; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1653596071}<LEND>[argument 454; litteral](integer){1210818999}<LEND>[argument 455; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){670376827}<LEND>[argument 456; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){731102808}<LEND>[argument 457; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){777216526}<LEND>[argument 458; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){898296394}<LEND>[argument 459; litteral](integer){1561615746}<LSEP>[argument 460; litteral](integer){1831006025}<LSEP>[argument 461; litteral](integer){1111556347}<LEND>[argument 462; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){263246572}<LEND>[argument 463; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1163356183}<LEND>[argument 464; litteral](integer){467276676}<LSEP>[argument 465; litteral](integer){203500682}<LSEP>[argument 466; litteral](integer){359485269}<LSEP>[argument 467; litteral](integer){705462960}<LSEP>[argument 468; litteral](integer){927838281}<LEND>[argument 469; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1782081487}<LEND>[argument 470; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){950942864}<LEND>[argument 471; litteral](integer){976412356}<LSEP>[argument 472; litteral](integer){400905896}<LEND>[argument 473; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){733281316}<LEND>[argument 474; litteral](integer){1068664818}<LSEP>[argument 475; litteral](integer){451303149}<LEND>[argument 476; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1103801678}<LEND>[argument 477; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1088841592}<LEND>[argument 478; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){228673413}<LEND>[argument 479; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1869543477}<LEND>[argument 480; litteral](integer){866383748}<LEND>[argument 481; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){409689948}<LEND>[argument 482; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1612116215}<LEND>[argument 483; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){190246274}<LEND>[argument 484; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){194509423}<LEND>[argument 485; litteral](integer){1206603931}<LSEP>[argument 486; litteral](integer){117067584}<LEND>[argument 487; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1613500060}<LEND>[argument 488; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1541486997}<LEND>[argument 489; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1473099121}<LEND>[argument 490; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){475673387}<LEND>[argument 491; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1245551072}<LEND>[argument 492; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){851373953}<LEND>[argument 493; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1408246220}<LEND>[argument 494; litteral](integer){1457745360}<LEND>[argument 495; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){248399565}<LEND>[argument 496; litteral](integer){624674363}<LEND>[argument 497; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){923955119}<LEND>[argument 498; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){492808034}<LEND>[argument 499; litteral](integer){616737261}<LEND>[argument 500; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){145960398}<LEND>[argument 501; litteral](integer){465456997}<LSEP>[argument 502; litteral](integer){832542447}<LEND>[argument 503; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){764063146}<LEND>[argument 504; litteral](integer){813069861}<LEND>[argument 505; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){527647017}<LEND>[argument 506; litteral](integer){1766834209}<LSEP>[argument 507; litteral](integer){101117051}<LEND>[argument 508; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){722236970}<LEND>[argument 509; litteral](integer){931218381}<LEND>[argument 510; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1629313845}<LEND>[argument 511; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2106158277}<LEND>[argument 512; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1000293403}<LEND>[argument 513; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){182009680}<LEND>[argument 514; litteral](integer){1436681922}<LEND>[argument 515; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){662110697}<LEND>[argument 516; litteral](integer){1089360825}<LSEP>[argument 517; litteral](integer){1998180686}<LSEP>[argument 518; litteral](integer){15467122}<LEND>[argument 519; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2007092026}<LEND>[argument 520; litteral](integer){64293585}<LEND>[argument 521; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1862660341}<LEND>[argument 522; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1166834028}<LEND>[argument 523; litteral](integer){1325299447}<LSEP>[argument 524; litteral](integer){1033331624}<LSEP>[argument 525; litteral](integer){613513384}<LEND>[argument 526; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){244292668}<LEND>[argument 527; litteral](integer){1556122232}<LEND>[argument 528; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1471134068}<LEND>[argument 529; litteral](integer){1782351979}<LSEP>[argument 530; litteral](integer){1275930866}<LEND>[argument 531; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1944590852}<LEND>[argument 532; litteral](integer){566724409}<LSEP>[argument 533; litteral](integer){371640717}<LSEP>[argument 534; litteral](integer){202304414}<LEND>[argument 535; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1723675232}<LEND>[argument 536; litteral](integer){648615189}<LSEP>[argument 537; litteral](integer){159081694}<LEND>[argument 538; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){793714735}<LEND>[argument 539; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1940374247}<LEND>[argument 540; litteral](integer){129919944}<LEND>[argument 541; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){700447199}<LEND>[argument 542; litteral](integer){1229273040}<LEND>[argument 543; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){133109680}<LEND>[argument 544; litteral](integer){447051902}<LSEP>[argument 545; litteral](integer){343010603}<LEND>[argument 546; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1520726198}<LEND>[argument 547; litteral](integer){1289811180}<LEND>[argument 548; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1831549669}<LEND>[argument 549; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){54375447}<LEND>[argument 550; litteral](integer){207499460}<LEND>[argument 551; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){926501899}<LEND>[argument 552; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){36679808}<LEND>[argument 553; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){346957311}<LEND>[argument 554; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){517667264}<LEND>[argument 555; litteral](integer){1412720009}<LSEP>[argument 556; litteral](integer){780240589}<LSEP>[argument 557; litteral](integer){1698566688}<LEND>[argument 558; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){587072300}<LEND>[argument 559; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1627535114}<LEND>[argument 560; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1776369547}<LEND>[argument 561; litteral](integer){1352056769}<LSEP>[argument 562; litteral](integer){1249221095}<LSEP>[argument 563; litteral](integer){2030017608}<LEND>[argument 564; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){189665187}<LEND>[argument 565; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1914942373}<LEND>[argument 566; litteral](integer){1529193725}<LEND>[argument 567; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1361527196}<LEND>[argument 568; litteral](integer){2056450823}<LSEP>[argument 569; litteral](integer){1548689335}<LSEP>[argument 570; litteral](integer){407292182}<LEND>[argument 571; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){97738409}<LEND>[argument 572; litteral](integer){1476271457}<LSEP>[argument 573; litteral](integer){2049889656}<LEND>[argument 574; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1234310459}<LEND>[argument 575; litteral](integer){613419929}<LSEP>[argument 576; litteral](integer){1313559959}<LSEP>[argument 577; litteral](integer){1843280481}<LSEP>[argument 578; litteral](integer){68659415}<LEND>[argument 579; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2003968968}<LEND>[argument 580; litteral](integer){298833804}<LEND>[argument 581; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){967490466}<LEND>[argument 582; litteral](integer){1587269028}<LEND>[argument 583; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1406278687}<LEND>[argument 584; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){907344964}<LEND>[argument 585; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1369424299}<LEND>[argument 586; litteral](integer){1374519002}<LEND>[argument 587; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1170529598}<LEND>[argument 588; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1020031440}<LEND>[argument 589; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){841821598}<LEND>[argument 590; litteral](integer){892971175}<LSEP>[argument 591; litteral](integer){582131352}<LEND>[argument 592; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){856201933}<LEND>[argument 593; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1923603158}<LEND>[argument 594; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){554907061}<LEND>[argument 595; litteral](integer){528470058}<LEND>[argument 596; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){520620721}<LEND>[argument 597; litteral](integer){1858375074}<LSEP>[argument 598; litteral](integer){1260200833}<LSEP>[argument 599; litteral](integer){884420306}<LSEP>[argument 600; litteral](integer){170422965}<LEND>[argument 601; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1091509229}<LEND>[argument 602; litteral](integer){1341083156}<LSEP>[argument 603; litteral](integer){614714942}<LSEP>[argument 604; litteral](integer){713550238}<LEND>[argument 605; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){262468024}<LEND>[argument 606; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){998188749}<LEND>[argument 607; litteral](integer){1217726001}<LSEP>[argument 608; litteral](integer){2055208521}<LSEP>[argument 609; litteral](integer){1173791159}<LSEP>[argument 610; litteral](integer){192457121}<LSEP>[argument 611; litteral](integer){389959635}<LSEP>[argument 612; litteral](integer){1032159058}<LSEP>[argument 613; litteral](integer){73799583}<LEND>[argument 614; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1353392281}<LEND>[argument 615; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){324182679}<LEND>[argument 616; litteral](integer){1627248569}<LEND>[argument 617; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1412578450}<LEND>[argument 618; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){778744804}<LEND>[argument 619; litteral](integer){1750339766}<LEND>[argument 620; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1851563057}<LEND>[argument 621; litteral](integer){2012418753}<LEND>[argument 622; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1369889007}<LEND>[argument 623; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){891159728}<LEND>[argument 624; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){557149156}<LEND>[argument 625; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1931825328}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){.Random.seed}<LSEP>[](symbol){saved_seed}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.970000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.970000}<LEND>[argument 2; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.970000}<LEND>[argument 3; litteral](real){1.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 8; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){testRes}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){paleotree}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LEND>[](symbol){record}<LEND>[statement 5; call](){}<LSEP>[](symbol){expect_true}<LSEP>[](symbol){testRes}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){quick example of birth-death s...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.100000}<LSEP>[argument 3; litteral](real){1.000000}<LSEP>[argument 4; litteral](real){50.000000}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[statement 3; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){record}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//quick_simFossil...}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){cladogeneticTraitCont function...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){444.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[argument 4; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){trait}<LEND>[call](){}<LSEP>[](symbol){cladogeneticTraitCont}<LSEP>[](symbol){taxa}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){taxa2phylo}<LSEP>[](symbol){taxa}<LEND>[statement 5; call](){}<LSEP>[](symbol){plotTraitgram}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){record2}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[argument 5; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){taxa2}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record2}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){trait2}<LEND>[call](){}<LSEP>[](symbol){cladogeneticTraitCont}<LSEP>[](symbol){taxa2}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){taxa2phylo}<LSEP>[](symbol){taxa2}<LEND>[statement 10; call](){}<LSEP>[](symbol){plotTraitgram}<LSEP>[](symbol){trait2}<LSEP>[](symbol){tree2}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 11; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 12; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 13; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){trait}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//cladogeneticTra...}<LEND>[statement 14; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//cladogeneticTra...}<LEND>[statement 15; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){trait2}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//cladogeneticTra...}<LEND>[statement 16; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){tree2}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//cladogeneticTra...}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){minBranchLength are not stocha...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){read.tree}<LSEP>[argument 0; litteral](str){(((Spinosaurus,Angaturama,Irri...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ages}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){98.500000}<LSEP>[argument 1; litteral](real){106.750000}<LSEP>[argument 2; litteral](real){106.750000}<LSEP>[argument 3; litteral](real){119.650000}<LSEP>[argument 4; litteral](real){129.675000}<LSEP>[argument 5; litteral](real){163.750000}<LSEP>[argument 6; litteral](real){168.800000}<LSEP>[argument 7; litteral](real){169.850000}<LSEP>[argument 8; litteral](real){167.200000}<LSEP>[argument 9; litteral](real){160.400000}<LSEP>[argument 10; litteral](real){163.750000}<LSEP>[argument 11; litteral](real){168.850000}<LSEP>[argument 12; litteral](real){167.200000}<LSEP>[argument 13; litteral](real){154.700000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){98.500000}<LSEP>[argument 1; litteral](real){106.750000}<LSEP>[argument 2; litteral](real){106.750000}<LSEP>[argument 3; litteral](real){119.650000}<LSEP>[argument 4; litteral](real){129.675000}<LSEP>[argument 5; litteral](real){163.750000}<LSEP>[argument 6; litteral](real){154.250000}<LSEP>[argument 7; litteral](real){169.850000}<LSEP>[argument 8; litteral](real){167.200000}<LSEP>[argument 9; litteral](real){156.000000}<LSEP>[argument 10; litteral](real){163.750000}<LSEP>[argument 11; litteral](real){168.850000}<LSEP>[argument 12; litteral](real){167.200000}<LSEP>[argument 13; litteral](real){148.550000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){ages}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Spinosaurus}<LSEP>[argument 1; litteral](str){Angaturama}<LSEP>[argument 2; litteral](str){Irritator}<LSEP>[argument 3; litteral](str){Suchomimus}<LSEP>[argument 4; litteral](str){Baryonyx}<LSEP>[argument 5; litteral](str){Eustreptospondylus}<LSEP>[argument 6; litteral](str){Afrovenator}<LSEP>[argument 7; litteral](str){Magnosaurus}<LSEP>[argument 8; litteral](str){Dubreuillosaurus}<LSEP>[argument 9; litteral](str){Leshansaurus}<LSEP>[argument 10; litteral](str){Piveaeausaurus}<LSEP>[argument 11; litteral](str){Duriavenator}<LSEP>[argument 12; litteral](str){Megalosaurus}<LSEP>[argument 13; litteral](str){Torvosaurus}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timetreesMBL}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timetreesMBL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){timePaleoPhy}<LSEP>[](symbol){tree}<LSEP>[](symbol){ages}<LSEP>[argument 2; litteral](str){mbl}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){testEqual}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){timetreesMBL}<LSEP>[](symbol){all.equal}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timetreesMBL}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){expect_true}<LSEP>[](symbol){testEqual}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord counts taxa in...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){saved_seed}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](integer){10403}<LSEP>[argument 1; litteral](integer){303}<LSEP>[argument 2; litteral](integer){1036177046}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){725760437}<LEND>[argument 4; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){603627585}<LEND>[argument 5; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2122159062}<LEND>[argument 6; litteral](integer){1171112377}<LSEP>[argument 7; litteral](integer){1813269596}<LSEP>[argument 8; litteral](integer){1251795192}<LEND>[argument 9; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){213283628}<LEND>[argument 10; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){282099126}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1747914946}<LEND>[argument 12; litteral](integer){1479354505}<LEND>[argument 13; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){226129111}<LEND>[argument 14; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1120084489}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1844943529}<LEND>[argument 16; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){394320296}<LEND>[argument 17; litteral](integer){1482511303}<LSEP>[argument 18; litteral](integer){520906459}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1951809137}<LEND>[argument 20; litteral](integer){1363632276}<LSEP>[argument 21; litteral](integer){798494342}<LEND>[argument 22; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2007130438}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){329083480}<LEND>[argument 24; litteral](integer){101103537}<LEND>[argument 25; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1804498241}<LEND>[argument 26; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){52036596}<LEND>[argument 27; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){129149475}<LEND>[argument 28; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2092284404}<LEND>[argument 29; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1512309709}<LEND>[argument 30; litteral](integer){1832373955}<LSEP>[argument 31; litteral](integer){485517067}<LEND>[argument 32; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){374388006}<LEND>[argument 33; litteral](integer){911286622}<LEND>[argument 34; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){174795653}<LEND>[argument 35; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){325613373}<LEND>[argument 36; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2107933316}<LEND>[argument 37; litteral](integer){277623990}<LSEP>[argument 38; litteral](integer){1126034325}<LSEP>[argument 39; litteral](integer){967219322}<LEND>[argument 40; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){622684168}<LEND>[argument 41; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1823542214}<LEND>[argument 42; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){551718064}<LEND>[argument 43; litteral](integer){1617509018}<LSEP>[argument 44; litteral](integer){1812905781}<LEND>[argument 45; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1516266781}<LEND>[argument 46; litteral](integer){1813298003}<LSEP>[argument 47; litteral](integer){1527126533}<LSEP>[argument 48; litteral](integer){2029334767}<LSEP>[argument 49; litteral](integer){1508293823}<LSEP>[argument 50; litteral](integer){573491295}<LSEP>[argument 51; litteral](integer){2030201913}<LSEP>[argument 52; litteral](integer){1429423985}<LEND>[argument 53; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){664131862}<LEND>[argument 54; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1679318866}<LEND>[argument 55; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1872359163}<LEND>[argument 56; litteral](integer){265285104}<LSEP>[argument 57; litteral](integer){531042338}<LEND>[argument 58; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1517572259}<LEND>[argument 59; litteral](integer){1723827471}<LSEP>[argument 60; litteral](integer){1044677938}<LSEP>[argument 61; litteral](integer){201398378}<LEND>[argument 62; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1180780811}<LEND>[argument 63; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){534061217}<LEND>[argument 64; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1359132116}<LEND>[argument 65; litteral](integer){1990560448}<LSEP>[argument 66; litteral](integer){1329557495}<LEND>[argument 67; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){370074826}<LEND>[argument 68; litteral](integer){2014199603}<LSEP>[argument 69; litteral](integer){1868774009}<LSEP>[argument 70; litteral](integer){1179426044}<LEND>[argument 71; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1892744141}<LEND>[argument 72; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){436358876}<LEND>[argument 73; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1469361412}<LEND>[argument 74; litteral](integer){736044398}<LEND>[argument 75; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){813026776}<LEND>[argument 76; litteral](integer){557992276}<LEND>[argument 77; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1932790469}<LEND>[argument 78; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){245804683}<LEND>[argument 79; litteral](integer){1942411579}<LEND>[argument 80; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2089574479}<LEND>[argument 81; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1229172885}<LEND>[argument 82; litteral](integer){928752528}<LSEP>[argument 83; litteral](integer){1832764069}<LSEP>[argument 84; litteral](integer){612961041}<LSEP>[argument 85; litteral](integer){1093393989}<LEND>[argument 86; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1206948333}<LEND>[argument 87; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1614768400}<LEND>[argument 88; litteral](integer){741416391}<LEND>[argument 89; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){14895279}<LEND>[argument 90; litteral](integer){2137581486}<LEND>[argument 91; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1917328695}<LEND>[argument 92; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){695024185}<LEND>[argument 93; litteral](integer){1880390052}<LSEP>[argument 94; litteral](integer){1631603462}<LEND>[argument 95; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){360094324}<LEND>[argument 96; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){348004426}<LEND>[argument 97; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){16043754}<LEND>[argument 98; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){345223205}<LEND>[argument 99; litteral](integer){232485093}<LSEP>[argument 100; litteral](integer){958748896}<LSEP>[argument 101; litteral](integer){1926422718}<LSEP>[argument 102; litteral](integer){1561630779}<LEND>[argument 103; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){188456126}<LEND>[argument 104; litteral](integer){1666740166}<LSEP>[argument 105; litteral](integer){398615854}<LEND>[argument 106; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1847754280}<LEND>[argument 107; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1014863579}<LEND>[argument 108; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1882484763}<LEND>[argument 109; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1292100414}<LEND>[argument 110; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){323235067}<LEND>[argument 111; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1767230762}<LEND>[argument 112; litteral](integer){1729797189}<LSEP>[argument 113; litteral](integer){192023476}<LEND>[argument 114; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){997950437}<LEND>[argument 115; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){923635969}<LEND>[argument 116; litteral](integer){330197793}<LEND>[argument 117; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1741808408}<LEND>[argument 118; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){647487620}<LEND>[argument 119; litteral](integer){1669006421}<LEND>[argument 120; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){737753468}<LEND>[argument 121; litteral](integer){367880042}<LEND>[argument 122; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1377892731}<LEND>[argument 123; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){98615161}<LEND>[argument 124; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1354440600}<LEND>[argument 125; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1012883369}<LEND>[argument 126; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){494649046}<LEND>[argument 127; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1098265353}<LEND>[argument 128; litteral](integer){979223029}<LSEP>[argument 129; litteral](integer){1969861207}<LEND>[argument 130; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1860937136}<LEND>[argument 131; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){542474266}<LEND>[argument 132; litteral](integer){526670415}<LSEP>[argument 133; litteral](integer){1592982404}<LEND>[argument 134; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1536130542}<LEND>[argument 135; litteral](integer){1997554069}<LEND>[argument 136; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){733554927}<LEND>[argument 137; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){445414682}<LEND>[argument 138; litteral](integer){449671441}<LEND>[argument 139; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){686865517}<LEND>[argument 140; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1820400993}<LEND>[argument 141; litteral](integer){1217427759}<LEND>[argument 142; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){722062750}<LEND>[argument 143; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){967057183}<LEND>[argument 144; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){250129821}<LEND>[argument 145; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1329064563}<LEND>[argument 146; litteral](integer){1735120055}<LSEP>[argument 147; litteral](integer){1471134075}<LEND>[argument 148; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){596551551}<LEND>[argument 149; litteral](integer){400278485}<LEND>[argument 150; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){808935108}<LEND>[argument 151; litteral](integer){1973326804}<LEND>[argument 152; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){672078377}<LEND>[argument 153; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1247275109}<LEND>[argument 154; litteral](integer){704941579}<LEND>[argument 155; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1550040087}<LEND>[argument 156; litteral](integer){743138592}<LSEP>[argument 157; litteral](integer){930990651}<LEND>[argument 158; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1607917878}<LEND>[argument 159; litteral](integer){2060963439}<LSEP>[argument 160; litteral](integer){488682191}<LEND>[argument 161; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1434272503}<LEND>[argument 162; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){978515500}<LEND>[argument 163; litteral](integer){1771885101}<LEND>[argument 164; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1677639025}<LEND>[argument 165; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1654052608}<LEND>[argument 166; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1101520546}<LEND>[argument 167; litteral](integer){902509822}<LEND>[argument 168; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1401523511}<LEND>[argument 169; litteral](integer){327926094}<LEND>[argument 170; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1030629990}<LEND>[argument 171; litteral](integer){2022730738}<LSEP>[argument 172; litteral](integer){515803255}<LSEP>[argument 173; litteral](integer){769626375}<LSEP>[argument 174; litteral](integer){1598251218}<LSEP>[argument 175; litteral](integer){534851199}<LSEP>[argument 176; litteral](integer){148219296}<LEND>[argument 177; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){304163521}<LEND>[argument 178; litteral](integer){1576747397}<LSEP>[argument 179; litteral](integer){1186404999}<LSEP>[argument 180; litteral](integer){956828826}<LEND>[argument 181; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){870403419}<LEND>[argument 182; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){244447980}<LEND>[argument 183; litteral](integer){558774041}<LEND>[argument 184; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1298988907}<LEND>[argument 185; litteral](integer){1582514961}<LSEP>[argument 186; litteral](integer){2092505395}<LSEP>[argument 187; litteral](integer){496186877}<LEND>[argument 188; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){671051319}<LEND>[argument 189; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1211957854}<LEND>[argument 190; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2083981219}<LEND>[argument 191; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1228808038}<LEND>[argument 192; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1687467628}<LEND>[argument 193; litteral](integer){570329149}<LSEP>[argument 194; litteral](integer){1438490807}<LEND>[argument 195; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){839725046}<LEND>[argument 196; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){195148353}<LEND>[argument 197; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1831062019}<LEND>[argument 198; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){526424982}<LEND>[argument 199; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1403433410}<LEND>[argument 200; litteral](integer){1959280201}<LSEP>[argument 201; litteral](integer){1900142734}<LEND>[argument 202; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1538855153}<LEND>[argument 203; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){237828605}<LEND>[argument 204; litteral](integer){309866360}<LSEP>[argument 205; litteral](integer){1070678719}<LEND>[argument 206; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1923175181}<LEND>[argument 207; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){22056925}<LEND>[argument 208; litteral](integer){1436768120}<LSEP>[argument 209; litteral](integer){488972697}<LSEP>[argument 210; litteral](integer){1563872704}<LSEP>[argument 211; litteral](integer){692764883}<LEND>[argument 212; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1262136728}<LEND>[argument 213; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){259531523}<LEND>[argument 214; litteral](integer){742157953}<LEND>[argument 215; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){278832557}<LEND>[argument 216; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1912370876}<LEND>[argument 217; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1725114612}<LEND>[argument 218; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2017225921}<LEND>[argument 219; litteral](integer){1786469420}<LEND>[argument 220; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){714778879}<LEND>[argument 221; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){386754820}<LEND>[argument 222; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){289194725}<LEND>[argument 223; litteral](integer){1991342509}<LSEP>[argument 224; litteral](integer){748149039}<LEND>[argument 225; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1730807078}<LEND>[argument 226; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){986115353}<LEND>[argument 227; litteral](integer){1379519120}<LEND>[argument 228; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1636906231}<LEND>[argument 229; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1098353257}<LEND>[argument 230; litteral](integer){1175377114}<LSEP>[argument 231; litteral](integer){739371747}<LEND>[argument 232; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){774448289}<LEND>[argument 233; litteral](integer){36333629}<LSEP>[argument 234; litteral](integer){1695467443}<LEND>[argument 235; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){808656582}<LEND>[argument 236; litteral](integer){788592911}<LEND>[argument 237; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1999354502}<LEND>[argument 238; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){727953197}<LEND>[argument 239; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1451370889}<LEND>[argument 240; litteral](integer){578104954}<LSEP>[argument 241; litteral](integer){2090480299}<LEND>[argument 242; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){205444724}<LEND>[argument 243; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2026816015}<LEND>[argument 244; litteral](integer){377378048}<LSEP>[argument 245; litteral](integer){1595574605}<LSEP>[argument 246; litteral](integer){2096603925}<LSEP>[argument 247; litteral](integer){1133713232}<LSEP>[argument 248; litteral](integer){529713193}<LSEP>[argument 249; litteral](integer){1066966412}<LSEP>[argument 250; litteral](integer){170149274}<LEND>[argument 251; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){452020930}<LEND>[argument 252; litteral](integer){1319893381}<LEND>[argument 253; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){468923166}<LEND>[argument 254; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1387018709}<LEND>[argument 255; litteral](integer){315724425}<LSEP>[argument 256; litteral](integer){1771839137}<LEND>[argument 257; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1076429625}<LEND>[argument 258; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){594124435}<LEND>[argument 259; litteral](integer){1764573655}<LSEP>[argument 260; litteral](integer){2126400933}<LSEP>[argument 261; litteral](integer){1175462653}<LEND>[argument 262; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){735341159}<LEND>[argument 263; litteral](integer){776851440}<LEND>[argument 264; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){593085224}<LEND>[argument 265; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){321080038}<LEND>[argument 266; litteral](integer){232951242}<LSEP>[argument 267; litteral](integer){53159976}<LSEP>[argument 268; litteral](integer){761226266}<LSEP>[argument 269; litteral](integer){1132230380}<LSEP>[argument 270; litteral](integer){156003327}<LSEP>[argument 271; litteral](integer){291871859}<LEND>[argument 272; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1365420732}<LEND>[argument 273; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){434704293}<LEND>[argument 274; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){710699094}<LEND>[argument 275; litteral](integer){1945550183}<LEND>[argument 276; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){338164208}<LEND>[argument 277; litteral](integer){1061636523}<LSEP>[argument 278; litteral](integer){787014732}<LSEP>[argument 279; litteral](integer){375052835}<LEND>[argument 280; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1042702321}<LEND>[argument 281; litteral](integer){294963721}<LEND>[argument 282; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1659043318}<LEND>[argument 283; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){805206448}<LEND>[argument 284; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){795524141}<LEND>[argument 285; litteral](integer){2042561387}<LEND>[argument 286; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){295607247}<LEND>[argument 287; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2024779994}<LEND>[argument 288; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){918154772}<LEND>[argument 289; litteral](integer){417230217}<LEND>[argument 290; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1118697097}<LEND>[argument 291; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1943909346}<LEND>[argument 292; litteral](integer){2057226244}<LEND>[argument 293; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2072304295}<LEND>[argument 294; litteral](integer){949559705}<LSEP>[argument 295; litteral](integer){178723448}<LEND>[argument 296; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1356796307}<LEND>[argument 297; litteral](integer){715277674}<LSEP>[argument 298; litteral](integer){1998981989}<LSEP>[argument 299; litteral](integer){927560545}<LEND>[argument 300; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){944019214}<LEND>[argument 301; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1807447796}<LEND>[argument 302; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1067174394}<LEND>[argument 303; litteral](integer){929760665}<LEND>[argument 304; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){969411345}<LEND>[argument 305; litteral](integer){1299327975}<LEND>[argument 306; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){170000888}<LEND>[argument 307; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){168641432}<LEND>[argument 308; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1624203151}<LEND>[argument 309; litteral](integer){1614982366}<LEND>[argument 310; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1102979733}<LEND>[argument 311; litteral](integer){526444388}<LEND>[argument 312; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1237966628}<LEND>[argument 313; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){59359861}<LEND>[argument 314; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){7557844}<LEND>[argument 315; litteral](integer){1728637406}<LSEP>[argument 316; litteral](integer){1804982761}<LSEP>[argument 317; litteral](integer){1951396818}<LSEP>[argument 318; litteral](integer){1824627493}<LEND>[argument 319; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1081218533}<LEND>[argument 320; litteral](integer){957385966}<LEND>[argument 321; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){82687539}<LEND>[argument 322; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1107928069}<LEND>[argument 323; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){760534415}<LEND>[argument 324; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){747053325}<LEND>[argument 325; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2043224827}<LEND>[argument 326; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){142649540}<LEND>[argument 327; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1237090611}<LEND>[argument 328; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2090174091}<LEND>[argument 329; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){546057316}<LEND>[argument 330; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1364368341}<LEND>[argument 331; litteral](integer){2139897899}<LSEP>[argument 332; litteral](integer){2029754430}<LSEP>[argument 333; litteral](integer){312901099}<LEND>[argument 334; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1624639036}<LEND>[argument 335; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){426243303}<LEND>[argument 336; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){58536998}<LEND>[argument 337; litteral](integer){2139596980}<LEND>[argument 338; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1350752873}<LEND>[argument 339; litteral](integer){759504442}<LEND>[argument 340; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1245417258}<LEND>[argument 341; litteral](integer){1965208412}<LEND>[argument 342; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1025890175}<LEND>[argument 343; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){288698290}<LEND>[argument 344; litteral](integer){1229142901}<LEND>[argument 345; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1845366857}<LEND>[argument 346; litteral](integer){138047863}<LEND>[argument 347; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1645968706}<LEND>[argument 348; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){883944772}<LEND>[argument 349; litteral](integer){1983029056}<LSEP>[argument 350; litteral](integer){2123088736}<LEND>[argument 351; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1036855518}<LEND>[argument 352; litteral](integer){1040522211}<LEND>[argument 353; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){130790537}<LEND>[argument 354; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){669375180}<LEND>[argument 355; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1542718749}<LEND>[argument 356; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1627453842}<LEND>[argument 357; litteral](integer){1242443435}<LSEP>[argument 358; litteral](integer){289588620}<LSEP>[argument 359; litteral](integer){1917801621}<LEND>[argument 360; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){92759993}<LEND>[argument 361; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1162805136}<LEND>[argument 362; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1818574900}<LEND>[argument 363; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1900424812}<LEND>[argument 364; litteral](integer){2076434870}<LSEP>[argument 365; litteral](integer){1122995521}<LSEP>[argument 366; litteral](integer){57838530}<LEND>[argument 367; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){21748160}<LEND>[argument 368; litteral](integer){1654745439}<LSEP>[argument 369; litteral](integer){309697198}<LSEP>[argument 370; litteral](integer){1981688554}<LSEP>[argument 371; litteral](integer){959837411}<LSEP>[argument 372; litteral](integer){2025789341}<LEND>[argument 373; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){238794708}<LEND>[argument 374; litteral](integer){655024344}<LSEP>[argument 375; litteral](integer){704126179}<LEND>[argument 376; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1768600698}<LEND>[argument 377; litteral](integer){1530823687}<LSEP>[argument 378; litteral](integer){470642353}<LSEP>[argument 379; litteral](integer){628088689}<LEND>[argument 380; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1634098529}<LEND>[argument 381; litteral](integer){2100775251}<LEND>[argument 382; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1831693367}<LEND>[argument 383; litteral](integer){803932160}<LSEP>[argument 384; litteral](integer){269186350}<LEND>[argument 385; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1427162903}<LEND>[argument 386; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){275859568}<LEND>[argument 387; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1907002927}<LEND>[argument 388; litteral](integer){944926036}<LSEP>[argument 389; litteral](integer){1261943794}<LSEP>[argument 390; litteral](integer){234591008}<LSEP>[argument 391; litteral](integer){2015259243}<LSEP>[argument 392; litteral](integer){1466389722}<LEND>[argument 393; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){814811631}<LEND>[argument 394; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){301244554}<LEND>[argument 395; litteral](integer){933571263}<LEND>[argument 396; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){919295077}<LEND>[argument 397; litteral](integer){643740555}<LSEP>[argument 398; litteral](integer){1982189819}<LEND>[argument 399; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){92886009}<LEND>[argument 400; litteral](integer){1839445112}<LSEP>[argument 401; litteral](integer){530726933}<LEND>[argument 402; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){30429027}<LEND>[argument 403; litteral](integer){909139425}<LSEP>[argument 404; litteral](integer){1675092771}<LSEP>[argument 405; litteral](integer){1525325303}<LEND>[argument 406; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1012012860}<LEND>[argument 407; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2129076508}<LEND>[argument 408; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1275547874}<LEND>[argument 409; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){786794670}<LEND>[argument 410; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){634020966}<LEND>[argument 411; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1380552024}<LEND>[argument 412; litteral](integer){1799434876}<LEND>[argument 413; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){373432374}<LEND>[argument 414; litteral](integer){2106397479}<LSEP>[argument 415; litteral](integer){1438206358}<LSEP>[argument 416; litteral](integer){25617167}<LSEP>[argument 417; litteral](integer){1683848708}<LEND>[argument 418; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){975738690}<LEND>[argument 419; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){893024067}<LEND>[argument 420; litteral](integer){1422919542}<LEND>[argument 421; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1039873266}<LEND>[argument 422; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){836020924}<LEND>[argument 423; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2014220417}<LEND>[argument 424; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){51227525}<LEND>[argument 425; litteral](integer){959414432}<LEND>[argument 426; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){263064426}<LEND>[argument 427; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1571923444}<LEND>[argument 428; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){384174176}<LEND>[argument 429; litteral](integer){931713660}<LEND>[argument 430; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1377280537}<LEND>[argument 431; litteral](integer){783269020}<LEND>[argument 432; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1755017000}<LEND>[argument 433; litteral](integer){2108519123}<LSEP>[argument 434; litteral](integer){1075384373}<LSEP>[argument 435; litteral](integer){1533131586}<LSEP>[argument 436; litteral](integer){107649287}<LEND>[argument 437; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1036482435}<LEND>[argument 438; litteral](integer){1454661956}<LSEP>[argument 439; litteral](integer){7111678}<LSEP>[argument 440; litteral](integer){877069561}<LEND>[argument 441; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1178965150}<LEND>[argument 442; litteral](integer){988096567}<LEND>[argument 443; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1592701019}<LEND>[argument 444; litteral](integer){1369993623}<LEND>[argument 445; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1239830980}<LEND>[argument 446; litteral](integer){1900397670}<LEND>[argument 447; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2006451502}<LEND>[argument 448; litteral](integer){66598832}<LSEP>[argument 449; litteral](integer){1634584859}<LEND>[argument 450; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){494843585}<LEND>[argument 451; litteral](integer){1546245710}<LEND>[argument 452; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1259964741}<LEND>[argument 453; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1511929382}<LEND>[argument 454; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1699382782}<LEND>[argument 455; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1569135383}<LEND>[argument 456; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1855288679}<LEND>[argument 457; litteral](integer){1572531575}<LSEP>[argument 458; litteral](integer){1188833347}<LSEP>[argument 459; litteral](integer){77292316}<LEND>[argument 460; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){293804264}<LEND>[argument 461; litteral](integer){1369171035}<LSEP>[argument 462; litteral](integer){624721134}<LSEP>[argument 463; litteral](integer){1447971223}<LSEP>[argument 464; litteral](integer){367352974}<LSEP>[argument 465; litteral](integer){1453153865}<LSEP>[argument 466; litteral](integer){780218206}<LEND>[argument 467; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1193171626}<LEND>[argument 468; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1297126278}<LEND>[argument 469; litteral](integer){728806201}<LEND>[argument 470; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1236394289}<LEND>[argument 471; litteral](integer){1490635819}<LEND>[argument 472; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1335919000}<LEND>[argument 473; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1441203162}<LEND>[argument 474; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){214059630}<LEND>[argument 475; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){126767481}<LEND>[argument 476; litteral](integer){249373431}<LSEP>[argument 477; litteral](integer){121651816}<LSEP>[argument 478; litteral](integer){527802137}<LSEP>[argument 479; litteral](integer){1710661605}<LEND>[argument 480; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1889962302}<LEND>[argument 481; litteral](integer){1920053701}<LSEP>[argument 482; litteral](integer){282929555}<LEND>[argument 483; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){209979458}<LEND>[argument 484; litteral](integer){1650023316}<LSEP>[argument 485; litteral](integer){828380226}<LSEP>[argument 486; litteral](integer){1840536757}<LSEP>[argument 487; litteral](integer){361814822}<LEND>[argument 488; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1351058151}<LEND>[argument 489; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){650317475}<LEND>[argument 490; litteral](integer){523383454}<LEND>[argument 491; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1269330190}<LEND>[argument 492; litteral](integer){1035012273}<LSEP>[argument 493; litteral](integer){1951314297}<LEND>[argument 494; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){76348151}<LEND>[argument 495; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){748546156}<LEND>[argument 496; litteral](integer){1736320939}<LSEP>[argument 497; litteral](integer){249694082}<LSEP>[argument 498; litteral](integer){769260960}<LSEP>[argument 499; litteral](integer){1189335726}<LEND>[argument 500; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){61995093}<LEND>[argument 501; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){908805405}<LEND>[argument 502; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1672687623}<LEND>[argument 503; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){846566850}<LEND>[argument 504; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1514984348}<LEND>[argument 505; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){326300704}<LEND>[argument 506; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1203336601}<LEND>[argument 507; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1832777826}<LEND>[argument 508; litteral](integer){998974845}<LSEP>[argument 509; litteral](integer){958642958}<LEND>[argument 510; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1191035094}<LEND>[argument 511; litteral](integer){1232705919}<LSEP>[argument 512; litteral](integer){1946895008}<LEND>[argument 513; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1116554897}<LEND>[argument 514; litteral](integer){119948481}<LSEP>[argument 515; litteral](integer){206278501}<LSEP>[argument 516; litteral](integer){1055406888}<LEND>[argument 517; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1126905267}<LEND>[argument 518; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1381529674}<LEND>[argument 519; litteral](integer){1715390604}<LEND>[argument 520; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){403226326}<LEND>[argument 521; litteral](integer){1657557274}<LEND>[argument 522; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1745452427}<LEND>[argument 523; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){653279441}<LEND>[argument 524; litteral](integer){305535934}<LEND>[argument 525; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){633168821}<LEND>[argument 526; litteral](integer){1599674569}<LEND>[argument 527; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){57359847}<LEND>[argument 528; litteral](integer){1823007512}<LEND>[argument 529; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1209471627}<LEND>[argument 530; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1524930416}<LEND>[argument 531; litteral](integer){620060603}<LSEP>[argument 532; litteral](integer){1369009780}<LEND>[argument 533; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){612403887}<LEND>[argument 534; litteral](integer){1967985996}<LEND>[argument 535; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1102448112}<LEND>[argument 536; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){457474425}<LEND>[argument 537; litteral](integer){193098413}<LEND>[argument 538; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1962273302}<LEND>[argument 539; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){293008069}<LEND>[argument 540; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){88771549}<LEND>[argument 541; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){941710644}<LEND>[argument 542; litteral](integer){1089071670}<LSEP>[argument 543; litteral](integer){941829365}<LSEP>[argument 544; litteral](integer){387168351}<LEND>[argument 545; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1919321224}<LEND>[argument 546; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){459663973}<LEND>[argument 547; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){295030194}<LEND>[argument 548; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1101331958}<LEND>[argument 549; litteral](integer){7766846}<LSEP>[argument 550; litteral](integer){1049045926}<LSEP>[argument 551; litteral](integer){2024131963}<LEND>[argument 552; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1863745508}<LEND>[argument 553; litteral](integer){420922347}<LEND>[argument 554; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1309789455}<LEND>[argument 555; litteral](integer){110069083}<LSEP>[argument 556; litteral](integer){1420482287}<LEND>[argument 557; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){69061584}<LEND>[argument 558; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){504516225}<LEND>[argument 559; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1642672094}<LEND>[argument 560; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1402916323}<LEND>[argument 561; litteral](integer){76197491}<LEND>[argument 562; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1098139476}<LEND>[argument 563; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){39726048}<LEND>[argument 564; litteral](integer){23168622}<LSEP>[argument 565; litteral](integer){161227673}<LEND>[argument 566; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){661774720}<LEND>[argument 567; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1254507383}<LEND>[argument 568; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){557156308}<LEND>[argument 569; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){833527324}<LEND>[argument 570; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){301900797}<LEND>[argument 571; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){591795567}<LEND>[argument 572; litteral](integer){1495512376}<LEND>[argument 573; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1737531957}<LEND>[argument 574; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1170814733}<LEND>[argument 575; litteral](integer){283407367}<LSEP>[argument 576; litteral](integer){757289171}<LSEP>[argument 577; litteral](integer){1077703134}<LEND>[argument 578; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){837133495}<LEND>[argument 579; litteral](integer){1073376497}<LSEP>[argument 580; litteral](integer){985534916}<LSEP>[argument 581; litteral](integer){220745082}<LEND>[argument 582; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){441865274}<LEND>[argument 583; litteral](integer){1486110261}<LSEP>[argument 584; litteral](integer){767013297}<LSEP>[argument 585; litteral](integer){1039305711}<LSEP>[argument 586; litteral](integer){570113302}<LSEP>[argument 587; litteral](integer){713240113}<LEND>[argument 588; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1082876692}<LEND>[argument 589; litteral](integer){707479413}<LEND>[argument 590; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2145507191}<LEND>[argument 591; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1892230792}<LEND>[argument 592; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1061457644}<LEND>[argument 593; litteral](integer){527032848}<LEND>[argument 594; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1111744620}<LEND>[argument 595; litteral](integer){568047372}<LEND>[argument 596; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){335434225}<LEND>[argument 597; litteral](integer){2113378135}<LEND>[argument 598; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1029827013}<LEND>[argument 599; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1006580140}<LEND>[argument 600; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1547069777}<LEND>[argument 601; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1189203543}<LEND>[argument 602; litteral](integer){1721744819}<LEND>[argument 603; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){73242054}<LEND>[argument 604; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){67077446}<LEND>[argument 605; litteral](integer){1637380594}<LEND>[argument 606; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1152070973}<LEND>[argument 607; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1453961669}<LEND>[argument 608; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1858835533}<LEND>[argument 609; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){932574288}<LEND>[argument 610; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1944796885}<LEND>[argument 611; litteral](integer){538023003}<LSEP>[argument 612; litteral](integer){329757059}<LSEP>[argument 613; litteral](integer){1893611092}<LSEP>[argument 614; litteral](integer){521907510}<LSEP>[argument 615; litteral](integer){1460378420}<LSEP>[argument 616; litteral](integer){753252322}<LEND>[argument 617; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1241359828}<LEND>[argument 618; litteral](integer){1491406989}<LSEP>[argument 619; litteral](integer){85741714}<LEND>[argument 620; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2048718018}<LEND>[argument 621; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1021418552}<LEND>[argument 622; litteral](integer){1828813134}<LEND>[argument 623; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){125060567}<LEND>[argument 624; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1933879857}<LEND>[argument 625; litteral](integer){1757722544}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){.Random.seed}<LSEP>[](symbol){saved_seed}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.100000}<LSEP>[argument 3; litteral](real){10.000000}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](logical){TRUE}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 6; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//countFinalTaxa/...}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){timeSliceTree shifts root age ...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){444.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){30.000000}<LSEP>[argument 1; litteral](real){40.000000}<LEND>[argument 4; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){taxa2phylo}<LSEP>[](symbol){taxa}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree950}<LEND>[call](){}<LSEP>[](symbol){timeSliceTree}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](real){950.000000}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tree950_NoExtinct}<LEND>[call](){}<LSEP>[](symbol){timeSliceTree}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](real){950.000000}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; call](){}<LSEP>[](symbol){expect_false}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree950}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree950_NoExtinct}<LSEP>[](symbol){root.time}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord is returning r...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.100000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){50.000000}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 5; litteral](real){30.000000}<LSEP>[argument 6; litteral](real){10.000000}<LSEP>[argument 7; litteral](real){15.000000}<LSEP>[argument 8; litteral](logical){FALSE}<LSEP>[argument 9; litteral](logical){TRUE}<LSEP>[argument 10; litteral](logical){TRUE}<LEND>[statement 2; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){record}<LEND>[argument 1; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord is returning r...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 2; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.100000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){50.000000}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 5; litteral](real){30.000000}<LSEP>[argument 6; litteral](real){10.000000}<LSEP>[argument 7; litteral](real){15.000000}<LSEP>[argument 8; litteral](logical){TRUE}<LSEP>[argument 9; litteral](logical){TRUE}<LSEP>[argument 10; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){rejected}<LEND>[](symbol){divCurveFossilRecordSim}<LEND>[statement 5; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){record}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){expect_identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){record}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){accepted}<LSEP>[argument 1; litteral](str){rejected}<LEND>[statement 7; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){accepted}<LEND>[argument 1; litteral](real){3.000000}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord doesn't return...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 2; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 3; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.100000}<LSEP>[argument 3; litteral](real){10.000000}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1000.000000}<LSEP>[argument 6; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){anyLive}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){z}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){anyLive}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Runs have extant taxa under co...}<LEND>[statement 7; call](){}<LSEP>[](symbol){expect_false}<LSEP>[](symbol){anyLive}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){timeSliceTree tip label option...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 1; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){444.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){30.000000}<LSEP>[argument 1; litteral](real){40.000000}<LEND>[argument 4; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){taxa2phylo}<LSEP>[](symbol){taxa}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree950}<LEND>[call](){}<LSEP>[](symbol){timeSliceTree}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](real){950.000000}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tree950_AD}<LEND>[call](){}<LSEP>[](symbol){timeSliceTree}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](real){950.000000}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){allDesc}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 7; call](){}<LSEP>[](symbol){expect_false}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree950}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree950_AD}<LSEP>[](symbol){tip.label}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){simFossilRecord doesn't return...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 2; call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){paleotree}<LEND>[statement 3; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){10.000000}<LSEP>[argument 4; litteral](real){10.000000}<LSEP>[argument 5; litteral](real){1000.000000}<LSEP>[argument 6; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){anyDead}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){z}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){anyDead}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Runs have extinct taxa under c...}<LEND>[statement 7; call](){}<LSEP>[](symbol){expect_false}<LSEP>[](symbol){anyDead}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){test involving examing the ret...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 1; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.100000}<LSEP>[argument 3; litteral](real){10.000000}<LSEP>[argument 4; litteral](real){10.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){30.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){30.000000}<LEND>[argument 7; litteral](logical){TRUE}<LSEP>[argument 8; litteral](logical){TRUE}<LSEP>[argument 9; litteral](logical){TRUE}<LEND>[statement 3; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){accepted}<LEND>[argument 1; litteral](real){10.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){totalTaxa_rej}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){rejected}<LEND>[](symbol){length}<LEND>[statement 5; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){totalTaxa_rej}<LEND>[statement 6; call](){}<LSEP>[](symbol){divCurveFossilRecordSim}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){rejected}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){totalTaxa_rej}<LEND>[](symbol){totalTaxa_rej}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){rejected}<LEND>[](symbol){divCurveFossilRecordSim}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){getDuration}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){record}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){maxAge}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){orig.time}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){minAge}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){ext.time}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){cladeDuration}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){maxAge}<LSEP>[](symbol){minAge}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){cladeDuration}<LEND>[statement 9; call](){}<LSEP>[](symbol){expect_true}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){record}<LSEP>[](symbol){accepted}<LEND>[](symbol){getDuration}<LEND>[argument 1; litteral](real){10.000000}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){cal3 datetreatment is consiste...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){test_identical_tip_ages}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){trees}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){trees}<LSEP>[argument 1; litteral](str){multiPhylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){trees is not class multiphylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trees}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fewer than two trees given}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){node_dates}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){trees}<LSEP>[](symbol){dateNodes}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tip_dates}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node_dates}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){node_dates}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){trees}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){trees}<LSEP>[](symbol){i}<LEND>[](symbol){tip.label}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){all_nearly_identical}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){tip_dates}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){isTRUE}<LEND>[argument 0; call](){}<LSEP>[](symbol){all.equal}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tip_dates}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){all_nearly_identical}<LEND>[statement 1; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){444.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){30.000000}<LSEP>[argument 1; litteral](real){40.000000}<LEND>[argument 4; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rangesCont}<LEND>[call](){}<LSEP>[](symbol){sampleRanges}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){cladogram}<LEND>[call](){}<LSEP>[](symbol){taxa2cladogram}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){rangesCont_pointocc}<LSEP>[](symbol){rangesCont}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesCont_pointocc}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){likFun}<LEND>[call](){}<LSEP>[](symbol){make_durationFreqCont}<LSEP>[](symbol){rangesCont}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){srRes}<LEND>[call](){}<LSEP>[](symbol){optim}<LEND>[argument 0; call](){}<LSEP>[](symbol){parInit}<LSEP>[](symbol){likFun}<LEND>[](symbol){likFun}<LEND>[argument 2; call](){}<LSEP>[](symbol){parLower}<LSEP>[](symbol){likFun}<LEND>[argument 3; call](){}<LSEP>[](symbol){parUpper}<LSEP>[](symbol){likFun}<LEND>[argument 4; litteral](str){L-BFGS-B}<LEND>[argument 5; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){1000000.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){sRate}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){srRes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){divRate}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){srRes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ttrees_1}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont_pointocc}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){firstLast}<LSEP>[argument 6; litteral](logical){FALSE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 13; call](){}<LSEP>[](symbol){expect_true}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_1}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){ttrees_2}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont_pointocc}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){minMax}<LSEP>[argument 6; litteral](logical){FALSE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 15; call](){}<LSEP>[](symbol){expect_true}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_2}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){ttrees_3a}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){firstLast}<LSEP>[argument 6; litteral](logical){FALSE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 17; call](){}<LSEP>[](symbol){expect_true}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_3a}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){ttrees_3b}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){minMax}<LSEP>[argument 6; litteral](logical){FALSE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 19; call](){}<LSEP>[](symbol){expect_false}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_3b}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){ttrees_4a}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){firstLast}<LSEP>[argument 6; litteral](logical){TRUE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 21; call](){}<LSEP>[](symbol){expect_true}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_4a}<LEND>[statement 22; call](){}<LSEP>[](symbol){expect_error}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){ttrees_4b}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){minMax}<LSEP>[argument 6; litteral](logical){TRUE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 23; call](){}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_4b}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){ttrees_5a}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){randObs}<LSEP>[argument 6; litteral](logical){FALSE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 25; call](){}<LSEP>[](symbol){expect_false}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_5a}<LEND>[statement 26; call](){}<LSEP>[](symbol){expect_error}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){ttrees_5b}<LEND>[call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){cladogram}<LSEP>[](symbol){rangesCont}<LSEP>[](symbol){divRate}<LSEP>[](symbol){divRate}<LSEP>[](symbol){sRate}<LSEP>[argument 5; litteral](str){randObs}<LSEP>[argument 6; litteral](logical){TRUE}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[statement 27; call](){}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){test_identical_tip_ages}<LSEP>[](symbol){ttrees_5b}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){obtainDatedPosteriorTreesMrB w...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fileTest}<LSEP>[litteral](str){data//retio_dating.run1.t}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){MCCT}<LEND>[call](){}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LSEP>[](symbol){fileTest}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](str){MCCT}<LSEP>[argument 5; litteral](NULL){NULL}<LEND>[statement 2; call](){}<LSEP>[](symbol){expect_message}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){MAP}<LEND>[call](){}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LSEP>[](symbol){fileTest}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](str){MAPosteriori}<LSEP>[argument 5; litteral](NULL){NULL}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){MAPr}<LEND>[call](){}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LSEP>[](symbol){fileTest}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](str){MAPriori}<LSEP>[argument 5; litteral](NULL){NULL}<LEND>[statement 4; call](){}<LSEP>[](symbol){expect_message}<LEND>[argument 0; call](){}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){MaxLike}<LEND>[call](){}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LSEP>[](symbol){fileTest}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](str){MaxLikelihood}<LSEP>[argument 5; litteral](NULL){NULL}<LEND>[statement 5; call](){}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){setRootAge}<LSEP>[](symbol){MCCT}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){hundredRandomlySelectedTrees}<LEND>[call](){}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LSEP>[](symbol){fileTest}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){TRUE}<LSEP>[argument 5; litteral](real){100.000000}<LSEP>[argument 6; litteral](NULL){NULL}<LEND>[statement 7; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 9; call](){}<LSEP>[](symbol){expect_equal_to_reference}<LSEP>[](symbol){hundredRandomlySelectedTrees}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){.//references//datedPosteriorT...}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){inverseSurv works at high para...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){444.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){30.000000}<LSEP>[argument 1; litteral](real){40.000000}<LEND>[argument 4; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rangesCont}<LEND>[call](){}<LSEP>[](symbol){sampleRanges}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rangesDisc}<LEND>[call](){}<LSEP>[](symbol){binTimeData}<LSEP>[](symbol){rangesCont}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){likFun}<LEND>[call](){}<LSEP>[](symbol){make_inverseSurv}<LSEP>[](symbol){rangesDisc}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){constrFun}<LEND>[call](){}<LSEP>[](symbol){constrainParPaleo}<LSEP>[](symbol){likFun}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){match.all}<LSEP>[](symbol){match.all}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){optim}<LEND>[argument 0; call](){}<LSEP>[](symbol){parInit}<LSEP>[](symbol){likFun}<LEND>[](symbol){likFun}<LEND>[argument 2; call](){}<LSEP>[](symbol){parLower}<LSEP>[](symbol){likFun}<LEND>[argument 3; call](){}<LSEP>[](symbol){parUpper}<LSEP>[](symbol){likFun}<LEND>[argument 4; litteral](str){L-BFGS-B}<LEND>[argument 5; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[statement 8; call](){}<LSEP>[](symbol){expect_false}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plotSinglePhyloPic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){whichTip}<LSEP>[](symbol){XX}<LSEP>[](symbol){YY}<LSEP>[](symbol){sizeScale}<LSEP>[](symbol){offsetPic}<LSEP>[](symbol){orientation}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){taxonColor}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picAspRatio}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){picPNG}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){picPNG}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xyCoords}<LEND>[call](){}<LSEP>[](symbol){getCoordsPhyloPic}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){XX}<LSEP>[](symbol){whichTip}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){YY}<LSEP>[](symbol){whichTip}<LEND>[](symbol){sizeScale}<LSEP>[](symbol){offsetPic}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){picAspRatio}<LSEP>[](symbol){orientation}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){picPNG_raster}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){as.raster}<LEND>[](symbol){picPNG}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxonColor}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG_raster}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){picPNG_raster}<LSEP>[argument 1; litteral](str){#000000FF}<LEND>[](symbol){taxonColor}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){graphics}<LSEP>[](symbol){rasterImage}<LEND>[](symbol){picPNG_raster}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xyCoords}<LSEP>[](symbol){xleft}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xyCoords}<LSEP>[](symbol){ybottom}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xyCoords}<LSEP>[](symbol){xright}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xyCoords}<LSEP>[](symbol){ytop}<LEND>[argument 5; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){getCoordsPhyloPic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xx}<LSEP>[](symbol){yy}<LSEP>[](symbol){sizeScale}<LSEP>[](symbol){offsetPic}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){picAspRatio}<LSEP>[](symbol){orientation}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){picAspRatio}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picSize}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sizeScale}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){picAspRatio}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picSize}<LSEP>[](symbol){sizeScale}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xx}<LSEP>[](symbol){offsetPic}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LSEP>[](symbol){yy}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xAdj}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){picSize}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){picAspRatio}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){yAdj}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){picSize}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){picAspRatio}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picSize}<LSEP>[](symbol){sizeScale}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picSize}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sizeScale}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){picAspRatio}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LSEP>[](symbol){xx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){yy}<LSEP>[](symbol){offsetPic}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xAdj}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){picSize}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){yAdj}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){picSize}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){picAspRatio}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){finalCoords}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){xAdj}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LSEP>[](symbol){yAdj}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){x}<LSEP>[](symbol){xAdj}<LEND>[argument 3; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){y}<LSEP>[](symbol){yAdj}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalCoords}<LEND>[assign](){<-}<LSEP>[](symbol){prepPhyloPic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){noiseThreshold}<LSEP>[](symbol){rescalePNG}<LSEP>[](symbol){trimPNG}<LSEP>[](symbol){colorGradient}<LSEP>[](symbol){plotComparison}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sliceOriginal}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){rescalePNG}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){picPNG}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){picPNG}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sliceContrasted}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){trimPNG}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sliceContrasted}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){sliceContrasted}<LSEP>[](symbol){noiseThreshold}<LEND>[litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){saveRows}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){sliceContrasted}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){sliceContrasted}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){saveCols}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){sliceContrasted}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){sliceContrasted}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){saveRows}<LSEP>[](symbol){saveCols}<LSEP>[](symbol){}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){colorGradient}<LSEP>[argument 1; litteral](str){trueMonochrome}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){picPNG}<LSEP>[argument 1; litteral](real){0.001000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){picPNG}<LSEP>[argument 1; litteral](real){0.200000}<LEND>[litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){picPNG}<LSEP>[argument 1; litteral](real){0.200000}<LEND>[litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){colorGradient}<LSEP>[argument 1; litteral](str){increaseDisparity}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){picPNG}<LSEP>[argument 1; litteral](real){0.001000}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){plotComparison}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){graphics}<LSEP>[](symbol){image}<LEND>[](symbol){sliceOriginal}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){graphics}<LSEP>[](symbol){image}<LEND>[](symbol){sliceContrasted}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){graphics}<LSEP>[](symbol){image}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){picPNG}<LEND>[assign](){<-}<LSEP>[](symbol){matchTaxaColor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaColorOld}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){transparency}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaColorNew}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaNames}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){taxaColorOld}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){taxaColorOld}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxaColor must be either NULL ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaColorOld}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaColorOld}<LSEP>[](symbol){taxaNames}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaColorNew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){taxaColorOld}<LEND>[litteral](str){red}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaColorNew}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){taxaColorOld}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaNames}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaColorOld}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If taxaColor is not NULL or le...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaColorNew}<LSEP>[](symbol){taxaColorOld}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaColorNew}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){transparency}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){transparency}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){transparency}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaNames}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){transparency}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If transparency is not length ...}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaColorNew}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaColorNew}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){convertColor2Hex}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaColorNew}<LSEP>[](symbol){i}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxaColorNew}<LEND>[assign](){<-}<LSEP>[](symbol){convertColor2Hex}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){colorName}<LSEP>[](symbol){transparency}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){transparency}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){transparency}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){transparency values must be be...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){transparency}<LSEP>[argument 1; litteral](real){255.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newColor}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){col2rgb}<LEND>[](symbol){colorName}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newColor}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){rgb}<LEND>[](symbol){newColor}<LSEP>[](symbol){alpha}<LSEP>[argument 2; litteral](real){255.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newColor}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){nodeDates2branchLengths}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nodeDates}<LSEP>[](symbol){tree}<LSEP>[](symbol){allTipsModern}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.lengths}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){input tree has $edge.lengths p...}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){allTipsModern}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nodeDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nodeDates must be same length ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){allAges}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[](symbol){nodeDates}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nodeDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nodeDates must be same length ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){allAges}<LSEP>[](symbol){nodeDates}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){allAges}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){allAges}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some input ages appear to be N...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){momAges}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){allAges}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){childAges}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){allAges}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){edgeLengths}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){momAges}<LSEP>[](symbol){childAges}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){edgeLengths}<LEND>[litteral](NULL){NULL}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){edgeLengths}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Check ages - some edges are ca...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){edgeLengths}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Caution: some edges are calcul...}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){edgeLengths}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){allAges}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){checkRootTimeRes}<LEND>[call](){}<LSEP>[](symbol){checkRootTime}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getPhyloPicPNG}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){picID_PBDB}<LSEP>[](symbol){cacheDir}<LSEP>[](symbol){cacheImage}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){notCached}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){picPNG}<LSEP>[litteral](NULL){NULL}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){cacheDir}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cachePath}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){cacheDir}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){picID_PBDB}<LSEP>[argument 1; litteral](str){.png}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){cachePath}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){png}<LSEP>[](symbol){readPNG}<LEND>[](symbol){cachePath}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){notCached}<LSEP>[litteral](logical){TRUE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){picPNG}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picUID}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){https://paleobiodb.org/data1.2...}<LSEP>[](symbol){picID_PBDB}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){picUID}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){picUID}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){picUID}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){picUID}<LSEP>[](symbol){uid}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){getPhyloPicFromPhyloPic}<LSEP>[](symbol){picUID}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){picPNG}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){getPhyloPicPNG_PBDB}<LSEP>[](symbol){picID_PBDB}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){cacheImage}<LSEP>[](symbol){notCached}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){dir.exists}<LSEP>[](symbol){cacheDir}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){dir.create}<LSEP>[](symbol){cacheDir}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){png}<LSEP>[](symbol){writePNG}<LEND>[](symbol){picPNG}<LEND>[argument 1; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){cacheDir}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){picID_PBDB}<LSEP>[argument 1; litteral](str){.png}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){picPNG}<LEND>[assign](){<-}<LSEP>[](symbol){getPhyloPicUIDsTableFromPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){picIDs}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){imgNumAPIurl}<LSEP>[litteral](str){https://paleobiodb.org/data1.2...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){URLwithNums}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){imgNumAPIurl}<LSEP>[](symbol){picIDs}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){URLwithNums}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){picIDs}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){rbind}<LEND>[argument 1; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){URLwithNums}<LSEP>[](symbol){read.csv}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){getPhyloPicFromPhyloPic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){picUID}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picInfoURL}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://phylopic.org/api/a/image/}<LSEP>[](symbol){picUID}<LSEP>[argument 2; litteral](str){?options=credit+licenseURL+png...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RCurl}<LSEP>[](symbol){url.exists}<LEND>[](symbol){picInfoURL}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picInfo}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){jsonlite}<LSEP>[](symbol){fromJSON}<LEND>[](symbol){picInfoURL}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){picInfo}<LSEP>[](symbol){result}<LEND>[](symbol){pngFiles}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picPNGurl}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){picInfo}<LSEP>[](symbol){result}<LEND>[](symbol){pngFiles}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){picInfo}<LSEP>[](symbol){result}<LEND>[](symbol){pngFiles}<LEND>[](symbol){url}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){picPNGurl}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://phylopic.org}<LSEP>[](symbol){picPNGurl}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RCurl}<LSEP>[](symbol){url.exists}<LEND>[](symbol){picPNGurl}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pngContent}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RCurl}<LSEP>[](symbol){getURLContent}<LEND>[](symbol){picPNGurl}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pngContent}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){png}<LSEP>[](symbol){readPNG}<LEND>[](symbol){pngContent}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pngContent}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pngContent}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pngContent}<LSEP>[litteral](NULL){NULL}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){pngContent}<LEND>[assign](){<-}<LSEP>[](symbol){getPhyloPicPNG_PBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){picID_PBDB}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){Sys.sleep}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){apiPicURL}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data1.2/...}<LSEP>[](symbol){picID_PBDB}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){png}<LSEP>[](symbol){readPNG}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RCurl}<LSEP>[](symbol){getURLContent}<LEND>[](symbol){apiPicURL}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){picPNG}<LEND>[assign](){<-}<LSEP>[](symbol){getPhyloPicIDNumFromPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){tree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){taxaData}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tiptaxa}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; litteral](str){,}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){apiAddressTaxa}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data1.2/...}<LSEP>[](symbol){tiptaxa}<LSEP>[argument 2; litteral](str){&rel=exact&show=img}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaData}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){apiAddressTaxa}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){image_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){taxon_name}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){image_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){taxon_name}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){If provided, phylopicIDsPBDB m...}<LSEP>[argument 1; litteral](str){ length as the number of tips ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot coerce phylopicIDsPBDB ...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If provided, phylopicIDsPBDB c...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){phylopicIDsPBDB}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If provided, phylopicIDsPBDB c...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){If provided, phylopicIDsPBDB m...}<LSEP>[argument 1; litteral](str){ labels matching the tree's ti...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){phylopicIDsPBDB}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getSortedMinMaxStratRanges}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeTree}<LSEP>[](symbol){rangesFourDate}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rangesMinMax}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesFourDate}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstapp_max_ma}<LSEP>[argument 1; litteral](str){lastapp_min_ma}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rangesMinMax}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){rangesMinMax}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rangesMinMax}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rangesFourDate}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rangesMinMaxSorted}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){timeTree}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){timeTree}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whichRanges}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rangesMinMax}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timeTree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesMinMaxSorted}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesMinMax}<LSEP>[](symbol){whichRanges}<LSEP>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){rangesMinMaxSorted}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstMax}<LSEP>[argument 1; litteral](str){lastMin}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rangesMinMaxSorted}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timeTree}<LSEP>[](symbol){tip.label}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){rangesMinMaxSorted}<LEND>[assign](){<-}<LSEP>[](symbol){plotTaxonStratDurations}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rangesMinMax}<LSEP>[](symbol){orientation}<LSEP>[](symbol){XX}<LSEP>[](symbol){YY}<LSEP>[](symbol){boxWidth}<LSEP>[](symbol){boxCol}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boxCol}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){boxCol}<LEND>[litteral](str){#000000FF}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){rangesMinMax}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){yCent}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){YY}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ageMax}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesMinMax}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){firstMax}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ageMin}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesMinMax}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){lastMin}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){graphics}<LSEP>[](symbol){rect}<LEND>[](symbol){ageMax}<LSEP>[](symbol){ageMin}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){yCent}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){boxWidth}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yCent}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){boxWidth}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boxCol}<LSEP>[](symbol){i}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boxCol}<LSEP>[](symbol){i}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){XX}<LSEP>[](symbol){i}<LEND>[](symbol){ageMin}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){YY}<LSEP>[](symbol){i}<LEND>[](symbol){yCent}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){rangesMinMax}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xCent}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){XX}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ageMax}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesMinMax}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){firstMax}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ageMin}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rangesMinMax}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){lastMin}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){graphics}<LSEP>[](symbol){rect}<LEND>[](symbol){ageMin}<LSEP>[](symbol){ageMax}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){xCent}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){boxWidth}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xCent}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){boxWidth}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boxCol}<LSEP>[](symbol){i}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boxCol}<LSEP>[](symbol){i}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){XX}<LSEP>[](symbol){i}<LEND>[](symbol){xCent}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){YY}<LSEP>[](symbol){i}<LEND>[](symbol){ageMin}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newXY}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){XX}<LSEP>[](symbol){YY}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newXY}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){divCurveFossilRecordSim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){merge.cryptic}<LSEP>[](symbol){plotLegend}<LSEP>[](symbol){legendPosition}<LSEP>[](symbol){curveColors}<LSEP>[](symbol){curveLineTypes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaConvert}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){fossilRecord}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){areSampled}<LEND>[call](){}<LSEP>[](symbol){whichSampledInPast}<LSEP>[](symbol){fossilRecord}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){areSampled}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fossilRanges}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilRanges}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){merge.cryptic}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){curveList}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxaConvert}<LSEP>[](symbol){fossilRanges}<LEND>[statement 2; call](){}<LSEP>[](symbol){multiDiv}<LSEP>[](symbol){curveList}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){merge.cryptic}<LSEP>[](symbol){curveColors}<LSEP>[](symbol){curveLineTypes}<LSEP>[argument 5; litteral](str){}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){plotLegend}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){legendPosition}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){True Richness}<LSEP>[argument 1; litteral](str){Sampled Richness}<LEND>[](symbol){curveColors}<LSEP>[](symbol){curveLineTypes}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){taxicDivCont}<LSEP>[](symbol){taxaConvert}<LSEP>[argument 1; litteral](real){0.200000}<LEND>[assign](){<-}<LSEP>[](symbol){whichSampledInPast}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){areSamp}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){areLive}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nExtant}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){areLive}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){areSamp}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nExtant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){possModernTime}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){areLive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sampOnce}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sampModernOnly}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){possModernTime}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){areSamp}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){sampModernOnly}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){areSamp}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){makePBDBtaxonTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){rankTaxon}<LSEP>[](symbol){method}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LSEP>[](symbol){annotatedDuplicateNames}<LSEP>[](symbol){APIversion}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){method}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){method}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){method must be a single charac...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Linnean}<LSEP>[argument 1; litteral](str){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){method must be one of either '...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxaDataPBDB isn't a data.frame}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rankTaxon}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){rankTaxon}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){rankTaxon must be a single cha...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){species}<LSEP>[argument 1; litteral](str){genus}<LSEP>[argument 2; litteral](str){family}<LSEP>[argument 3; litteral](str){order}<LSEP>[argument 4; litteral](str){class}<LSEP>[argument 5; litteral](str){phylum}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){rankTaxon}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){rankTaxon must be one of 'spec...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dataTransform}<LEND>[call](){}<LSEP>[](symbol){translatePBDBtaxa}<LSEP>[](symbol){taxaDataPBDB}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){dataTransform}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){dataTransform}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tipSet}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipSet}<LSEP>[litteral](str){nonParents}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parData}<LEND>[call](){}<LSEP>[](symbol){getAllParents}<LSEP>[](symbol){dataTransform}<LSEP>[argument 1; litteral](str){all}<LSEP>[](symbol){annotatedDuplicateNames}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tipIDs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){taxon_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){taxon_rank}<LEND>[](symbol){rankTaxon}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tipIDs}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){tipIDs}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){whichTip}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){tipIDs}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){subsetParDataPBDB}<LSEP>[](symbol){tipIDs}<LSEP>[](symbol){parData}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){constructParentChildMatrixPBDB}<LSEP>[](symbol){pcMat}<LSEP>[](symbol){parData}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pcMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){convertParentChildMatNames}<LSEP>[](symbol){parData}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){NODE}<LEND>[](symbol){}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){parentChild2taxonTree}<LSEP>[](symbol){pcMat}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){parentChild}<LEND>[](symbol){pcMat}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){Linnean}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){getLinneanTaxonTreePBDB}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LSEP>[](symbol){rankTaxon}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){parentChildOldMergeRoot}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){parentChildOldQueryPBDB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){parentChildPBDBOld}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LSEP>[](symbol){method}<LSEP>[](symbol){APIversion}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){taxaDataPBDB}<LEND>[](symbol){taxaDataPBDB}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}<LEND>[assign](){<-}<LSEP>[](symbol){plotTaxaTreePBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){edgeLength}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){edgeLength}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){taxaTree}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){taxaTree}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){edgeLength}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){root.edge}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){edgeLength}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[statement 3; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){taxaTree}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.200000}<LEND>[statement 4; call](){}<LSEP>[](symbol){nodelabels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){node.label}<LEND>[argument 1; litteral](real){0.500000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.100000}<LSEP>[argument 1; litteral](real){0.500000}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){simFossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){anag.rate}<LSEP>[](symbol){prop.bifurc}<LSEP>[](symbol){prop.cryptic}<LSEP>[](symbol){modern.samp.prob}<LSEP>[](symbol){startTaxa}<LSEP>[](symbol){nruns}<LSEP>[](symbol){maxAttempts}<LSEP>[](symbol){totalTime}<LSEP>[](symbol){nTotalTaxa}<LSEP>[](symbol){nExtant}<LSEP>[](symbol){nSamp}<LSEP>[](symbol){returnAllRuns}<LSEP>[](symbol){tolerance}<LSEP>[](symbol){maxStepTime}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[](symbol){count.cryptic}<LSEP>[](symbol){negRatesAsZero}<LSEP>[](symbol){print.runs}<LSEP>[](symbol){sortNames}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nruns}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){maxAttempts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nruns and maxAttempts must be ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){startTaxa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){startTaxa must be at least 1}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){nruns}<LSEP>[](symbol){startTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nruns and startTaxa must coerc...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){prop.bifurc}<LSEP>[](symbol){prop.cryptic}<LSEP>[](symbol){modern.samp.prob}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){prop.bifurc}<LSEP>[](symbol){prop.cryptic}<LSEP>[](symbol){modern.samp.prob}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){bad parameters input:\n}<LSEP>[argument 1; litteral](str){ prop.bifurc, prop.cryptic an...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prop.bifurc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){prop.cryptic}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Prop.bifurc greater than 0 whe...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nSamp}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Minimum number of required sam...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){count.cryptic}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){unreachableConstraints}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){prop.cryptic}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){anag.rate}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nTotalTaxa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nExtant}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nSamp}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){unreachableConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Minimum number of required nT...}<LSEP>[argument 1; litteral](str){ but these constraints canno...}<LSEP>[argument 2; litteral](str){ count.cryptic = FALSE, prop...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){count.cryptic}<LSEP>[](symbol){negRatesAsZero}<LSEP>[](symbol){print.runs}<LSEP>[](symbol){sortNames}<LSEP>[](symbol){plot}<LEND>[](symbol){is.logical}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){count.cryptic, negRatesAsZero,...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){nTotalTaxa}<LSEP>[](symbol){nExtant}<LSEP>[](symbol){nSamp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nTotalTaxa, nExtant, nSamp mus...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){runConditions}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){totalTime}<LSEP>[](symbol){nTotalTaxa}<LSEP>[](symbol){nExtant}<LSEP>[](symbol){nSamp}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){is.numeric}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Run condition arguments must b...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Run condition arguments must b...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){runConditions}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){runConditions}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){x}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[](symbol){x}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){runConditions}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Run Condition values must be e...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){runConditions}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Run condition misordered:\n}<LSEP>[argument 1; litteral](str){ Values given as a range must...}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){getBranchRate}<LEND>[call](){}<LSEP>[](symbol){makeParFunct}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){getExtRate}<LEND>[call](){}<LSEP>[](symbol){makeParFunct}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){getSampRate}<LEND>[call](){}<LSEP>[](symbol){makeParFunct}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){getAnagRate}<LEND>[call](){}<LSEP>[](symbol){makeParFunct}<LSEP>[](symbol){anag.rate}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){isTimeDep}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){getBranchRate}<LSEP>[](symbol){getExtRate}<LSEP>[](symbol){getSampRate}<LSEP>[](symbol){getAnagRate}<LEND>[](symbol){attr}<LSEP>[argument 2; litteral](str){timeDep}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){acceptedSimulations}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 21; control flow](){if}<LSEP>[](symbol){returnAllRuns}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rejectedSimulations}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){ntries}<LSEP>[litteral](real){0.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){nAccepted}<LSEP>[litteral](real){0.000000}<LEND>[statement 24; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nruns}<LSEP>[](symbol){nAccepted}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){accept}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){isRejectedRun}<LSEP>[litteral](logical){FALSE}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){accept}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntries}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ntries}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){ntries}<LSEP>[](symbol){maxAttempts}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Maximum number of attempts (}<LSEP>[](symbol){maxAttempts}<LSEP>[argument 2; litteral](str){) has been exceeded with only }<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nAccepted}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 4; litteral](str){ run(s) successful.}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){timePassed}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){currentTime}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){initiateTaxa}<LSEP>[](symbol){startTaxa}<LSEP>[](symbol){currentTime}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){startVitals}<LEND>[call](){}<LSEP>[](symbol){getRunVitals}<LSEP>[](symbol){taxa}<LSEP>[](symbol){count.cryptic}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){timePassed}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){startVitals}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){continue}<LEND>[call](){}<LSEP>[](symbol){testContinue}<LSEP>[](symbol){startVitals}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){runConditions}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){continue}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Initial starting point already...}<LEND>[statement 9; control flow](){while}<LSEP>[](symbol){continue}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timePassed}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){currentTime}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaDurations}<LEND>[call](){}<LSEP>[](symbol){getTaxonDurations}<LSEP>[](symbol){taxa}<LSEP>[](symbol){currentTime}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rateMatrix}<LEND>[call](){}<LSEP>[](symbol){getRateMatrix}<LSEP>[](symbol){taxa}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){taxaDurations}<LSEP>[](symbol){getBranchRate}<LSEP>[](symbol){getExtRate}<LSEP>[](symbol){getSampRate}<LSEP>[](symbol){getAnagRate}<LSEP>[](symbol){prop.cryptic}<LSEP>[](symbol){prop.bifurc}<LSEP>[](symbol){negRatesAsZero}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){changeTime}<LEND>[call](){}<LSEP>[](symbol){rexp}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){rateMatrix}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){isTimeDep}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){changeTime}<LSEP>[](symbol){maxStepTime}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){changeTime}<LSEP>[](symbol){maxStepTime}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newTime}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){currentTime}<LSEP>[](symbol){changeTime}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newTimePassed}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){changeTime}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eventProbMatrix}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){rateMatrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){rateMatrix}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sampledCell}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rateMatrix}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){eventProbMatrix}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sampledCell}<LEND>[call](){}<LSEP>[](symbol){arrayInd}<LSEP>[](symbol){sampledCell}<LEND>[argument 1; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){rateMatrix}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){event}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){rateMatrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampledCell}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){target}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){rateMatrix}<LSEP>[argument 1; litteral](str){whichExtant}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampledCell}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){newTime}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){currentTime}<LSEP>[](symbol){changeTime}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){newTimePassed}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){changeTime}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){eventOccurs}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){event}<LSEP>[](symbol){newTime}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){currentVitals}<LEND>[call](){}<LSEP>[](symbol){getRunVitals}<LSEP>[](symbol){taxa}<LSEP>[](symbol){count.cryptic}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){continue}<LEND>[call](){}<LSEP>[](symbol){testContinue}<LSEP>[](symbol){currentVitals}<LSEP>[](symbol){newTimePassed}<LSEP>[](symbol){runConditions}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){currentVitals}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){newTimePassed}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){currentVitals}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){currentVitals}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){currentTime}<LSEP>[](symbol){newTime}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){worthyVitals}<LEND>[call](){}<LSEP>[](symbol){worthCheckingVitalsRecord}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){runConditions}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){worthyVitals}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){seqVitals}<LEND>[call](){}<LSEP>[](symbol){testVitalsRecord}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){tolerance}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){seqVitals}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){accept}<LSEP>[litteral](logical){TRUE}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){returnAllRuns}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){accept}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){accept}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){isRejectedRun}<LSEP>[litteral](logical){TRUE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){returnAllRuns}<LSEP>[](symbol){isRejectedRun}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){fossilRecordSimulation}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){taxa}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){slicingDate}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){currentTime}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){timeSliceFossilRecord}<LSEP>[](symbol){taxa}<LSEP>[](symbol){slicingDate}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[](symbol){modern.samp.prob}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){passedDate}<LEND>[call](){}<LSEP>[](symbol){sampleSeqVitals}<LSEP>[](symbol){seqVitals}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){slicingDate}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){passedDate}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){fossilRecordSimulation}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){taxa}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){timeSliceFossilRecord}<LSEP>[](symbol){taxa}<LSEP>[](symbol){slicingDate}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[](symbol){modern.samp.prob}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){finalTest}<LEND>[call](){}<LSEP>[](symbol){testFinal}<LSEP>[](symbol){taxa}<LSEP>[](symbol){passedDate}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){count.cryptic}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){anag.rate}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){prop.cryptic}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){startTaxa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaIDsTest}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){namesIdenticalTest}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaIDsTest}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaIDsTest}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){namesIdenticalTest}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Non-cryptic taxa created in a ...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){checkNegDates}<LEND>[call](){}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LSEP>[](symbol){taxa}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){getTaxaNames}<LSEP>[](symbol){taxa}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){sortNames}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){taxa}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){returnAllRuns}<LSEP>[](symbol){isRejectedRun}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nextRejected}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rejectedSimulations}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rejectedSimulations}<LSEP>[](symbol){nextRejected}<LEND>[](symbol){taxa}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nAccepted}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nAccepted}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){acceptedSimulations}<LSEP>[](symbol){nAccepted}<LEND>[](symbol){taxa}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){divCurveFossilRecordSim}<LSEP>[](symbol){taxa}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nruns}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){title}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Run Number }<LSEP>[](symbol){nAccepted}<LSEP>[argument 2; litteral](str){ of }<LSEP>[](symbol){nruns}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){acceptedSimulations}<LEND>[](symbol){nAccepted}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of accepted simulat...}<LEND>[statement 26; control flow](){if}<LSEP>[](symbol){print.runs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){runNumMessage}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nruns}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){1 run}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){nruns}<LSEP>[argument 1; litteral](str){ runs}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){runNumMessage}<LSEP>[argument 1; litteral](str){ accepted from }<LSEP>[](symbol){ntries}<LSEP>[argument 3; litteral](str){ total runs (}<LEND>[argument 4; call](){}<LSEP>[](symbol){signif}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){nruns}<LSEP>[](symbol){ntries}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 5; litteral](str){ Acceptance Probability)}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nruns}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){acceptedSimulations}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one run accepted des...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){acceptedSimulations}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){acceptedSimulations}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 28; control flow](){if}<LSEP>[](symbol){returnAllRuns}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){acceptedSimulations}<LSEP>[](symbol){rejectedSimulations}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){results}<LSEP>[](symbol){acceptedSimulations}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){perCapitaRates}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LSEP>[](symbol){plot}<LSEP>[](symbol){logRates}<LSEP>[](symbol){drop.extant}<LSEP>[](symbol){isExtant}<LSEP>[](symbol){jitter}<LSEP>[](symbol){legendPosition}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not of matrix or...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not of matrix or...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){intMat}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intMat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not in intervals...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[1]] <0 ?}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not in intervals...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[2]] <0 ?}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){modInt}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){modInt}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){modInt}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){isExtant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){isExtant}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){modInt}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){altMod}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){modInt}<LEND>[argument 2; litteral](real){1.000000}<LEND>[](symbol){altMod}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){modInt}<LEND>[argument 2; litteral](real){2.000000}<LEND>[](symbol){altMod}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){intMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modInt}<LEND>[](symbol){}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){isExtant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){isExtant}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){timeData}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){isSequential_1}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intMat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){x}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){isNonRep}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intMat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){x}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){isSequential_2}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){isSequential_1}<LSEP>[](symbol){isSequential_2}<LEND>[](symbol){isNonRep}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Sorry, intervals need to be se...}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){intlen}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intMat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){isExtant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){isExtant}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intMat}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){Nbt}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){NbL}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){NFt}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){NFL}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){NbL}<LEND>[](symbol){NFt}<LEND>[](symbol){NFL}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){pRate}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){Nbt}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Nbt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){NFt}<LEND>[](symbol){intlen}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){qRate}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){Nbt}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Nbt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){NbL}<LEND>[](symbol){intlen}<LEND>[statement 26; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){int.start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.end}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){jigger}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LSEP>[](symbol){times1}<LEND>[argument 1; litteral](real){10.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){pRate}<LSEP>[](symbol){pRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){q1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){qRate}<LSEP>[](symbol){qRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){logRates}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){q1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ylims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.500000}<LEND>[statement 3; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){p1}<LSEP>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](str){y}<LSEP>[argument 4; litteral](real){4.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](real){5.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[](symbol){ylims}<LSEP>[argument 9; litteral](str){Time (Before Present)}<LSEP>[argument 10; litteral](str){Instantaneous Per-Capita Rate ...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ylims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.200000}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){p1}<LSEP>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](real){4.000000}<LSEP>[argument 4; litteral](real){2.000000}<LSEP>[argument 5; litteral](real){5.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[](symbol){ylims}<LSEP>[argument 8; litteral](str){Time (Before Present)}<LSEP>[argument 9; litteral](str){Instantaneous Per-Capita Rate ...}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){jitter}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){times1}<LSEP>[](symbol){jigger}<LEND>[](symbol){q1}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){times1}<LSEP>[](symbol){q1}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){2.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){legendPosition}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){legendPosition}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Origination}<LSEP>[argument 1; litteral](str){Extinction}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){intMat}<LSEP>[](symbol){intlen}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){NbL}<LSEP>[](symbol){NFt}<LSEP>[](symbol){NFL}<LSEP>[](symbol){N}<LSEP>[](symbol){pRate}<LSEP>[](symbol){qRate}<LEND>[statement 28; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){parnames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parnames}<LEND>[assign](){<-}<LSEP>[](symbol){parnames.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[assign](){<-}<LSEP>[](symbol){parnames.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[assign](){<-}<LSEP>[](symbol){parnames<-}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parnames<-}<LEND>[assign](){<-}<LSEP>[](symbol){parnames<-.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot set parnames on a const...}<LEND>[assign](){<-}<LSEP>[](symbol){parnames<-.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){np}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){value}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){value}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){value}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new parnames not equ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){value}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in parnames replacement}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){value}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicated names in parnames r...}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[](symbol){value}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){parbounds}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parbounds}<LEND>[assign](){<-}<LSEP>[](symbol){parbounds.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[assign](){<-}<LSEP>[](symbol){parbounds.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[assign](){<-}<LSEP>[](symbol){parbounds<-}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parbound<-}<LEND>[assign](){<-}<LSEP>[](symbol){parbounds<-.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot set parbounds on a cons...}<LEND>[assign](){<-}<LSEP>[](symbol){parbounds<-.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){np}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){value}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){value}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parbounds needs to be a list c...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lower}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){value}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new lower parbounds ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){lower}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in lower parbounds r...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){upper}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){value}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){upper}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new upper parbounds ...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){upper}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in upper parbounds r...}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[](symbol){value}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){parLower}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parLower}<LEND>[assign](){<-}<LSEP>[](symbol){parLower.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){parLower.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){parLower<-}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parLower<-}<LEND>[assign](){<-}<LSEP>[](symbol){parLower<-.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot set parLower on a const...}<LEND>[assign](){<-}<LSEP>[](symbol){parLower<-.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){np}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lower}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){value}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new lower parbounds ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){lower}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in lower parbounds r...}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){value}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){parUpper}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parUpper}<LEND>[assign](){<-}<LSEP>[](symbol){parUpper.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){parUpper.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){parUpper<-}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parUpper<-}<LEND>[assign](){<-}<LSEP>[](symbol){parUpper<-.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot set parUpper on a const...}<LEND>[assign](){<-}<LSEP>[](symbol){parUpper<-.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){np}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){upper}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){value}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){upper}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new upper parbounds ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){upper}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in upper parbounds r...}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){value}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){parInit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){parInit}<LEND>[assign](){<-}<LSEP>[](symbol){parInit.constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){runif}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){res}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){parInit.paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){runif}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){res}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){parnames}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){dateNodes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){rootAge}<LSEP>[](symbol){labelDates}<LSEP>[](symbol){tolerance}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree does not appear to have e...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nodeRelTimes}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){rootAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rootAge}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){nodeRelTimes}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Root age not given; treating t...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){rootAge}<LSEP>[](symbol){nodeRelTimes}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tolerance}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Some dates are negati...}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){labelDates}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){tree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[argument 1; litteral](str){ }<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plotTraitgram}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree}<LSEP>[](symbol){main}<LSEP>[](symbol){conf.int}<LSEP>[](symbol){lwd}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trait}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){No names for trait data, assum...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){trait}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){trait}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){noNodes}<LSEP>[litteral](logical){TRUE}<LEND>[statement 2; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Plotting ancestral reconstruct...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){noNodes}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trait}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length(trait) not equal to num...}<LEND>[statement 2; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Plotting internal node values ...}<LEND>[statement 3; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){assuming trait data in same or...}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){noNodes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){asr}<LEND>[call](){}<LSEP>[](symbol){ace}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree}<LSEP>[argument 2; litteral](str){pic}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tr1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){trait}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){asr}<LSEP>[](symbol){ace}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tr1}<LSEP>[](symbol){trait}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){conf.int}<LSEP>[litteral](logical){FALSE}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){conf.int}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ci}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){asr}<LSEP>[](symbol){CI95}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xlims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){tr1}<LSEP>[](symbol){ci}<LEND>[argument 1; litteral](real){0.100000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){tr1}<LSEP>[](symbol){ci}<LEND>[argument 1; litteral](real){0.100000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){tr1}<LEND>[argument 1; litteral](real){0.100000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){tr1}<LEND>[argument 1; litteral](real){0.100000}<LEND>[statement 6; call](){}<LSEP>[](symbol){plot}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](str){n}<LSEP>[](symbol){xlims}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times}<LEND>[argument 5; litteral](str){Trait Values}<LSEP>[argument 6; litteral](str){Time (Before Present)}<LSEP>[](symbol){main}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anc}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){desc}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tr1}<LSEP>[](symbol){anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tr1}<LSEP>[](symbol){desc}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times}<LSEP>[](symbol){anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times}<LSEP>[](symbol){desc}<LEND>[](symbol){lwd}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){conf.int}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ci}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ci}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[](symbol){lwd}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){occData2timeList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){occList}<LSEP>[](symbol){intervalType}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){intervalType}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){occRange}<LSEP>[argument 1; litteral](str){dateRange}<LSEP>[argument 2; litteral](str){zoneOverlap}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){intervalType must be one of 'd...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaInt}<LEND>[call](){}<LSEP>[](symbol){pullOccListData}<LSEP>[](symbol){occList}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){intervalType}<LSEP>[argument 1; litteral](str){occRange}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaMin}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaInt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaMax}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaInt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaMin}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaMin}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaMax}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaMax}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[](symbol){x}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){taxaMin}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaMin}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaMin}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){taxaMax}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaMax}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaMax}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){intervalType}<LSEP>[argument 1; litteral](str){dateRange}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaMin}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaInt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){max}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaMax}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaInt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){min}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){intervalType}<LSEP>[argument 1; litteral](str){zoneOverlap}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaMin}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaInt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaMax}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaInt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaMin}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaMin}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaMax}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaMax}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){fourDate}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){taxaMin}<LSEP>[](symbol){taxaMax}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){timeList}<LEND>[call](){}<LSEP>[](symbol){fourDate2timeList}<LSEP>[](symbol){fourDate}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timeList}<LSEP>[](symbol){taxonTimes}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){occList}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){timeList}<LEND>[assign](){<-}<LSEP>[](symbol){pullOccListData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){occList}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){occList}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){occList is not a list?}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){inherits}<LSEP>[argument 2; litteral](str){data.frame}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){inherits}<LSEP>[argument 2; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){All elements of occList must b...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){exOcc}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){occList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){exOcc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not all occList entries have s...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){ageSelector}<LSEP>[litteral](NULL){NULL}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](str){early_age}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](str){late_age}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ageSelector}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){early_age}<LSEP>[argument 1; litteral](str){late_age}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](str){eag}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](str){lag}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ageSelector}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){eag}<LSEP>[argument 1; litteral](str){lag}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](str){max_ma}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](str){min_ma}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ageSelector}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){max_ma}<LSEP>[argument 1; litteral](str){min_ma}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ageSelector}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){exOcc}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ageSelector}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Data is not a two-column matri...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){taxaOcc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){occList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){ageSelector}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxaOcc}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){taxonTable2taxonTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){cleanTree}<LSEP>[](symbol){rootLabel}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){taxonTable}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){taxonTable}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxonTable must be a matrix of...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){taxonTable}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxonTable must have multiple ...}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxonTable}<LEND>[litteral](str){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){constantCol}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){taxonTable}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rootColumn}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){constantCol}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constantCol}<LSEP>[](symbol){rootColumn}<LEND>[litteral](logical){FALSE}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LSEP>[](symbol){rootColumn}<LEND>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LSEP>[](symbol){rootColumn}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){rootLabel}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxonTable}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){taxonTable}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Must have at least one varying...}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxonTable}<LSEP>[argument 1; litteral](str){}<LEND>[litteral](logical){NA}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){taxonTable}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing tip taxon names in tax...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){labels}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){taxonTable}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){labels}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Duplicated labels found for ta...}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){labels}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){levels}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){taxonTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){level}<LSEP>[](symbol){levels}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newNodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LSEP>[](symbol){level}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LSEP>[](symbol){level}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){node}<LSEP>[](symbol){newNodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){labels}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){labels}<LSEP>[](symbol){node}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nodeID}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){labels}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){whichDesc}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LSEP>[](symbol){level}<LEND>[](symbol){node}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){descTaxRow}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){whichDesc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){level}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){descTax}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){descTaxRow}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){descTax}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){descTax}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){descID}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){descTax}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){labels}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){descID}<LEND>[litteral](NULL){NULL}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){newEdge}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){nodeID}<LSEP>[](symbol){descID}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edge}<LSEP>[](symbol){newEdge}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){edge}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){Nnode}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){tip.label}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonTable}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){taxonTable}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){node.label}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tip.label}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){Ntip}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tip.label}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Ntip}<LEND>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Ntip}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){nodes}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){root}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nodes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){root}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Multiple (}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){root}<LEND>[argument 2; litteral](str){) roots found in data??}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){root}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){Ntip}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Root isn't renumbering correctly}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edge}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){edge}<LSEP>[](symbol){tip.label}<LSEP>[](symbol){edge.length}<LSEP>[](symbol){Nnode}<LEND>[argument 4; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){node.label}<LEND>[statement 31; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){phylo}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){tree}<LEND>[statement 32; control flow](){if}<LSEP>[](symbol){cleanTree}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){cleanNewPhylo}<LSEP>[](symbol){tree}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxonTable}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Taxa number changed while clea...}<LEND>[statement 34; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){timeList2fourDate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](str){list}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList is not a list?}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){timeList}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList is not length = 2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){timeList}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){timeList}<LSEP>[](symbol){as.matrix}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){timeList}<LSEP>[](symbol){inherits}<LSEP>[argument 2; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList elements are not matr...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){timeList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList matrices do not have ...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){firstInt}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){x}<LSEP>[](symbol){}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){lastInt}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){x}<LSEP>[](symbol){}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){fourDate}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){firstInt}<LSEP>[](symbol){lastInt}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){fourDate}<LEND>[assign](){<-}<LSEP>[](symbol){fourDate2timeList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fourDate}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fourDate}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){fourDate}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){fourDate}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){fourDate}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fourDate must be a matrix with...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaFirst}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fourDate}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaLast}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fourDate}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){intTimes}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){taxaFirst}<LSEP>[](symbol){taxaLast}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){intTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intTimes}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intTimes}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){firstInt}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){taxaFirst}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){lastInt}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){taxaLast}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){taxonTimes}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){firstInt}<LSEP>[](symbol){lastInt}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){intTimes}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){startTime}<LSEP>[argument 1; litteral](str){endTime}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){taxonTimes}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstInt}<LSEP>[argument 1; litteral](str){lastInt}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){intTimes}<LSEP>[](symbol){taxonTimes}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){makeParFunct}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){par}<LSEP>[](symbol){isBranchRate}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){acceptedArg}<LEND>[control flow](){if}<LSEP>[](symbol){isBranchRate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){N}<LSEP>[argument 1; litteral](str){T}<LSEP>[argument 2; litteral](str){D}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){N}<LSEP>[argument 1; litteral](str){T}<LSEP>[argument 2; litteral](str){D}<LSEP>[argument 3; litteral](str){P}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){par}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){par}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){par}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){timeDepAttr}<LSEP>[litteral](logical){FALSE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){type.convert}<LSEP>[](symbol){par}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){type.convert}<LSEP>[](symbol){par}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){res}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){input rates must be at least 0...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){parFunct}<LEND>[control flow](){if}<LSEP>[](symbol){isBranchRate}<LEND>[true branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){N}<LSEP>[](symbol){T}<LSEP>[](symbol){D}<LEND>[body; block](){}<LEND>[false branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){N}<LSEP>[](symbol){T}<LSEP>[](symbol){D}<LSEP>[](symbol){P}<LEND>[body; block](){}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){body}<LSEP>[](symbol){parFunct}<LEND>[](symbol){res}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){parFunct}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){args}<LEND>[call](){}<LSEP>[](symbol){all.vars}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){XXdave~}<LSEP>[](symbol){par}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){args}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){args}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){args}<LSEP>[argument 1; litteral](str){XXdave}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){args}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){acceptedArg}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){isBranchRate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Incorrect parameterization of ...}<LSEP>[argument 1; litteral](str){Only N and T allowed as variables}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Incorrect parameterization of ...}<LSEP>[argument 1; litteral](str){Only P, N and T allowed as var...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){args}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){T}<LSEP>[argument 1; litteral](str){D}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeDepAttr}<LSEP>[litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){parFunct}<LEND>[control flow](){if}<LSEP>[](symbol){isBranchRate}<LEND>[true branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){N}<LSEP>[](symbol){T}<LSEP>[](symbol){D}<LEND>[body; block](){}<LEND>[false branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){N}<LSEP>[](symbol){T}<LSEP>[](symbol){D}<LSEP>[](symbol){P}<LEND>[body; block](){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){body}<LSEP>[](symbol){parFunct}<LEND>[call](){}<LSEP>[](symbol){parse}<LSEP>[](symbol){par}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){parFunct}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](str){timeDep}<LEND>[](symbol){timeDepAttr}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){getRateMatrix}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){taxaDurations}<LSEP>[](symbol){getBranchRate}<LSEP>[](symbol){getExtRate}<LSEP>[](symbol){getSampRate}<LSEP>[](symbol){getAnagRate}<LSEP>[](symbol){prop.cryptic}<LSEP>[](symbol){prop.bifurc}<LSEP>[](symbol){negRatesAsZero}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whichExtant}<LEND>[call](){}<LSEP>[](symbol){whichLive}<LSEP>[](symbol){taxa}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nLive}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichExtant}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rateMat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[](symbol){nLive}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){rateMat}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){budd}<LSEP>[argument 1; litteral](str){bifurc}<LSEP>[argument 2; litteral](str){anag}<LSEP>[argument 3; litteral](str){crypt}<LSEP>[argument 4; litteral](str){ext}<LSEP>[argument 5; litteral](str){samp}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){rateMat}<LSEP>[argument 1; litteral](str){whichExtant}<LEND>[](symbol){whichExtant}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nLive}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxonDur}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDurations}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){branchRate}<LEND>[call](){}<LSEP>[](symbol){getBranchRate}<LSEP>[](symbol){nLive}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){taxonDur}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){extRate}<LEND>[call](){}<LSEP>[](symbol){getExtRate}<LSEP>[](symbol){nLive}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){taxonDur}<LSEP>[](symbol){branchRate}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sampRate}<LEND>[call](){}<LSEP>[](symbol){getSampRate}<LSEP>[](symbol){nLive}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){taxonDur}<LSEP>[](symbol){branchRate}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){anagRate}<LEND>[call](){}<LSEP>[](symbol){getAnagRate}<LSEP>[](symbol){nLive}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){taxonDur}<LSEP>[](symbol){branchRate}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){crypticRate}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){branchRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){prop.cryptic}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){morphRate}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){branchRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){prop.cryptic}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){buddRate}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){morphRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){prop.bifurc}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){bifurcRate}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){morphRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){prop.bifurc}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){rateVector}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){buddRate}<LSEP>[](symbol){bifurcRate}<LSEP>[](symbol){anagRate}<LSEP>[](symbol){crypticRate}<LSEP>[](symbol){extRate}<LSEP>[](symbol){sampRate}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rateVector}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){budd}<LSEP>[argument 1; litteral](str){bifurc}<LSEP>[argument 2; litteral](str){anag}<LSEP>[argument 3; litteral](str){crypt}<LSEP>[argument 4; litteral](str){ext}<LSEP>[argument 5; litteral](str){samp}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){rateVector}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){negRatesAsZero}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rateVector}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){rateVector}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){rateVector}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](str){rate calculated less than zero}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rateMat}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[](symbol){rateVector}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){rateMat}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Simulation found scenario in w...}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){rateMat}<LEND>[assign](){<-}<LSEP>[](symbol){initiateTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){startTaxa}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newTaxa}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){startTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){newTaxon}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){NA}<LSEP>[](symbol){time}<LSEP>[](symbol){x}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newTaxa}<LEND>[assign](){<-}<LSEP>[](symbol){newTaxon}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){newID}<LSEP>[](symbol){ancID}<LSEP>[](symbol){time}<LSEP>[](symbol){looksLike}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaData}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){newID}<LSEP>[](symbol){ancID}<LSEP>[](symbol){time}<LSEP>[argument 3; litteral](logical){NA}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[](symbol){looksLike}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){taxaData}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){taxon.id}<LSEP>[argument 1; litteral](str){ancestor.id}<LSEP>[argument 2; litteral](str){orig.time}<LSEP>[argument 3; litteral](str){ext.time}<LSEP>[argument 4; litteral](str){still.alive}<LSEP>[argument 5; litteral](str){looks.like}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxon}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){numeric}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxon}<LEND>[assign](){<-}<LSEP>[](symbol){origination}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){ancID}<LSEP>[](symbol){time}<LSEP>[](symbol){looksLike}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newID}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){looksLike}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){looksLike}<LSEP>[](symbol){newID}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){looksLike}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){looksLike}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newTaxonData}<LEND>[call](){}<LSEP>[](symbol){newTaxon}<LSEP>[](symbol){newID}<LSEP>[](symbol){ancID}<LSEP>[](symbol){time}<LSEP>[](symbol){looksLike}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newTaxa}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){newTaxonData}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newTaxa}<LEND>[assign](){<-}<LSEP>[](symbol){termination}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whichTarget}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){target}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichTarget}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxon IDs repeated??}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){whichTarget}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[](symbol){time}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){whichTarget}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){buddingEvent}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){origination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LSEP>[argument 3; litteral](NULL){NULL}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){crypticEvent}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){origination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LSEP>[](symbol){parent}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){anagEvent}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){origination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LSEP>[argument 3; litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){termination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){bifurcEvent}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){origination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LSEP>[argument 3; litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){origination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LSEP>[argument 3; litteral](NULL){NULL}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){termination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parent}<LSEP>[](symbol){time}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){extEvent}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){termination}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){sampEvent}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whichTarget}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){target}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){whichTarget}<LEND>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){whichTarget}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){time}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){eventOccurs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){type}<LSEP>[](symbol){time}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){budd}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){buddingEvent}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){bifurc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){bifurcEvent}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){anag}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){anagEvent}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){crypt}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){crypticEvent}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){ext}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){extEvent}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){samp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){sampEvent}<LSEP>[](symbol){taxa}<LSEP>[](symbol){target}<LSEP>[](symbol){time}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxa object contains taxa with...}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){whichLive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res2}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){res2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Disagreement on which taxa are...}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){res}<LEND>[argument 2; litteral](str){ taxa were coded as is.extant (}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](str){, }<LEND>[argument 4; litteral](str){)\n}<LEND>[argument 5; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){res2}<LEND>[argument 6; litteral](str){ taxa had NA or 0L extinction ...}<LEND>[argument 7; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){res2}<LEND>[argument 1; litteral](str){, }<LEND>[argument 8; litteral](str){)\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){whichSampled}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){res}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){getTaxonDurations}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){currentTime}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){areExtant}<LEND>[call](){}<LSEP>[](symbol){whichLive}<LSEP>[](symbol){taxa}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){durations}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){areExtant}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){currentTime}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){durations}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){negative durations calculated??}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){durations}<LEND>[assign](){<-}<LSEP>[](symbol){getRunVitals}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){count.cryptic}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){taxa}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){handed getRunVitals a taxa obj...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichExtant}<LEND>[call](){}<LSEP>[](symbol){whichLive}<LSEP>[](symbol){taxa}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){whichSamp}<LEND>[call](){}<LSEP>[](symbol){whichSampled}<LSEP>[](symbol){taxa}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){count.cryptic}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nTaxa}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nLive}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichExtant}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nSampled}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichSamp}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){looksLike}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nTaxa}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){looksLike}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nLive}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){looksLike}<LSEP>[](symbol){whichExtant}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nSampled}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){looksLike}<LSEP>[](symbol){whichSamp}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){vitals}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){nTaxa}<LSEP>[](symbol){nLive}<LSEP>[](symbol){nSampled}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){vitals}<LEND>[assign](){<-}<LSEP>[](symbol){testContinue}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){vitals}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){runConditions}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){totalExtinction}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitals}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tooMuchTime}<LEND>[call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){timePassed}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tooManyTaxa}<LEND>[call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitals}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){nTotalTaxa}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tooManySamp}<LEND>[call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitals}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){nSamp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){runStop}<LEND>[call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LSEP>[](symbol){totalExtinction}<LSEP>[](symbol){tooMuchTime}<LEND>[](symbol){tooManyTaxa}<LEND>[](symbol){tooManySamp}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){continue}<LEND>[call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){runStop}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){continue}<LEND>[assign](){<-}<LSEP>[](symbol){contiguousIntegerSeq}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){vector}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){vector}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){contiguousIntegerSeq handed a ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vector}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){contiguousIntegerSeq handed le...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vector}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){vector}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){starts}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vector}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){starts}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[](symbol){starts}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){starts}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector}<LSEP>[](symbol){starts}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ends}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vector}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ends}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){ends}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){ends}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector}<LSEP>[](symbol){ends}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){seqMat}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){starts}<LSEP>[](symbol){ends}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){seqMat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){seqMat isn't a matrix}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){seqMat}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){seqMat doesn't have 2 columns}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){seqMat}<LEND>[assign](){<-}<LSEP>[](symbol){insertRow}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){table}<LSEP>[](symbol){row}<LSEP>[](symbol){rownum}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){table}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){table}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){rownum}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[](symbol){row}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){table}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){rownum}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){table}<LEND>[assign](){<-}<LSEP>[](symbol){worthCheckingVitalsRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){runConditions}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){labMatch}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){runConditions}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){labMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){runConditions and vitalsRecord...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lastVitals}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){vitalsRecord}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){reachMin}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lastVitals}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){worthChecking}<LEND>[call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){reachMin}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){worthChecking}<LEND>[assign](){<-}<LSEP>[](symbol){testVitalsRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){tolerance}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){labMatch}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){runConditions}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){labMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){runConditions and vitalsRecord...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){isMinTime}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){isMinTime}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whereInsert}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newRow}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){whereInsert}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){newRow}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){isMaxTime}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){isMaxTime}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whereInsert}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newRow}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){totalTime}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){whereInsert}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){newRow}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){newVitalsRecord}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){pastIncrement}<LEND>[call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){pastIncrement}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pastIncrement}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pastIncrement}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){pastIncrement}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){1000.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pastIncrement}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){tolerance}<LSEP>[](symbol){pastIncrement}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pastIncrement}<LSEP>[](symbol){tolerance}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){newTimes}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newVitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){pastIncrement}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){newTimes}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){newTimes}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){newTimes}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newVitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){newTimes}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){newVitalsRecord}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){vitalsRecord}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){okayVitalsMat}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){var}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){varRange}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){i}<LEND>[statement 2; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){varRange}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){varRange}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){okayVitals}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){okayVitalsMat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){all}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){okayVitals}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whichOkay}<LEND>[call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){okayVitals}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichOkay}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){seqVitals}<LEND>[call](){}<LSEP>[](symbol){contiguousIntegerSeq}<LSEP>[](symbol){whichOkay}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){seqVitals}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){whichOkay}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){seqVitals}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){seqVitals}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vitalsRecord}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){seqVitals}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){seqVitals}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){seqVitals}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){seqVitals}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){seqVitals isn't a matrix}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){seqVitals}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){seqVitals doesn't have 2 columns}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){seqVitals}<LSEP>[litteral](logical){NA}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){seqVitals}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){seqVitals constructed incorrectly}<LEND>[statement 20; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){seqVitals}<LEND>[assign](){<-}<LSEP>[](symbol){sampleSeqVitals}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){seqVitals}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cumSumSeq}<LEND>[call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){seqVitals}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){totalSum}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){cumSumSeq}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){totalSum}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){placedDate}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){totalSum}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){findRow}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){cumSumSeq}<LSEP>[](symbol){placedDate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){earlierRowCumSum}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){findRow}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cumSumSeq}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){findRow}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){date}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){seqVitals}<LSEP>[](symbol){findRow}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){placedDate}<LEND>[](symbol){earlierRowCumSum}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){seqVitals}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){date}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){seqVitals}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){date}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){seqVitals}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){date}<LEND>[assign](){<-}<LSEP>[](symbol){getTaxaNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cryptIDs}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxonIDs}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){whichCrypt}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){cryptIDs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){cryptIDs}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newIDs}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxonIDs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichCrypt}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchCrypt}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){cryptIDs}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cryptIDs}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nCrypt}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonIDs}<LSEP>[](symbol){matchCrypt}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonIDs}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cryptIDs}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){.}<LSEP>[](symbol){nCrypt}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonIDs}<LSEP>[](symbol){x}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){newIDs}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){t}<LSEP>[](symbol){newIDs}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newIDs}<LEND>[assign](){<-}<LSEP>[](symbol){testFinal}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){count.cryptic}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whichExtant}<LEND>[call](){}<LSEP>[](symbol){whichLive}<LSEP>[](symbol){taxa}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichExtant}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){extantTime}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichExtant}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){extantTime}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){finalVitals}<LEND>[call](){}<LSEP>[](symbol){getRunVitals}<LSEP>[](symbol){taxa}<LSEP>[](symbol){count.cryptic}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){finalVitals}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){timePassed}<LSEP>[](symbol){finalVitals}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){okayVitals}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){var}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){finalVitals}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){varRange}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){runConditions}<LSEP>[](symbol){i}<LEND>[statement 2; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){varRange}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){varRange}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){okayVitals}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){taxa}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){finalVitals}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Accepted run is outside of bou...}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){runConditions}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){okayVitals}<LEND>[argument 2; litteral](str){, }<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){finalCheck}<LEND>[call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){okayVitals}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalVitals}<LEND>[assign](){<-}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hasNegFirstDate}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){orig.time}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hasNegLastDate}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){ext.time}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){ext.time}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){hasNegSampleDate}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){hasNegFirstDate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in origination times...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){hasNegLastDate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs returned when testin...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){hasNegSampleDate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs returned when testin...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){hasNegFirstDate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){fossilRecord object has taxon ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){badTaxa}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){hasNegFirstDate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){badTaxa}<LEND>[statement 3; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Something has gone very wrong.}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){hasNegLastDate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){fossilRecord object has taxon ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){badTaxa}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){hasNegLastDate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){badTaxa}<LEND>[statement 3; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Something has gone very wrong.}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){hasNegSampleDate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){fossilRecord object has taxon ...}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){hasNegSampleDate}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Something has gone very wrong.}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](logical){TRUE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getMrBFixedAgesFromNexus}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){origNexusFile}<LSEP>[](symbol){shouldEndWithNex}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){shouldEndWithNex}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){endNex}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){\\.nex$}<LSEP>[](symbol){origNexusFile}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){endNex}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origNexusFile}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){origNexusFile}<LSEP>[argument 1; litteral](str){.nex}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){scan}<LSEP>[](symbol){origNexusFile}<LEND>[argument 1; call](){}<LSEP>[](symbol){character}<LEND>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){[}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){readChar}<LSEP>[](symbol){origNexusFile}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.info}<LSEP>[](symbol){origNexusFile}<LEND>[](symbol){size}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){ }<LSEP>[argument 2; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){\t}<LSEP>[argument 2; litteral](str){}<LEND>[statement 5; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){\\[|\\]}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){\\[[^\\[\\]]*\\]}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){\r}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){\n}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){origNexus}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){origNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){hasCalibrate}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){calibrate}<LSEP>[](symbol){origNexus}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hasCalibrate}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){origNexus}<LSEP>[](symbol){hasCalibrate}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){hasCalibrate}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){hasCalibrate}<LSEP>[argument 1; litteral](str){calibrate}<LSEP>[argument 2; litteral](str){}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){hasFixed}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){=fixed\\(}<LSEP>[](symbol){hasCalibrate}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){hasFixed}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hasCalibrate}<LSEP>[](symbol){hasFixed}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){hasFixed}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){hasFixed}<LSEP>[argument 1; litteral](str){fixed\\(}<LSEP>[argument 2; litteral](str){}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){hasFixed}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){hasFixed}<LSEP>[argument 1; litteral](str){\\);}<LSEP>[argument 2; litteral](str){}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){fixedList}<LEND>[call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){hasFixed}<LSEP>[argument 1; litteral](str){=}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){fixedMatrix}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fixedList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[](symbol){x}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){fixedTable}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){fixedMatrix}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixedTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixedMatrix}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){fixedTable}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){No OTUs with fixed ages found ...}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){fixedTable}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){OTUname}<LSEP>[argument 1; litteral](str){fixedAge}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){fixedTable}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){make_inverseSurv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LSEP>[](symbol){groups}<LSEP>[](symbol){p_cont}<LSEP>[](symbol){q_cont}<LSEP>[](symbol){PA_n}<LSEP>[](symbol){PB_1}<LSEP>[](symbol){Nb}<LSEP>[](symbol){drop.extant}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){modernTest}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){modernTest}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){modernTest}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one modern interval ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modInt}<LEND>[call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){modernTest}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newInt}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){newInt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one interval stretch...}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){modDroppers}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){modInt}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){modDroppers}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sapply}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){modInt}<LEND>[true branch; block](){}<LSEP>[](symbol){newInt}<LEND>[false branch; block](){}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modInt}<LEND>[](symbol){}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){PA_n}<LSEP>[argument 1; litteral](str){fixed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){PA_n}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){PA_n}<LSEP>[argument 1; litteral](str){fixed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){PA_n}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){int.length}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){parNames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){p}<LSEP>[argument 1; litteral](str){q}<LSEP>[argument 2; litteral](str){r}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){parNames}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[argument 2; litteral](str){.}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){PB_1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parNames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){parNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){PB_1.0}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){PA_n}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parNames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){parNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){PA_n.0}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){drop.extant}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){modernTest}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modDroppers}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){number of rows in groups isn't...}<LEND>[argument 1; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){after modern taxa are dropped}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parNames}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){.}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){groups}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){ngroup}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groupings}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){breakNames}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){lowerBound}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.001000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parNames}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){upperBound}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parNames}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upperBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){PB_1}<LEND>[litteral](real){1.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upperBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){PA_n}<LEND>[litteral](real){1.000000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upperBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[litteral](real){1.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){parbounds}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){lowerBound}<LSEP>[](symbol){upperBound}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){obs_X_list}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 19; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngroup}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ranges}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ranges}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){groups}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){k}<LSEP>[](symbol){}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){obs_X}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n}<LSEP>[](symbol){n}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_X}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ranges}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ranges}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){j}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_X_list}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){obs_X}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){logL_invSurv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){par}<LSEP>[](symbol){altMode}<LSEP>[](symbol){plotPar}<LSEP>[](symbol){ratesPerInt}<LSEP>[](symbol){logRates}<LSEP>[](symbol){jitter}<LSEP>[](symbol){legendPosition}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of input parameters is ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){altMode}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){logLsum}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){z}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngroup}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){par}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){breakNames}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){z}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parnew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LSEP>[](symbol){selector}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){breaknew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){selector}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){p}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){r}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){int.length}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){int.length}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LSEP>[](symbol){int.length}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){obs_X}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obs_X_list}<LSEP>[](symbol){z}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){fR}<LEND>[call](){}<LSEP>[](symbol){footeValues}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){PA_n}<LSEP>[](symbol){PB_1}<LSEP>[](symbol){p_cont}<LSEP>[](symbol){q_cont}<LSEP>[](symbol){Nb}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){P_forw}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[](symbol){n}<LSEP>[](symbol){n}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_forw}<LSEP>[](symbol){j}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){XFL}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){XFt}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){XFL}<LEND>[](symbol){j}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LSEP>[litteral](logical){NA}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_forw}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_forw}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_bL}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_bt}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PA}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PA}<LEND>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_forw}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_forw}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_bL}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_bt}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PA}<LEND>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PA}<LEND>[](symbol){i}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){P_inv}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[](symbol){n}<LSEP>[](symbol){n}<LEND>[statement 15; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_inv}<LSEP>[](symbol){j}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){XFL}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){XbL}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){XFL}<LEND>[](symbol){i}<LEND>[statement 16; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LSEP>[litteral](logical){NA}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_inv}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_inv}<LSEP>[](symbol){j}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_Ft}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_bt}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PB}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PB}<LEND>[](symbol){j}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_inv}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_inv}<LSEP>[](symbol){j}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_Ft}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PD_bt}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PB}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fR}<LSEP>[](symbol){PB}<LEND>[](symbol){j}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){logL}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){n}<LSEP>[](symbol){n}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_X}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){logL}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_X}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_forw}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_X}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){P_inv}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){logLsum}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){logL}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){logLsum}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){logLsum}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){logLsum}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){plotPar}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){ngroup}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngroup}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Number of groups greater than ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){plotPar}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){z}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngroup}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){par}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){breakNames}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){z}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parnew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LSEP>[](symbol){selector}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){breaknew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){selector}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){p}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){r}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){ratesPerInt}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){int.length}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){int.length}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LSEP>[](symbol){int.length}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){rates}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rates}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rates}<LEND>[argument 1; litteral](str){p}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){results}<LSEP>[](symbol){z}<LEND>[](symbol){rates}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){plotPar}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){int.start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.end}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){jigger}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LSEP>[](symbol){times1}<LEND>[argument 1; litteral](real){10.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){q1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){q}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){r1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){r}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){logRates}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){q1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){r1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ylims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LSEP>[](symbol){r1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LSEP>[](symbol){r1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.500000}<LEND>[statement 4; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){p1}<LSEP>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](str){y}<LSEP>[argument 4; litteral](real){4.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](real){5.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[](symbol){ylims}<LSEP>[argument 9; litteral](str){Time (Before Present)}<LSEP>[argument 10; litteral](str){Instantaneous Per-Capita Rate ...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ylims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LSEP>[](symbol){r1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){p1}<LSEP>[](symbol){q1}<LSEP>[](symbol){r1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.500000}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){p1}<LSEP>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](real){4.000000}<LSEP>[argument 4; litteral](real){2.000000}<LSEP>[argument 5; litteral](real){5.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[](symbol){ylims}<LSEP>[argument 8; litteral](str){Time (Before Present)}<LSEP>[argument 9; litteral](str){Instantaneous Per-Capita Rate ...}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){jitter}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){times1}<LSEP>[](symbol){jigger}<LEND>[](symbol){q1}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){times1}<LSEP>[](symbol){jigger}<LEND>[](symbol){r1}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){6.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){times1}<LSEP>[](symbol){q1}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){times1}<LSEP>[](symbol){r1}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){6.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){legendPosition}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){legendPosition}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Origination}<LSEP>[argument 1; litteral](str){Extinction}<LSEP>[argument 2; litteral](str){Sampling}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ngroup}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){logL_invSurv}<LEND>[call](){}<LSEP>[](symbol){make_paleotreeFunc}<LSEP>[](symbol){logL_invSurv}<LSEP>[](symbol){parNames}<LSEP>[](symbol){parbounds}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){logL_invSurv}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){footeValues}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){PA_n}<LSEP>[](symbol){PB_1}<LSEP>[](symbol){p_cont}<LSEP>[](symbol){q_cont}<LSEP>[](symbol){Nb}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p is not same length as q!}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){r}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p is not same length as r!}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){q is not same length as r!}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Nbt}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Nbt}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){q}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NbL}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NbL}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LSEP>[](symbol){q}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFt}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFt}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFt}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFt}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){q}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){NFL}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){NFL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){NFL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFL}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFL}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NFL}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){PD_bt}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_bL}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_bL}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_Ft}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_Ft}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_FL}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PD_FL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){NFL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PD_FL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Nb}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){NFL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_FL}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){p}<LEND>[](symbol){r}<LEND>[](symbol){p}<LEND>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_FL}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){q}<LEND>[](symbol){r}<LEND>[](symbol){q}<LEND>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){q}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PD_FL}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){PA}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PA}<LSEP>[](symbol){n}<LEND>[](symbol){PA_n}<LEND>[statement 15; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){q_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PA_i}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LSEP>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PA_i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PA_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PD_bL}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PA}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PA_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PA}<LSEP>[](symbol){n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PA_i}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LSEP>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PA_i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PA_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PD_bL}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PA}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PA_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PA}<LSEP>[](symbol){n}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){PB}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PB}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){PB_1}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){p_cont}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PB_i}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LSEP>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PB_i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PB_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PD_Ft}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PB}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PB_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PB}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PB_i}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LSEP>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PB_i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PB_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PD_Ft}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PB}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){PB_i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PB}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){Xbt}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){PB}<LEND>[](symbol){PA}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){XbL}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NbL}<LSEP>[](symbol){PB}<LEND>[](symbol){PD_bL}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){PB}<LEND>[](symbol){PD_bt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PA}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){XFt}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NFt}<LSEP>[](symbol){PA}<LEND>[](symbol){PD_Ft}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nbt}<LSEP>[](symbol){PA}<LEND>[](symbol){PD_bt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PB}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){XFL}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NFL}<LSEP>[](symbol){PD_FL}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NbL}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PB}<LEND>[](symbol){PD_bL}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NFt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PA}<LEND>[](symbol){PD_Ft}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Nbt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PB}<LEND>[](symbol){PD_bt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PA}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){Nb}<LSEP>[](symbol){n}<LEND>[](symbol){Nbt}<LSEP>[](symbol){NbL}<LSEP>[](symbol){NFt}<LSEP>[](symbol){NFL}<LSEP>[](symbol){PD_bt}<LSEP>[](symbol){PD_bL}<LSEP>[](symbol){PD_Ft}<LSEP>[](symbol){PD_FL}<LSEP>[](symbol){PA}<LSEP>[](symbol){PB}<LSEP>[](symbol){Xbt}<LSEP>[](symbol){XbL}<LSEP>[](symbol){XFt}<LSEP>[](symbol){XFL}<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){tipDatingCompatabilitySummaryMrB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){runFile}<LSEP>[](symbol){nRuns}<LSEP>[](symbol){burnin}<LSEP>[](symbol){compatibilityThreshold}<LSEP>[](symbol){labelPostProb}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){compatibilityThreshold}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){compatibilityThreshold < 0.5:\...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){postBurnInTrees}<LEND>[call](){}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LSEP>[](symbol){runFile}<LSEP>[](symbol){nRuns}<LSEP>[](symbol){burnin}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LSEP>[argument 5; litteral](NULL){NULL}<LSEP>[argument 6; litteral](str){all}<LSEP>[argument 7; litteral](NULL){NULL}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){postBurnInTrees}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){postBurnInTrees}<LSEP>[](symbol){i}<LEND>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){finalTree}<LEND>[call](){}<LSEP>[](symbol){consensus}<LSEP>[](symbol){postBurnInTrees}<LSEP>[](symbol){compatibilityThreshold}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){finalTree}<LEND>[call](){}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){finalTree}<LSEP>[](symbol){postBurnInTrees}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalTree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){accioExhaustionCurve}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){phyloTree}<LSEP>[](symbol){charData}<LSEP>[](symbol){charTypes}<LSEP>[](symbol){outgroup}<LSEP>[](symbol){firstAppearances}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){inapplicableValue}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntaxa}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){charData}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ntaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){phyloTree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of tips on phylotree do...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mtree}<LSEP>[](symbol){phyloTree}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mtree}<LSEP>[](symbol){tip.label}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){phyloTree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){charData}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mtree}<LEND>[call](){}<LSEP>[](symbol){accio_matrix_tree_from_ape_tree}<LSEP>[](symbol){mtree}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){nchar}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){charData}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){nchar}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){charTypes}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){charTypes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){charTypes}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){charTypes}<LSEP>[](symbol){nchar}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of charTypes must be 1 ...}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){charData}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){charData}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outgroup}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outgroupID}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){outgroup}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){if given, outgroup must be of ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){outgroupID}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){phyloTree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){outgroup}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){outgroupID}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){There is no single match to th...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){char_history}<LEND>[call](){}<LSEP>[](symbol){accio_minimum_steps_history}<LSEP>[](symbol){mtree}<LSEP>[](symbol){charData}<LSEP>[](symbol){charTypes}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){inapplicableValue}<LSEP>[](symbol){outgroupID}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){firstAppearances}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){branch_order}<LEND>[call](){}<LSEP>[](symbol){accio_patristic_distance_from_base}<LSEP>[](symbol){mtree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){used_order}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){branch_order}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){branch_order}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){exhaust_order}<LEND>[call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){used_order}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ntaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){firstAppearances}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of firstAppearances doe...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){exhaust_order}<LEND>[assign](){<-}<LSEP>[](symbol){used_order}<LEND>[call](){}<LSEP>[](symbol){accio_branch_order_with_stratigraphy}<LSEP>[](symbol){mtree}<LSEP>[](symbol){firstAppearances}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){branches}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mtree}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){branch_derivs}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){branches}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){b}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){branches}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){branch_derivs}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_history}<LSEP>[](symbol){Changes}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){b}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){rel_branches}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){branch_derivs}<LSEP>[](symbol){exhaust_order}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){rb}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rel_branches}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){char_deriv}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nchar}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){exhaust_matrix}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_history}<LSEP>[](symbol){Changes}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_history}<LSEP>[](symbol){Changes}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){found}<LEND>[assign](){<-}<LSEP>[](symbol){total_steps}<LEND>[assign](){<-}<LSEP>[](symbol){novel_chars}<LEND>[assign](){<-}<LSEP>[](symbol){novel_states}<LSEP>[litteral](real){0.000000}<LEND>[statement 19; control flow](){for}<LSEP>[](symbol){b}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){rb}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){br}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rel_branches}<LSEP>[](symbol){b}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){local_change}<LEND>[call](){}<LSEP>[](symbol){subset}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_history}<LSEP>[](symbol){Changes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_history}<LSEP>[](symbol){Changes}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){br}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_deriv}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_deriv}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){novel_chars}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){novel_chars}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_deriv}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){d}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){branch_derivs}<LSEP>[](symbol){br}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){branch_derivs}<LSEP>[](symbol){br}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[](symbol){d}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){st}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[](symbol){d}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){st}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_change}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_matrix}<LSEP>[](symbol){ch}<LSEP>[](symbol){st}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_matrix}<LSEP>[](symbol){ch}<LSEP>[](symbol){st}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_matrix}<LSEP>[](symbol){ch}<LSEP>[](symbol){st}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){novel_states}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){novel_states}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){total_steps}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){total_steps}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){branch_derivs}<LSEP>[](symbol){br}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](real){10.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mtree}<LEND>[argument 1; litteral](real){10.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brnm}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){br_}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){mtree}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brnm}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){br_0}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brnm}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){br_00}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mtree}<LEND>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brnm}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){br_}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brnm}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){br_0}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaust_order}<LSEP>[](symbol){b}<LEND>[argument 2; litteral](str){}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){b}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){exhaustion}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){total_steps}<LSEP>[](symbol){novel_states}<LSEP>[](symbol){novel_chars}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){branch_names}<LSEP>[](symbol){brnm}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){exhaustion}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){exhaustion}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){total_steps}<LSEP>[](symbol){novel_states}<LSEP>[](symbol){novel_chars}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){branch_names}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){branch_names}<LSEP>[](symbol){brnm}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exhaustion}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Steps}<LSEP>[argument 1; litteral](str){Novel_States}<LSEP>[argument 2; litteral](str){Novel_Characters}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){exhaustion}<LEND>[](symbol){branch_names}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){exhaust_output}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){exhaustion}<LSEP>[](symbol){exhaust_matrix}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){exhaust_output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Exhaustion}<LSEP>[argument 1; litteral](str){State_Derivations}<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){exhaust_output}<LEND>[assign](){<-}<LSEP>[](symbol){accioBestAcquisitionModel}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){changesType}<LSEP>[](symbol){models}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){changesType}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){totalAcc}<LSEP>[argument 1; litteral](str){charAlt}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){changesType must be one of eit...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){changesType}<LSEP>[argument 1; litteral](str){totalAcc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){changes}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){rowSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){State_Derivations}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){changesType}<LSEP>[argument 1; litteral](str){charAlt}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){changes}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){array}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){State_Derivations}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){array}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){State_Derivations}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){best_H}<LEND>[assign](){<-}<LSEP>[](symbol){best_uniform}<LEND>[call](){}<LSEP>[](symbol){optimize_uniform_abundance}<LSEP>[](symbol){changes}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){best_model}<LSEP>[litteral](str){uniform}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){best_dist}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_H}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_H}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){exponential}<LSEP>[](symbol){models}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_exponential}<LEND>[call](){}<LSEP>[](symbol){optimize_geometric_abundance}<LSEP>[](symbol){changes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_exponential}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_exponential}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_H}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_H}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_H}<LSEP>[](symbol){best_exponential}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){best_model}<LSEP>[litteral](str){exponential}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_dist}<LEND>[call](){}<LSEP>[](symbol){geometric_distribution}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_exponential}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){gamma}<LSEP>[](symbol){models}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_gamma1}<LEND>[call](){}<LSEP>[](symbol){optimize_gamma_one_abundance}<LSEP>[](symbol){changes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_gamma1}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_gamma1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_H}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_H}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_H}<LSEP>[](symbol){best_gamma1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){best_model}<LSEP>[litteral](str){gamma}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_dist}<LEND>[call](){}<LSEP>[](symbol){gamma_distribution}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_gamma1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_gamma1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_gamma1}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){lognormal}<LSEP>[](symbol){models}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_lognormal}<LEND>[call](){}<LSEP>[](symbol){optimize_lognormal_abundance}<LSEP>[](symbol){changes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_lognormal}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_lognormal}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_H}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_H}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_H}<LSEP>[](symbol){best_lognormal}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){best_model}<LSEP>[litteral](str){lognormal}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_dist}<LEND>[call](){}<LSEP>[](symbol){lognormal_distribution}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_lognormal}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_lognormal}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){zipf}<LSEP>[](symbol){models}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_zipf}<LEND>[call](){}<LSEP>[](symbol){optimize_zipf_abundance}<LSEP>[](symbol){changes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_zipf}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_zipf}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_H}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){best_H}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_H}<LSEP>[](symbol){best_zipf}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){best_model}<LSEP>[litteral](str){zipf}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_dist}<LEND>[call](){}<LSEP>[](symbol){zipf_distribution}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_zipf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){best_zipf}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){best_model}<LSEP>[](symbol){best_H}<LSEP>[](symbol){best_dist}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Best_Model}<LSEP>[argument 1; litteral](str){Best_Model_Parameters}<LSEP>[argument 2; litteral](str){Best_Distribution}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){output}<LEND>[assign](){<-}<LSEP>[](symbol){charExhaustPlot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){changesType}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[](symbol){main}<LSEP>[](symbol){xsize}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){abcissa}<LSEP>[](symbol){xlab}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){changesType}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){totalAcc}<LSEP>[argument 1; litteral](str){charAlt}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){changesType must be one of eit...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){exhaustion}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){Exhaustion}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nstep}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){Exhaustion}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){best_exhaustion}<LEND>[call](){}<LSEP>[](symbol){accioBestAcquisitionModel}<LSEP>[](symbol){exhaustion_info}<LSEP>[](symbol){changesType}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){exponential}<LSEP>[argument 1; litteral](str){gamma}<LSEP>[argument 2; litteral](str){lognormal}<LSEP>[argument 3; litteral](str){zipf}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ba}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){best_exhaustion}<LSEP>[](symbol){Best_Distribution}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){after3}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaustion}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){hba}<LEND>[call](){}<LSEP>[](symbol){expected_exhaustion_curve}<LSEP>[](symbol){ba}<LSEP>[](symbol){nstep}<LSEP>[](symbol){after3}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ba}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){mxx}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaustion}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){10.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mxx}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mxx}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){xsize}<LSEP>[](symbol){xsize}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){changesType}<LSEP>[argument 1; litteral](str){totalAcc}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ordinate}<LSEP>[litteral](str){Novel States}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ordinate}<LSEP>[](symbol){ylab}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){main}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main_title}<LSEP>[litteral](str){State Accumulation}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main_title}<LSEP>[](symbol){main}<LEND>[statement 2; call](){}<LSEP>[](symbol){plot}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](str){n}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[](symbol){main_title}<LSEP>[](symbol){abcissa}<LSEP>[](symbol){ordinate}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[statement 3; call](){}<LSEP>[](symbol){draw_symmetric_axes}<LSEP>[](symbol){mxx}<LSEP>[](symbol){xsize}<LEND>[statement 4; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nstep}<LEND>[](symbol){hba}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){points}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaustion}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaustion}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](real){21.000000}<LSEP>[argument 3; litteral](str){green}<LSEP>[argument 4; litteral](real){1.250000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){changesType}<LSEP>[argument 1; litteral](str){charAlt}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ordinate}<LSEP>[litteral](str){Altered Characters}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ordinate}<LSEP>[](symbol){ylab}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){main}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main_title}<LSEP>[litteral](str){Character Alterations}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main_title}<LSEP>[](symbol){main}<LEND>[statement 2; call](){}<LSEP>[](symbol){plot}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](str){n}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[](symbol){main_title}<LSEP>[](symbol){abcissa}<LSEP>[](symbol){ordinate}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[statement 3; call](){}<LSEP>[](symbol){draw_symmetric_axes}<LSEP>[](symbol){mxx}<LSEP>[](symbol){xsize}<LEND>[statement 4; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nstep}<LEND>[](symbol){hba}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){points}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaustion}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exhaustion}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){21.000000}<LSEP>[argument 3; litteral](str){skyblue}<LSEP>[argument 4; litteral](real){1.250000}<LEND>[assign](){<-}<LSEP>[](symbol){accio_minimum_steps_history}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mtree}<LSEP>[](symbol){charData}<LSEP>[](symbol){charTypes}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){inapplicableValue}<LSEP>[](symbol){outgroupID}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){otus}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){charData}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Nnodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){mtree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nchar}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){charData}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){steps}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nchar}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){c}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nchar}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cvector}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){charData}<LSEP>[](symbol){}<LSEP>[](symbol){c}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){charTypes}<LSEP>[](symbol){c}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){char_evolution}<LEND>[call](){}<LSEP>[](symbol){Sankoff_character}<LSEP>[](symbol){mtree}<LSEP>[](symbol){cvector}<LSEP>[](symbol){type}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){inapplicableValue}<LSEP>[](symbol){outgroupID}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){steps}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_evolution}<LSEP>[](symbol){Steps}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){full_matrix}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_evolution}<LSEP>[](symbol){States}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){changes_matrix}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_evolution}<LSEP>[](symbol){Derivation}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){full_matrix}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){full_matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_evolution}<LSEP>[](symbol){States}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){changes_matrix}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){changes_matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){char_evolution}<LSEP>[](symbol){Derivation}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){char_labels}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nchar}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){c}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nchar}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nchar}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_labels}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ch_}<LSEP>[](symbol){c}<LSEP>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nchar}<LSEP>[argument 1; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nchar}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_labels}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ch_0}<LSEP>[](symbol){c}<LSEP>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_labels}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ch_00}<LSEP>[](symbol){c}<LSEP>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nchar}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_labels}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ch_}<LSEP>[](symbol){c}<LSEP>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_labels}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ch_0}<LSEP>[](symbol){c}<LSEP>[argument 2; litteral](str){}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ttl_br}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[](symbol){Nnodes}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){nonzero}<LSEP>[litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){rbr}<LSEP>[litteral](real){1.000000}<LEND>[statement 10; control flow](){for}<LSEP>[](symbol){br}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ttl_br}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nonzero}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){changes_matrix}<LSEP>[](symbol){br}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nonzero}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dch}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nchar}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){changes_matrix}<LSEP>[](symbol){br}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dst}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){changes_matrix}<LSEP>[](symbol){br}<LEND>[argument 2; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){changes_matrix}<LSEP>[](symbol){br}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dbr}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){br}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dch}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rbr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){branch_changes}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){dbr}<LSEP>[](symbol){dch}<LSEP>[](symbol){dst}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){branch_changes}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){branch_changes}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){dbr}<LSEP>[](symbol){dch}<LSEP>[](symbol){dst}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rbr}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){rbr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){branch_changes}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){branch_changes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){full_matrix}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){changes_matrix}<LEND>[](symbol){char_labels}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){steps}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){full_matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[](symbol){Nnodes}<LEND>[](symbol){}<LEND>[](symbol){branch_changes}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Steps}<LSEP>[argument 1; litteral](str){Ancestral_Reconstructions}<LSEP>[argument 2; litteral](str){Changes}<LEND>[statement 15; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){output}<LEND>[assign](){<-}<LSEP>[](symbol){Sankoff_character}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mtree}<LSEP>[](symbol){cvector}<LSEP>[](symbol){type}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){inapplicableValue}<LSEP>[](symbol){outgroupID}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obs_states}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){cvector}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ttl_states}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){obs_states}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Nnodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){mtree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){otus}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cvector}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){scored}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){otus}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){sankoff_matrix}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[](symbol){Nnodes}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; assign](){=}<LSEP>[](symbol){length}<LSEP>[](symbol){ttl_states}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){otus}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){s}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){st}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){s}<LEND>[](symbol){obs_states}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){s}<LSEP>[](symbol){st}<LEND>[litteral](real){0.000000}<LEND>[false branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){s}<LSEP>[](symbol){}<LEND>[litteral](real){0.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){cvector}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){cvector}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){Nnodes}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){node_rich}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){Nnodes}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){Nnodes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){missing}<LEND>[assign](){<-}<LSEP>[](symbol){gap}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rich}<LSEP>[](symbol){n}<LEND>[assign](){<-}<LSEP>[](symbol){f1}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[](symbol){otus}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[litteral](real){0.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LSEP>[](symbol){s}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){sp}<LEND>[](symbol){inapplicableValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){sp}<LEND>[](symbol){missingCharValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n_s}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_states}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){a_s}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_states}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){no_step}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){n_s}<LSEP>[](symbol){obs_states}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){add_step}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){a_s}<LSEP>[](symbol){obs_states}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){no_step}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){no_step}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){no_step}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){obs_states}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){add_step}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){add_step}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){sp}<LEND>[](symbol){inapplicableValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gap}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){gap}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){sp}<LEND>[](symbol){missingCharValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){missing}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){missing}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){missing}<LSEP>[](symbol){f1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){missingCharValue}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){scored}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){scored}<LSEP>[](symbol){ht}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gap}<LSEP>[](symbol){f1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){inapplicableValue}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){scored}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){scored}<LSEP>[](symbol){ht}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ast}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_states}<LSEP>[](symbol){ast}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){scored}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){scored}<LSEP>[](symbol){ht}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){ravel_polymorph}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_states}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){ht}<LSEP>[](symbol){}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){ch_steps}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){base}<LSEP>[](symbol){}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){base}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){base}<LEND>[](symbol){missingCharValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){base}<LEND>[](symbol){inapplicableValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){poss_starts}<LEND>[call](){}<LSEP>[](symbol){unravel_polymorph}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){base}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){outgroupID}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){outgroupID}<LEND>[](symbol){poss_starts}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){outgroupID}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){grab}<LEND>[call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){poss_starts}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poss_starts}<LSEP>[](symbol){grab}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){changes_above}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){Nnodes}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Nnodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[](symbol){otus}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){inapplicableValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){missingCharValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rich}<LSEP>[](symbol){n}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f1}<LEND>[](symbol){scored}<LEND>[](symbol){f1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anc_st}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){unscored}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f1}<LEND>[](symbol){scored}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){u}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){unscored}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){unscored}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unscored}<LSEP>[](symbol){u}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f2}<LSEP>[](symbol){unscored}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){anc_st}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){anc_st}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_states}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){f2}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LSEP>[](symbol){f2}<LSEP>[](symbol){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[](symbol){anc_st}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){anc_st}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){anc_st}<LSEP>[](symbol){missingCharValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){anc_st}<LSEP>[](symbol){inapplicableValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anc_poss}<LEND>[call](){}<LSEP>[](symbol){unravel_polymorph}<LSEP>[](symbol){anc_st}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){f2_poss}<LEND>[call](){}<LSEP>[](symbol){unravel_polymorph}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){reduced_poss}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f2_poss}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){f2_poss}<LSEP>[](symbol){anc_poss}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){reduced_poss}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[](symbol){reduced_poss}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){reduced_poss}<LEND>[argument 1; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){reduced_poss}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f2_poss}<LEND>[call](){}<LSEP>[](symbol){unravel_polymorph}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f2_poss}<LEND>[argument 1; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){f2_poss}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){changes_above}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sankoff_matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[](symbol){otus}<LEND>[](symbol){}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){cchanges}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cvector}<LEND>[statement 16; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Nnodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[](symbol){n}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){missingCharValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){inapplicableValue}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rich}<LSEP>[](symbol){n}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){f}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mtree}<LSEP>[](symbol){n}<LSEP>[](symbol){f}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[true branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[](symbol){missingCharValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[](symbol){inapplicableValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){missingCharValue}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[](symbol){inapplicableValue}<LEND>[true branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){ht}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cchanges}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cvector}<LSEP>[](symbol){f2}<LEND>[](symbol){obs_states}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ch_steps}<LSEP>[](symbol){cvector}<LSEP>[](symbol){cchanges}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Steps}<LSEP>[argument 1; litteral](str){States}<LSEP>[argument 2; litteral](str){Derivation}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){output}<LEND>[assign](){<-}<LSEP>[](symbol){accio_data_from_nexus_file}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nexus_file_name}<LSEP>[](symbol){polymorphs}<LSEP>[](symbol){missingCharValue}<LSEP>[](symbol){inapplicableValue}<LSEP>[](symbol){label_char_cols}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexus}<LEND>[call](){}<LSEP>[](symbol){scan}<LSEP>[](symbol){nexus_file_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){character}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){gp_scr}<LSEP>[litteral](str){-}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){unkn_scr}<LSEP>[litteral](str){?}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){BEGIN DATA;}<LSEP>[](symbol){nexus}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){BEGIN DATA;}<LSEP>[](symbol){nexus}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ln}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](str){ = }<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){notu}<LSEP>[litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){ }<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){notu}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){notu}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nchars}<LSEP>[litteral](real){0.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 8; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){;}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nchars}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){nchars}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ln}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 11; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){F}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](str){O}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){9.000000}<LEND>[argument 1; litteral](str){S}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[argument 1; litteral](str){Y}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ln}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](str){ = }<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){gp_scr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){unkn_scr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ln}<LEND>[assign](){<-}<LSEP>[](symbol){taxa_line}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){BEGIN TAXA;}<LSEP>[](symbol){nexus}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){found}<LSEP>[litteral](logical){FALSE}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){found}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ln}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){found}<LEND>[call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](str){I}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){M}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){notu}<LSEP>[litteral](real){0.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){ = }<LSEP>[](symbol){txt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; assign](){<-}<LSEP>[](symbol){notu}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){notu}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ln}<LEND>[assign](){<-}<LSEP>[](symbol){taxa_line}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){BEGIN CHARACTERS;}<LSEP>[](symbol){nexus}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){found}<LSEP>[litteral](logical){FALSE}<LEND>[statement 7; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){found}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ln}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){found}<LEND>[call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](str){I}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){M}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){nchars}<LSEP>[litteral](real){0.000000}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){ = }<LSEP>[](symbol){txt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; assign](){<-}<LSEP>[](symbol){nchars}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){nchars}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){found}<LSEP>[litteral](logical){FALSE}<LEND>[statement 11; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){found}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ln}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){found}<LEND>[call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){F}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](str){O}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){R}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){txt}<LSEP>[argument 1; litteral](str){ = }<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){gap_scr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){unkn_scr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){nexus_alt}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){\t}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){nexus}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){matrix_starts}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){MATRIX}<LSEP>[](symbol){nexus_alt}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ms}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){matrix_starts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_alt}<LSEP>[](symbol){ms}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){[}<LEND>[body; assign](){<-}<LSEP>[](symbol){ms}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ms}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){notu}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){chmatrix}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){notu}<LSEP>[](symbol){nchars}<LEND>[statement 10; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){notu}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ms}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){matrix_starts}<LSEP>[](symbol){n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){ms}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){\t}<LEND>[body; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){j}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){name}<LSEP>[litteral](str){}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){'}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){2.000000}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){'}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){\t}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){n}<LEND>[](symbol){name}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){\t}<LEND>[body; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){ch}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nchars}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[](symbol){unkn_scr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[](symbol){missingCharValue}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[](symbol){gap_scr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[](symbol){inapplicableValue}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){(}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){{}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){[}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LSEP>[litteral](real){0.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){)}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){}}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){]}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){,}<LEND>[body; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){9.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){convert_letter_state_to_numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){9.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){convert_letter_state_to_numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){n}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){nstates}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nchars}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){ch}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nchars}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){states}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){}<LSEP>[](symbol){ch}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){states}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){states}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){states}<LSEP>[](symbol){missingCharValue}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){states}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){states}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){states}<LSEP>[](symbol){inapplicableValue}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){states}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){polys}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){states}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){states}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){p}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){polys}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){states}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){states}<LEND>[argument 1; call](){}<LSEP>[](symbol){unravel_polymorph}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){polys}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){states}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){states}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){states}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nstates}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){states}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){outgroup}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){BEGIN SETS;}<LSEP>[](symbol){nexus}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tx_pt}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){BEGIN SETS;}<LSEP>[](symbol){nexus}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){splitNexusTxPt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){tx_pt}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){outgroup}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitNexusTxPt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){\t}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitNexusTxPt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitNexusTxPt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](str){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitNexusTxPt}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){X}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitNexusTxPt}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](str){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitNexusTxPt}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 1; litteral](str){A}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){tx_pt}<LEND>[argument 1; litteral](str){ }<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){Outgroup}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){otg}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){Outgroup}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){otg}<LEND>[argument 1; litteral](str){:}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){otg}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){otg}<LEND>[argument 1; litteral](str){}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){otg}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otg}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){j}<LSEP>[](symbol){otg}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){a}<LSEP>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){outgroup}<LSEP>[litteral](real){0.000000}<LEND>[statement 5; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LSEP>[](symbol){a}<LEND>[argument 1; litteral](str){,}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LSEP>[](symbol){a}<LEND>[argument 1; litteral](str){;}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outgroup}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){outgroup}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LSEP>[](symbol){a}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tx_pt}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){tx_pt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){splitNexusTxPt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus}<LSEP>[](symbol){tx_pt}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){CHARSTATELABELS }<LSEP>[](symbol){nexus_alt}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){char_names}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nchars}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){state_names}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](str){}<LSEP>[](symbol){nchars}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){nstates}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ln}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){CHARSTATELABELS }<LSEP>[](symbol){nexus_alt}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_alt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){ ; }<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_alt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){char_info}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_alt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ln}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){, }<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){ch}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nchars}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){txt}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_info}<LSEP>[](symbol){ch}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){ }<LEND>[body; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){'}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](str){'}<LEND>[body; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_names}<LSEP>[](symbol){ch}<LEND>[litteral](str){}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_names}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_names}<LSEP>[](symbol){ch}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){k}<LEND>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[body; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_names}<LSEP>[](symbol){ch}<LEND>[litteral](str){}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](str){ }<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){h}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){h}<LSEP>[](symbol){j}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){i}<LSEP>[](symbol){h}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_names}<LSEP>[](symbol){ch}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){char_names}<LSEP>[](symbol){ch}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){k}<LEND>[argument 2; litteral](str){}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](str){/}<LEND>[body; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){statenames}<LSEP>[litteral](str){}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){txt}<LEND>[body; assign](){<-}<LSEP>[](symbol){statenames}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){statenames}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){txt}<LSEP>[](symbol){k}<LEND>[argument 2; litteral](str){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sn}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){statenames}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){state_names}<LSEP>[](symbol){ch}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sn}<LEND>[](symbol){sn}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){char_names}<LEND>[assign](){<-}<LSEP>[](symbol){state_names}<LSEP>[litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){chmatrix}<LEND>[](symbol){taxa}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){char_names}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){label_char_cols}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){chmatrix}<LEND>[](symbol){char_names}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){char_names}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){outgroup}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxa}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){nstates}<LSEP>[](symbol){char_names}<LSEP>[](symbol){state_names}<LSEP>[](symbol){outgroup}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){OTUs}<LSEP>[argument 1; litteral](str){Matrix}<LSEP>[argument 2; litteral](str){States}<LSEP>[argument 3; litteral](str){Characters_Labels}<LSEP>[argument 4; litteral](str){States_Labels}<LSEP>[argument 5; litteral](str){Outgroup}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){char_names}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxa}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){nstates}<LSEP>[](symbol){char_names}<LSEP>[](symbol){state_names}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){OTUs}<LSEP>[argument 1; litteral](str){Matrix}<LSEP>[argument 2; litteral](str){States}<LSEP>[argument 3; litteral](str){Characters_Labels}<LSEP>[argument 4; litteral](str){States_Labels}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){outgroup}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxa}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){nstates}<LSEP>[](symbol){outgroup}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){OTUs}<LSEP>[argument 1; litteral](str){Matrix}<LSEP>[argument 2; litteral](str){States}<LSEP>[argument 3; litteral](str){Outgroup}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxa}<LSEP>[](symbol){chmatrix}<LSEP>[](symbol){nstates}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){OTUs}<LSEP>[argument 1; litteral](str){Matrix}<LSEP>[argument 2; litteral](str){States}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){output}<LEND>[assign](){<-}<LSEP>[](symbol){convert_letter_state_to_numeric}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){letterstate}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){A}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){10.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){B}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){11.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){C}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){12.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){D}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){13.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){E}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){14.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){F}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){15.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){G}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){16.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){H}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){17.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){J}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){18.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){K}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){19.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){L}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){20.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){M}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){21.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){N}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){22.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){P}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){23.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){Q}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){24.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){R}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){25.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){S}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){26.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){T}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){27.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){U}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){28.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){V}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){29.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){W}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){30.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){X}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){31.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){Y}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){32.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){letterstate}<LSEP>[argument 1; litteral](str){Z}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){state}<LSEP>[litteral](real){33.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){state}<LEND>[assign](){<-}<LSEP>[](symbol){unravel_polymorph}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){poly}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){poly}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){poly}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){combo}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){poly}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sts}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){combo}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){polymorphics}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){sts}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){sts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){sts}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){polymorphics}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){combo}<LEND>[](symbol){base}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){combo}<LEND>[call](){}<LSEP>[](symbol){%%}<LSEP>[](symbol){combo}<LSEP>[](symbol){base}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){polymorphics}<LEND>[assign](){<-}<LSEP>[](symbol){read_nexus_tree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nexustreefile}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexustree}<LEND>[call](){}<LSEP>[](symbol){scan}<LSEP>[](symbol){nexustreefile}<LEND>[argument 1; call](){}<LSEP>[](symbol){character}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nexus_string}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){nexustree}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nodes}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nexus_string}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){(}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nodes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){clades}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nodes}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){c}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nodes}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clades}<LSEP>[](symbol){c}<LEND>[](symbol){c}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){notu}<LEND>[assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){0.000000}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nexus_string}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){0}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){9}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){otu}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){otu}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){otu}<LSEP>[](symbol){notu}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){notu}<LSEP>[](symbol){otu}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[assign](){<-}<LSEP>[](symbol){otu}<LSEP>[litteral](real){0.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){vector_tree}<LEND>[call](){}<LSEP>[](symbol){vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){notu}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){clades}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){c}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nodes}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clades}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){cl}<LEND>[assign](){<-}<LSEP>[](symbol){c}<LSEP>[litteral](real){0.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){1.000000}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nexus_string}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){(}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sp}<LEND>[assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){cl}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){cl}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){notu}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clades}<LSEP>[](symbol){c}<LEND>[](symbol){notu}<LEND>[false branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){notu}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clades}<LSEP>[](symbol){c}<LEND>[](symbol){cl}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){)}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sp}<LEND>[assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){0.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){,}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sp}<LEND>[assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){0.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){0}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){9}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sp}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){0}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexus_string}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){9}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){notu}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clades}<LSEP>[](symbol){c}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){vector_tree}<LEND>[assign](){<-}<LSEP>[](symbol){accio_matrix_tree_from_vector_tree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){vector_tree}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){node_rosetta}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){vector_tree}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Nnodes}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node_rosetta}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){maxtomy}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){Nnodes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node_rosetta}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rosetta}<LSEP>[](symbol){n}<LEND>[](symbol){maxtomy}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){maxtomy}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rosetta}<LSEP>[](symbol){n}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){node_rich}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){Nnodes}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){matrix_tree}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){Nnodes}<LSEP>[](symbol){maxtomy}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vector_tree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rosetta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){node}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LSEP>[](symbol){i}<LEND>[](symbol){node_rosetta}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rich}<LSEP>[](symbol){node}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rich}<LSEP>[](symbol){node}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix_tree}<LSEP>[](symbol){node}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_rich}<LSEP>[](symbol){node}<LEND>[](symbol){i}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){matrix_tree}<LEND>[assign](){<-}<LSEP>[](symbol){ravel_polymorph}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){polies}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){polies}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){polies}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){poly}<LSEP>[litteral](real){0.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){polies}<LEND>[body; assign](){<-}<LSEP>[](symbol){poly}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){poly}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){polies}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){poly}<LEND>[assign](){<-}<LSEP>[](symbol){accio_branch_order_with_stratigraphy}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mtree}<LSEP>[](symbol){firstAppearances}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){branch_order}<LEND>[call](){}<LSEP>[](symbol){accio_patristic_distance_from_base}<LSEP>[](symbol){mtree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){used_order}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){branch_order}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){branch_order}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){strat_order}<LEND>[call](){}<LSEP>[](symbol){date_taxa_on_tree_simple}<LSEP>[](symbol){mtree}<LSEP>[](symbol){firstAppearances}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tosort}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){strat_order}<LSEP>[](symbol){used_order}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tosort}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tosort}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){accio_patristic_distance_from_base}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){atree}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttus}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){atree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pat_dist_from_base}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){ttus}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.array}<LSEP>[](symbol){atree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){atree}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Nnodes}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){atree}<LEND>[](symbol){base}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LSEP>[](symbol){base}<LEND>[litteral](real){0.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){ttus}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){n}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){s}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Nnodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){atree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){otus}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ttus}<LSEP>[](symbol){Nnodes}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){otus}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LSEP>[](symbol){base}<LEND>[litteral](real){0.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){t}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Nnodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f1}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){t}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){t}<LSEP>[](symbol){otus}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){f}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){t}<LSEP>[](symbol){f}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pat_dist_from_base}<LSEP>[](symbol){ht}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){pat_dist_from_base}<LEND>[assign](){<-}<LSEP>[](symbol){date_taxa_on_tree_simple}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){atree}<LSEP>[](symbol){firstAppearances}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttus}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){atree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dates}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){ttus}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){notu}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){firstAppearances}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.array}<LSEP>[](symbol){atree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){notu}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){end}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){firstAppearances}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){nd}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){base}<LSEP>[](symbol){ttus}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){nd}<LEND>[](symbol){end}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){sp}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){notu}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){sp}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){firstAppearances}<LSEP>[](symbol){sp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){anc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){sp}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){sp}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){anc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){sp}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){nd}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){ttus}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){nd}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){nd}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){nd}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){anc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){nd}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Nnodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){atree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){notu}<LEND>[](symbol){firstAppearances}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){Nnodes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f1}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){n}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[](symbol){notu}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){ht}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){atree}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f1}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){dates}<LEND>[assign](){<-}<LSEP>[](symbol){modified_AIC}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lnL}<LSEP>[](symbol){k}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[](symbol){k}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[](symbol){k}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[](symbol){k}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){inf}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){aic_c}<LEND>[call](){}<LSEP>[](symbol){AIC}<LSEP>[](symbol){lnL}<LSEP>[](symbol){k}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){aic_c}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[](symbol){lnL}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[](symbol){k}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){aic_c}<LEND>[assign](){<-}<LSEP>[](symbol){fisher_plot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){finds}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){finds}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){finds}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[](symbol){counts}<LEND>[assign](){<-}<LSEP>[](symbol){create_quantile_vector}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){N}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){expected_abundances}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){S}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){expected}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){nspec}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){t}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){S}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nspec}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){expected}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){expected}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){dbinom}<LSEP>[](symbol){i}<LSEP>[](symbol){nspec}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){t}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){expected}<LEND>[assign](){<-}<LSEP>[](symbol){expected_sampling_curve}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){S}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){exp_find}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nspec}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){exp_find}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){exp_find}<LEND>[argument 1; call](){}<LSEP>[](symbol){expected_sampled_richness}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){i}<LSEP>[](symbol){S}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){exp_find}<LEND>[assign](){<-}<LSEP>[](symbol){expected_exhaustion_curve}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nstep}<LSEP>[](symbol){after3}<LSEP>[](symbol){C}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){expected_sampling_curve}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nstep}<LSEP>[](symbol){C}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){xx}<LSEP>[](symbol){after3}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xfinds}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LSEP>[](symbol){d}<LEND>[statement 3; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){xfinds}<LSEP>[](symbol){after3}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d}<LSEP>[argument 1; litteral](real){0.010000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xfinds}<LEND>[call](){}<LSEP>[](symbol){expected_sampled_richness}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){d}<LSEP>[](symbol){C}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){d}<LSEP>[](symbol){after3}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){exp_states}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){after3}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){after3}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nstep}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){exp_states}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){exp_states}<LEND>[argument 1; call](){}<LSEP>[](symbol){expected_sampled_richness}<LSEP>[](symbol){rel_ab_dist}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[](symbol){dd}<LEND>[](symbol){C}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){exp_states}<LEND>[assign](){<-}<LSEP>[](symbol){expected_sampled_richness}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){S}<LSEP>[](symbol){MINNO}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){exp_find}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){t}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){S}<LEND>[body; assign](){<-}<LSEP>[](symbol){exp_find}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){exp_find}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){t}<LEND>[](symbol){nspec}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){exp_find}<LEND>[assign](){<-}<LSEP>[](symbol){distribution_loglikelihood_mul}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){observed}<LSEP>[](symbol){expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LSEP>[](symbol){MINNO}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mxfind}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){prop_expected}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){expected}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){mxfind}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){expected}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){prop_expected}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){prop_expected}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){MINNO}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lnlo}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){observed}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){prop_expected}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lnlo}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){lnlo}<LEND>[litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){sobs}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){lnlo}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){eS}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){expected}<LEND>[statement 7; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){eS}<LSEP>[](symbol){hS}<LEND>[body; assign](){<-}<LSEP>[](symbol){eS}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.999990}<LSEP>[](symbol){eS}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){hS}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){eS}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){hS}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lnls}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){lfactorial}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){lfactorial}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){hS}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){lfactorial}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){eS}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){hS}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){hS}<LSEP>[](symbol){eS}<LEND>[](symbol){hS}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lnls}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){MINNO}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){sobs}<LSEP>[](symbol){lnls}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_uniform_abundance}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LSEP>[](symbol){MAXNO}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){minS}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){oS}<LEND>[assign](){<-}<LSEP>[](symbol){hS}<LSEP>[](symbol){minS}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){observed}<LEND>[call](){}<LSEP>[](symbol){fisher_plot}<LSEP>[](symbol){counts}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mxlnl}<LEND>[assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){MAXNO}<LEND>[statement 5; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lnl}<LSEP>[](symbol){mxlnl}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rel_ab_dist}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){hS}<LEND>[](symbol){hS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){raw_expected}<LEND>[call](){}<LSEP>[](symbol){expected_abundances}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){distribution_loglikelihood_mul}<LSEP>[](symbol){observed}<LSEP>[](symbol){raw_expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){mxlnl}<LSEP>[](symbol){lnl}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){mxlnl}<LSEP>[](symbol){lnl}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){hS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){hS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){hS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){mxlnl}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){modified_AIC}<LSEP>[](symbol){mxlnl}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){nspec}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Uniform_S}<LSEP>[argument 1; litteral](str){Uniform_log-likelihood}<LSEP>[argument 2; litteral](str){Uniform_AICc}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){geometric_distribution}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){decay}<LSEP>[](symbol){MINEXPN}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){decay}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){decay}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){decay}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){S}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){MINEXPN}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){decay}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){decay}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ranks}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){S}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){prop}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){decay}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){decay}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ranks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){prop}<LEND>[assign](){<-}<LSEP>[](symbol){loglikelihood_geometric_rad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){decay}<LSEP>[](symbol){nspec}<LSEP>[](symbol){oS}<LSEP>[](symbol){observed}<LSEP>[](symbol){MINNO}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rel_ab_dist}<LEND>[call](){}<LSEP>[](symbol){geometric_distribution}<LSEP>[](symbol){decay}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hS}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rel_ab_dist}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){hS}<LSEP>[](symbol){oS}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){raw_expected}<LEND>[call](){}<LSEP>[](symbol){expected_abundances}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){distribution_loglikelihood_mul}<LSEP>[](symbol){observed}<LSEP>[](symbol){raw_expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){oS}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){MINNO}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){lnl}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_geometric_abundance}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){observed}<LEND>[call](){}<LSEP>[](symbol){fisher_plot}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){decay}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){counts}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){counts}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){max_decay}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){decay}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){min_decay}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){decay}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){counts}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){decay}<LSEP>[](symbol){loglikelihood_geometric_rad}<LSEP>[argument 2; litteral](str){L-BFGS-B}<LSEP>[](symbol){nspec}<LSEP>[](symbol){oS}<LSEP>[](symbol){observed}<LSEP>[](symbol){min_decay}<LSEP>[](symbol){max_decay}<LSEP>[](symbol){cl}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){par}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){value}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){modified_AIC}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){value}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){nspec}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Geometric_decay}<LSEP>[argument 1; litteral](str){Geometric_log-likelihood}<LSEP>[argument 2; litteral](str){Geometric_AICc}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){lognormal_distribution}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mag}<LSEP>[](symbol){S}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fi}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){S}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){S}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){prop}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){mag}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LSEP>[](symbol){fi}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){mag}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LSEP>[](symbol){fi}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){prop}<LEND>[assign](){<-}<LSEP>[](symbol){jack5_Fisher}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){observed}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntaxa}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){observed}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ss}<LSEP>[litteral](real){0.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[body; assign](){<-}<LSEP>[](symbol){ss}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){observed}<LSEP>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){S}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ntaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[](symbol){ss}<LEND>[argument 1; litteral](real){15.000000}<LEND>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){ss}<LSEP>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){70.000000}<LSEP>[](symbol){ss}<LEND>[argument 1; litteral](real){125.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){120.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){485.000000}<LSEP>[](symbol){ss}<LEND>[argument 1; litteral](real){660.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){ss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ss}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){S}<LEND>[assign](){<-}<LSEP>[](symbol){accio_min_and_max_lognormal_mag_given_hS}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LSEP>[](symbol){hS}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){observed}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mxfinds}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mnfinds}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){mxfinds}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rank_shifts}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){hS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){oS}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){local_m}<LEND>[assign](){<-}<LSEP>[](symbol){mag_shifts}<LEND>[call](){}<LSEP>[](symbol){vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){oS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){oS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mag_shifts}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){counts}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){counts}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){local_m}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mag_shifts}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank_shifts}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank_shifts}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){observed}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){min_mag}<LEND>[call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){local_m}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){min_mag}<LSEP>[litteral](real){1.010000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){max_mag}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){prod}<LSEP>[](symbol){local_m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){local_m}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){max_mag}<LSEP>[](symbol){min_mag}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LSEP>[](symbol){min_mag}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){min_mag}<LSEP>[](symbol){max_mag}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){max_mag}<LSEP>[](symbol){m}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){min_mag}<LSEP>[](symbol){max_mag}<LEND>[assign](){<-}<LSEP>[](symbol){loglikelihood_lognormal_rad_for_optim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){rand_no}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){min_mag}<LSEP>[](symbol){max_mag}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mag}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){min_mag}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){rand_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){max_mag}<LSEP>[](symbol){min_mag}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rel_ab_dist}<LEND>[call](){}<LSEP>[](symbol){lognormal_distribution}<LSEP>[](symbol){mag}<LSEP>[](symbol){hS}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){raw_expected}<LEND>[call](){}<LSEP>[](symbol){expected_abundances}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){distribution_loglikelihood_mul}<LSEP>[](symbol){observed}<LSEP>[](symbol){raw_expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){lnl}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){loglikelihood_lognormal_rad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){mag}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rad}<LEND>[call](){}<LSEP>[](symbol){lognormal_distribution}<LSEP>[](symbol){mag}<LSEP>[](symbol){hS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){raw_expected}<LEND>[call](){}<LSEP>[](symbol){expected_abundances}<LSEP>[](symbol){rad}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){distribution_loglikelihood_mul}<LSEP>[](symbol){observed}<LSEP>[](symbol){raw_expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){lnl}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_lognormal_abundance_given_hS}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LSEP>[](symbol){hS}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){observed}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[](symbol){observed}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mxfinds}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mnfinds}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){mxfinds}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mm}<LEND>[call](){}<LSEP>[](symbol){accio_min_and_max_lognormal_mag_given_hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LSEP>[](symbol){hS}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){mag}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){prod}<LSEP>[](symbol){mm}<LEND>[argument 1; litteral](real){0.500000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){rand_no}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mag}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){rand_no}<LSEP>[](symbol){loglikelihood_lognormal_rad_for_optim}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](str){L-BFGS-B}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 9; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[](symbol){cl}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){par}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mm}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){par}<LEND>[](symbol){hS}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){value}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Lognormal_magnitude}<LSEP>[argument 1; litteral](str){Lognormal_S}<LSEP>[argument 2; litteral](str){Lognormal_log-likelihood}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_lognormal_abundance}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){observed}<LEND>[call](){}<LSEP>[](symbol){fisher_plot}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){counts}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){span}<LSEP>[litteral](real){5.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){oS}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){enS}<LSEP>[](symbol){span}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){0.000000}<LEND>[statement 8; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hS}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){stS}<LSEP>[](symbol){enS}<LSEP>[](symbol){incr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){hS}<LSEP>[](symbol){optimize_lognormal_abundance_given_hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mlnl}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mlSc}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mlS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[](symbol){}<LSEP>[](symbol){mlSc}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){spn}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mlSc}<LSEP>[](symbol){spn}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){peak}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){oS}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hS2}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mlS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){results2}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){hS2}<LSEP>[](symbol){optimize_lognormal_abundance_given_hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[](symbol){span}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){modified_AIC}<LSEP>[](symbol){mlnl}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){nspec}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){Lognormal_AICc}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){zipf_distribution}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){zm}<LSEP>[](symbol){S}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){S}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){zm}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){S}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){zm}<LEND>[assign](){<-}<LSEP>[](symbol){loglikelihood_zipf_rad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){zm}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rel_ab_dist}<LEND>[call](){}<LSEP>[](symbol){zipf_distribution}<LSEP>[](symbol){zm}<LSEP>[](symbol){hS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){raw_expected}<LEND>[call](){}<LSEP>[](symbol){expected_abundances}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){distribution_loglikelihood_mul}<LSEP>[](symbol){observed}<LSEP>[](symbol){raw_expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){lnl}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_zipf_abundance_given_hS}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LSEP>[](symbol){observed}<LSEP>[](symbol){max_zipf}<LSEP>[](symbol){hS}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){observed}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[](symbol){observed}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mxfinds}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mnfinds}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){mxfinds}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){observed}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){inzm}<LEND>[assign](){<-}<LSEP>[](symbol){zm}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){mxfinds}<LSEP>[](symbol){mnfinds}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){oS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){zm}<LSEP>[](symbol){loglikelihood_zipf_rad}<LSEP>[argument 2; litteral](str){L-BFGS-B}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LSEP>[argument 7; litteral](real){0.000000}<LSEP>[](symbol){max_zipf}<LSEP>[](symbol){cl}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){par}<LEND>[](symbol){hS}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){value}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Zipf_log-log_decay}<LSEP>[argument 1; litteral](str){Zipf_hypothesized_richness}<LSEP>[argument 2; litteral](str){Zipf_log-likelihood}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){accio_max_zipf_decay}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){oS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){yy}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){counts}<LSEP>[](symbol){nspec}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nspec}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){zz}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){yy}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){xx}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){zz}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_zipf_abundance}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LSEP>[](symbol){span}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){observed}<LEND>[call](){}<LSEP>[](symbol){fisher_plot}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){oS}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){enS}<LSEP>[](symbol){span}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){0.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){counts}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){max_zipf}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){accio_max_zipf_decay}<LSEP>[](symbol){counts}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){pa}<LSEP>[litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){pz}<LSEP>[](symbol){span}<LEND>[statement 10; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hS}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){stS}<LSEP>[](symbol){enS}<LSEP>[](symbol){incr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){pa}<LSEP>[](symbol){pz}<LEND>[](symbol){optimize_zipf_abundance_given_hS}<LSEP>[](symbol){counts}<LSEP>[](symbol){observed}<LSEP>[](symbol){max_zipf}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pa}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){bH}<LSEP>[](symbol){results}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){pz}<LSEP>[](symbol){span}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){results}<LSEP>[](symbol){bH}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mlnl}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mlSc}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){mlS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[](symbol){}<LSEP>[](symbol){mlSc}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){spn}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mlSc}<LSEP>[](symbol){spn}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){peak}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pa}<LSEP>[litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pz}<LSEP>[](symbol){span}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){oS}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){pa}<LSEP>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){pz}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){pa}<LSEP>[litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){pz}<LSEP>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hS2}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mlS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){results2}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){hS2}<LSEP>[](symbol){optimize_zipf_abundance_given_hS}<LSEP>[](symbol){counts}<LSEP>[](symbol){observed}<LSEP>[](symbol){max_zipf}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS2}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){enS}<LEND>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){pa}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){pz}<LSEP>[](symbol){span}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS2}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[](symbol){span}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){enS}<LEND>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){pa}<LSEP>[litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){pz}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){modified_AIC}<LSEP>[](symbol){mlnl}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){nspec}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){Lognormal_AICc}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){gamma_distribution}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LSEP>[](symbol){S}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p0}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){S}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p0}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){S}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){S}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){S}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p0}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){S}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){prop}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){qgamma}<LSEP>[](symbol){p0}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){qgamma}<LSEP>[](symbol){p0}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){prop}<LEND>[assign](){<-}<LSEP>[](symbol){accio_minimum_alpha_for_gamma_one}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){hS}<LSEP>[](symbol){MINNO}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){min_alpha}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){iS}<LSEP>[](symbol){hS}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){iS}<LSEP>[](symbol){hS}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rel_ab_dist}<LEND>[call](){}<LSEP>[](symbol){gamma_distribution}<LSEP>[](symbol){min_alpha}<LSEP>[](symbol){min_alpha}<LSEP>[](symbol){hS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){iS}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){MINNO}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){iS}<LSEP>[](symbol){hS}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){min_alpha}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){min_alpha}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){min_alpha}<LEND>[assign](){<-}<LSEP>[](symbol){loglikelihood_gamma_one_rad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){alpha}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){MINNO}<LSEP>[](symbol){MAXNO}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rel_ab_dist}<LEND>[call](){}<LSEP>[](symbol){gamma_distribution}<LSEP>[](symbol){alpha}<LSEP>[](symbol){alpha}<LSEP>[](symbol){hS}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){MINNO}<LEND>[](symbol){hS}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){raw_expected}<LEND>[call](){}<LSEP>[](symbol){expected_abundances}<LSEP>[](symbol){rel_ab_dist}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){distribution_loglikelihood_mul}<LSEP>[](symbol){observed}<LSEP>[](symbol){raw_expected}<LSEP>[](symbol){oS}<LSEP>[](symbol){hS}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){lnl}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){MAXNO}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){lnl}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_gamma_one_abundance_given_hS}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LSEP>[](symbol){hS}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){observed}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){observed}<LEND>[](symbol){observed}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){alpha}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){min_alpha}<LEND>[call](){}<LSEP>[](symbol){accio_minimum_alpha_for_gamma_one}<LSEP>[](symbol){hS}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){alpha}<LSEP>[](symbol){loglikelihood_gamma_one_rad}<LSEP>[argument 2; litteral](str){L-BFGS-B}<LSEP>[](symbol){oS}<LSEP>[](symbol){nspec}<LSEP>[](symbol){hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){min_alpha}<LSEP>[argument 8; litteral](real){10000.000000}<LSEP>[](symbol){cl}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){par}<LEND>[](symbol){hS}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){w}<LSEP>[](symbol){value}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Gamma_alpha = beta}<LSEP>[argument 1; litteral](str){Gamma_S}<LSEP>[argument 2; litteral](str){Gamma_log-likelihood}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){optimize_gamma_one_abundance}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){counts}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[assign](){<-}<LSEP>[](symbol){oS}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){observed}<LEND>[call](){}<LSEP>[](symbol){fisher_plot}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nspec}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){counts}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){span}<LSEP>[litteral](real){5.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){oS}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){enS}<LSEP>[](symbol){span}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){0.000000}<LEND>[statement 8; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hS}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){stS}<LSEP>[](symbol){enS}<LSEP>[](symbol){incr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){hS}<LSEP>[](symbol){optimize_gamma_one_abundance_given_hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mlnl}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mlSc}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mlS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[](symbol){}<LSEP>[](symbol){mlSc}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){spn}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mlSc}<LSEP>[](symbol){spn}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){peak}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stS}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){oS}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){spn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){spn}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){incr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){peak}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hS2}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mlS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){results2}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){hS2}<LSEP>[](symbol){optimize_lognormal_abundance_given_hS}<LSEP>[](symbol){observed}<LSEP>[](symbol){counts}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){span}<LSEP>[](symbol){incr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){mlnl}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){results2}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stS}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LSEP>[](symbol){mlSc}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){enS}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hS}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mlSc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){incr}<LSEP>[](symbol){span}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[](symbol){span}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){enS}<LSEP>[](symbol){stS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){incr}<LSEP>[litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){bH}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bH}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){modified_AIC}<LSEP>[](symbol){mlnl}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){nspec}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){bH}<LEND>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){Gamma_AICc}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bH}<LEND>[assign](){<-}<LSEP>[](symbol){draw_symmetric_axes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mxx}<LSEP>[](symbol){xsize}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brks}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){5.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[argument 6; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){prn}<LSEP>[litteral](logical){TRUE}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){prn}<LSEP>[litteral](logical){FALSE}<LEND>[statement 9; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[](symbol){prn}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[argument 6; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[](symbol){prn}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 13; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){200.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brks}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){20.000000}<LSEP>[argument 1; litteral](real){10.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[argument 6; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 8; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 11; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){mxx}<LSEP>[argument 1; litteral](real){500.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brks}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){50.000000}<LSEP>[argument 1; litteral](real){25.000000}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[argument 6; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 8; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 11; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brks}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){100.000000}<LSEP>[argument 1; litteral](real){50.000000}<LSEP>[argument 2; litteral](real){10.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){1.100000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[argument 6; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.300000}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xsize}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 8; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.200000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tcs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){mxx}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brks}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LEND>[statement 11; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tcs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.100000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.100000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){accio_matrix_tree_from_ape_tree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ape}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ape}<LSEP>[](symbol){edge}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){notu}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){yyy}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ape}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ape}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){yyy}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){notu}<LEND>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ape}<LSEP>[](symbol){tip.label}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){zzz}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){yyy}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){yyy}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){vector_tree}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zzz}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zzz}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){vector_tree}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vector_tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){base}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vector_tree}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){mtree}<LEND>[call](){}<LSEP>[](symbol){accio_matrix_tree_from_vector_tree}<LSEP>[](symbol){vector_tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){seqTimeList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LSEP>[](symbol){nruns}<LSEP>[](symbol){weightSampling}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lap}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){lap}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Your timeList doesn't have any...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){noLap}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){nInts}<LEND>[assign](){<-}<LSEP>[](symbol){nTaxa}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){savedLists}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nruns}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nruns}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){valid}<LSEP>[](symbol){noLap}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){invalid}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){valid}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){candidate}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){valid}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){candidate}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){candidate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){weightSampling}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){weights}<LEND>[call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){candidate}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){weights}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){weights}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){weights}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){draw}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){candidate}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){weights}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){draw}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){candidate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){valid}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){valid}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){candidate}<LSEP>[](symbol){draw}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){drawInt}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){candidate}<LSEP>[](symbol){draw}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){candidate}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){candidate}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){draw}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){candInt}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){candidate}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){badInt}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){candInt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drawInt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drawInt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){invalid}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){invalid}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){candidate}<LSEP>[](symbol){badInt}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){candidate}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){candidate}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){badInt}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){candidate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){valid}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){valid}<LSEP>[](symbol){candidate}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){valid}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){valid}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){newInts}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){valid}<LSEP>[](symbol){}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){newInts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newInts}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newInts}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){WHAT!}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){validTaxa}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){valid}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){valid}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){cropTaxa}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){validTaxa}<LSEP>[](symbol){}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){newTaxa}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cropTaxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){valid}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cropTaxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){valid}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nInts}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newInts}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nTaxa}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newTaxa}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){savedLists}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){newInts}<LSEP>[](symbol){newTaxa}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){nInts}<LSEP>[](symbol){nTaxa}<LSEP>[](symbol){savedLists}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){optimPaleo}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){modelFun}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){modelFun}<LSEP>[argument 1; litteral](str){paleotreeFunc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Given function does not appear...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){optim}<LEND>[argument 0; call](){}<LSEP>[](symbol){parInit}<LSEP>[](symbol){modelFun}<LEND>[](symbol){modelFun}<LEND>[argument 2; call](){}<LSEP>[](symbol){parLower}<LSEP>[](symbol){modelFun}<LEND>[argument 3; call](){}<LSEP>[](symbol){parUpper}<LSEP>[](symbol){modelFun}<LEND>[argument 4; litteral](str){L-BFGS-B}<LEND>[argument 5; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){1000000.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){pairwiseSpearmanRho}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){dropAbsent}<LSEP>[](symbol){asDistance}<LSEP>[](symbol){diag}<LSEP>[](symbol){upper}<LSEP>[](symbol){na.rm}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x must be a matrix, with sampl...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dropPar}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){bothAbsent}<LSEP>[argument 1; litteral](str){eitherAbsent}<LSEP>[argument 2; litteral](str){noDrop}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dropAbsent}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dropPar}<LEND>[argument 1; call](){}<LSEP>[](symbol){pmatch}<LSEP>[](symbol){dropAbsent}<LSEP>[](symbol){dropPar}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){asDistance}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){diag}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){diag}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){upper}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){upper}<LSEP>[litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){diag}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){diag}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){upper}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){upper}<LSEP>[litteral](logical){TRUE}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){dropAbsent}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){dropAbsent must be one of }<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){dropPar}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){rhos}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){na.rm}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[](symbol){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhos}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhos}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){na.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LSEP>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dropAbsent}<LSEP>[argument 1; litteral](str){bothAbsent}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){selector}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dropAbsent}<LSEP>[argument 1; litteral](str){eitherAbsent}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){selector}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){selector}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhos}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhos}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){samp1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){selector}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){samp2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LSEP>[](symbol){selector}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rho}<LEND>[call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){cor.test}<LSEP>[](symbol){samp1}<LSEP>[](symbol){samp2}<LSEP>[argument 2; litteral](str){spearman}<LEND>[](symbol){estimate}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhos}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhos}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[](symbol){rho}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){rhos}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){rhos}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){asDistance}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rhos}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){rhos}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){rhos}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){result}<LSEP>[argument 1; litteral](str){Diag}<LEND>[](symbol){diag}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){result}<LSEP>[argument 1; litteral](str){Upper}<LEND>[](symbol){upper}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[](symbol){rhos}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){HurlbertPIE}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){nAnalyze}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nAnalyze}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){nAnalyze}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nAnalyze}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nAnalyze must be a numeric vec...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){nAnalyze}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.integer}<LSEP>[](symbol){nAnalyze}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nAnalyze2}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){nAnalyze}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){nAnalyze2}<LSEP>[](symbol){nAnalyze}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nAnalyze must be a whole number}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nAnalyze}<LSEP>[](symbol){nAnalyze2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){PIE}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){samp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){nAnalyze}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){samp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){samp}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){rank}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){samp}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nAnalyze}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){samp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){samp}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){samp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){diversity}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){samp}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){diversity}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){propAbund}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){samp}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){samp}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PIE}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){diversity}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){diversity}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){propAbund}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PIE}<LSEP>[](symbol){i}<LEND>[litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){PIE}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){x}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){PIE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getCladeTaxaPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxon}<LSEP>[](symbol){showTaxa}<LSEP>[](symbol){status}<LSEP>[](symbol){urlOnly}<LSEP>[](symbol){stopIfMissing}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxon}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Input 'taxon' should only be a...}<LSEP>[argument 1; litteral](str){ A single name of a higher t...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){requestURLPBDB}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/}<LSEP>[argument 1; litteral](str){data1.2/taxa/list.txt?base_name=}<LSEP>[](symbol){taxon}<LSEP>[argument 3; litteral](str){&show=}<LEND>[argument 4; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){showTaxa}<LSEP>[argument 1; litteral](str){,}<LEND>[argument 5; litteral](str){&taxon_status=}<LSEP>[](symbol){status}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){urlOnly}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){requestURLPBDB}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){getPBDBtaxaCSV}<LSEP>[](symbol){requestURLPBDB}<LSEP>[](symbol){stopIfMissing}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){getSpecificTaxaPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){showTaxa}<LSEP>[](symbol){status}<LSEP>[](symbol){urlOnly}<LSEP>[](symbol){stopIfMissing}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){taxa}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){duplicates}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){taxa}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){duplicates}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){duplicates}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 2; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Duplicated taxa found in input...}<LSEP>[](symbol){duplicates}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){taxa}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaMerged}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](str){,}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaMerged}<LSEP>[](symbol){taxa}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){requestURLPBDB}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data1.2/...}<LSEP>[](symbol){taxaMerged}<LSEP>[argument 2; litteral](str){&show=}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){showTaxa}<LSEP>[argument 1; litteral](str){,}<LEND>[argument 4; litteral](str){&taxon_status=}<LSEP>[](symbol){status}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){urlOnly}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){requestURLPBDB}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){getPBDBtaxaCSV}<LSEP>[](symbol){requestURLPBDB}<LSEP>[](symbol){stopIfMissing}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Fewer taxon records returned (}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){res}<LEND>[argument 2; litteral](str){) than the number of unique ta...}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[argument 4; litteral](str){).\n}<LSEP>[argument 5; litteral](str){ This may reflect missing tax...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){stopIfMissing}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Terminated as stopIfMissing = ...}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){getPBDBtaxaCSV}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){requestURL}<LSEP>[](symbol){stopIfMissing}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){linesOut}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[](symbol){requestURL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){linesOut}<LSEP>[argument 1; litteral](str){"THIS REQUEST RETURNED NO REC...}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){For this query, the PBDB API r...}<LSEP>[argument 1; litteral](str){"THIS REQUEST RETURNED NO REC...}<LSEP>[argument 2; litteral](str){\n Presumably this means a tax...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){linesOut}<LSEP>[argument 1; litteral](str){"Records:"}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){isWarning}<LEND>[call](){}<LSEP>[](symbol){startsWith}<LSEP>[](symbol){linesOut}<LSEP>[argument 1; litteral](str){"Warning:",}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){isWarning}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){errorMsg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linesOut}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){errorMsg}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){"Warning:","}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){errorMsg}<LEND>[statement 2; call](){}<LSEP>[](symbol){warning}<LSEP>[](symbol){errorMsg}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){stopIfMissing}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Some taxa not found in PBDB ta...}<LSEP>[argument 1; litteral](str){ see warnings and check API re...}<LSEP>[](symbol){requestURL}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lineRemove}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){isWarning}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){linesOut}<LSEP>[argument 1; litteral](str){"Records:"}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){linesOut}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linesOut}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){lineRemove}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){linesOut}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){getPBDBocc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){showOccs}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](str){,}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){taxa}<LSEP>[argument 1; litteral](str){_}<LEND>[argument 1; litteral](str){%20}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){showOccs}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){showOccs}<LSEP>[argument 1; litteral](str){,}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){command}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data1.2/...}<LSEP>[](symbol){taxa}<LSEP>[argument 2; litteral](str){&show=}<LSEP>[](symbol){showOccs}<LSEP>[argument 4; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){command}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){command}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 1; litteral](str){%20}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){downData}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[](symbol){command}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){grep}<LSEP>[argument 0; litteral](str){Warning}<LSEP>[](symbol){downData}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){start}<LEND>[call](){}<LSEP>[](symbol){grep}<LSEP>[argument 0; litteral](str){Records}<LSEP>[](symbol){downData}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){warn}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){downData}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){start}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){warn}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){warn}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){"}<LEND>[argument 1; litteral](str){,}<LEND>[argument 1; litteral](str){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){warn}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){warn}<LSEP>[argument 1; litteral](str){\n}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){warn}<LEND>[litteral](NULL){NULL}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){downData}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){start}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LEND>[argument 0; call](){}<LSEP>[](symbol){textConnection}<LSEP>[](symbol){mat}<LEND>[statement 7; call](){}<LSEP>[](symbol){message}<LSEP>[](symbol){warn}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mat}<LSEP>[](symbol){downData}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LEND>[argument 0; call](){}<LSEP>[](symbol){textConnection}<LSEP>[](symbol){mat}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){mat}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){isTimeListSequential}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LSEP>[](symbol){threshold}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){testTimeList}<LSEP>[](symbol){timeList}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList isn't a TimeList}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){intTimes}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){intTimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){threshold}<LEND>[argument 1; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intTimes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){testTimeList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){timeList}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList isn't a list}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){timeList}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList isn't of length 2}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not in intervals...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not in intervals...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList <0 ?}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some of these interval numbers...}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](logical){TRUE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){branchClasses}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){whichExtant}<LSEP>[](symbol){tol}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dists}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){whichExtant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dists1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dists}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){modern}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dists1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){modern}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){modern.tips}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){dists1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modern}<LSEP>[](symbol){tol}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dead.tips}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){dists1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modern}<LSEP>[](symbol){tol}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichExtant}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Length of whichExtant is not e...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modern.tips}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichExtant}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dead.tips}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichExtant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){int.edges}<LEND>[call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){live.edges}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){modern.tips}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dead.edges}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){dead.tips}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){depths}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dists}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dists}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){depths}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dists}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){brlen.all}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){brlen.all}<LEND>[](symbol){depths}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){brlen.int}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){int.edges}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){brlen.int}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){depths}<LSEP>[](symbol){int.edges}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){brlen.live}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){live.edges}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){brlen.live}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){depths}<LSEP>[](symbol){live.edges}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){brlen.dead}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){dead.edges}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){brlen.dead}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){depths}<LSEP>[](symbol){dead.edges}<LEND>[statement 15; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){brlen.all}<LSEP>[](symbol){brlen.int}<LSEP>[](symbol){brlen.live}<LSEP>[](symbol){brlen.dead}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){nearestNeighborDist}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){distMat}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){distMat}<LSEP>[argument 1; litteral](str){dist}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){distMat}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){distMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Diagonal is nonzero and not NA...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){isSymmetric}<LSEP>[](symbol){distMat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not a Symmetric Distance Matrix?}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){distMat}<LSEP>[](symbol){distMat}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not a matrix, not a 'dist' obj...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){distMat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){distMat}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){NND}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){distMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distMat}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){NND}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){labels}<LSEP>[](symbol){distMat}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){NND}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){depthRainbow}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree isn't of class phylo}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ndepth}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){edepth}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ndepth}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){col_edge}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){edepth}<LEND>[](symbol){edepth}<LEND>[statement 5; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){col_edge}<LEND>[statement 6; call](){}<LSEP>[](symbol){axisPhylo}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){parentChild2taxonTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tipSet}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){tipSet}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipSet must be a single charac...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){parentChild isn't of class cha...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parentChild}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){parentChild}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.character}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){parentChild}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parentChild must be a matrix o...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){parentChild}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){parentChild}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parentChild must be a matrix o...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){testParentChild}<LSEP>[](symbol){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parentChild relationships are ...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){continue}<LSEP>[litteral](logical){TRUE}<LEND>[statement 5; control flow](){while}<LSEP>[](symbol){continue}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){unqIDs}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ultimateAnc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqIDs}<LSEP>[](symbol){getUltimateAnc}<LSEP>[](symbol){parentChild}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){ultimateAnc}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ultAnc1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ultimateAnc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parentChild constructed improp...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){descEdge}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){ultAnc1}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){descEdge}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Removing singular node leading...}<LSEP>[](symbol){ultAnc1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parentChild}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){descEdge}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){parentChild}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No branching nodes found?!}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){continue}<LSEP>[litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nodeNames}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){whichRoot}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nodeNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){identical}<LEND>[argument 2; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichRoot}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Not all taxable are traceable ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichRoot}<LEND>[argument 2; litteral](str){possible roots found:}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeNames}<LSEP>[](symbol){whichRoot}<LEND>[argument 1; litteral](str){, }<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nodeNames}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeNames}<LSEP>[](symbol){whichRoot}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){whichRoot}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){tipSet}<LSEP>[argument 1; litteral](str){nonParents}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tipSet}<LSEP>[argument 1; litteral](str){all}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parentChild}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){parentChild}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){nodeNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){(}<LSEP>[](symbol){nodeNames}<LSEP>[argument 2; litteral](str){)}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipSet must be one of either '...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){notParents}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){identical}<LEND>[argument 2; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){x}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){tipNames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){notParents}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){parentChild}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){parentChild}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){taxonNames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){tipNames}<LSEP>[](symbol){nodeNames}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){nUniquePC}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxonNames}<LEND>[](symbol){nUniquePC}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of tip and node names d...}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxonNames}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxonNames}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){testParentChild}<LSEP>[](symbol){edge}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){created edge relationships are...}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){edge}<LSEP>[](symbol){tipNames}<LSEP>[argument 2; litteral](NULL){NULL}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nodeNames}<LEND>[](symbol){nodeNames}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){phylo}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){tree}<LEND>[statement 23; control flow](){if}<LSEP>[](symbol){cleanTree}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){cleanNewPhylo}<LSEP>[](symbol){tree}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tipNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Taxa number changed while clea...}<LEND>[statement 25; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}<LEND>[assign](){<-}<LSEP>[](symbol){getUltimateAnc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){parentChild}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){count}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){identical}<LEND>[argument 2; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some parents are listed as chi...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){count}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parentChild}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Breaking while() loop: cannot ...}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxa}<LEND>[assign](){<-}<LSEP>[](symbol){charEdge2numeric}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){parentChild}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parentChild has to be characte...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){unqIDs}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){parentChild2}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){parentChild}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqIDs}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqIDs}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){parentChild2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parentChild not coercing corre...}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){parentChild2}<LEND>[assign](){<-}<LSEP>[](symbol){testParentChild}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){parentChild}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){edge/parentChild matrix must b...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){parentChild}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){edge/parentChild matrix must h...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){parentChild}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parentChild}<LEND>[call](){}<LSEP>[](symbol){charEdge2numeric}<LSEP>[](symbol){parentChild}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){input must be of type numeric ...}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){parentChild}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){parentChild}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){parentMatch}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){parentMatch}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){More than one apparent root; \n}<LSEP>[argument 1; litteral](str){more than one parent without t...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){parentANDchild}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){parentChild}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){x}<LEND>[statement 1; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){parentANDchild}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some pairs with same ID listed...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){unqIDs}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){ultimateAnc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqIDs}<LSEP>[](symbol){getUltimateAnc}<LSEP>[](symbol){parentChild}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){ultimateAnc}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){IDs trace back to more than on...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Some IDs are listed as a desce...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](str){, }<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){parentMatch}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentChild}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){parentMatch}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){More than one apparent root; \n}<LSEP>[argument 1; litteral](str){more than ancestor without an ...}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](logical){TRUE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){timeSliceFossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){sliceTime}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[](symbol){modern.samp.prob}<LSEP>[](symbol){tolerance}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){checkResult}<LEND>[call](){}<LSEP>[](symbol){checkFossilRecord}<LSEP>[](symbol){fossilRecord}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){sliceTime}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sliceTime}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){sliceTime must be a single num...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){sliceTime}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){sliceTime cannot be a negative...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){shiftPar}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](str){withExtantOnly}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){shiftRoot4TimeSlice}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){shiftPar}<LEND>[argument 1; call](){}<LSEP>[](symbol){pmatch}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[](symbol){shiftPar}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){shiftRoot4TimeSlice}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){shiftRoot4TimeSlice must be a ...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){sliceTime}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){droppers}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fossilRecord}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){All taxa appear to originate *...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){fossilRecord}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fossilRecord}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){droppers}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){sliceTime}<LSEP>[](symbol){tolerance}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){isAlive}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[](symbol){sliceTime}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){sliceTime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LEND>[](symbol){tolerance}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](logical){FALSE}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[argument 1; litteral](str){withExtantOnly}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){isAlive}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shiftRoot4TimeSlice}<LSEP>[litteral](logical){FALSE}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){shiftRoot4TimeSlice}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){isAlive}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){sliceTime}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newStartEndTime_extinct}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){sliceTime}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){newStartEndTime_extinct}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){withinTolerance}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){newStartEndTime_extinct}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){newStartEndTime_extinct}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tolerance}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newStartEndTime_extinct}<LSEP>[](symbol){withinTolerance}<LEND>[litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){newStartEndTime_extinct}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Extinct taxon dates being shif...}<LSEP>[argument 1; litteral](str){ rescale modern time to zero,...}<LSEP>[argument 2; litteral](str){ - Old FAD & LAD are: }<LEND>[argument 3; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){ }<LEND>[argument 4; litteral](str){\n}<LSEP>[argument 5; litteral](str){ - sliceTime is: }<LSEP>[](symbol){sliceTime}<LSEP>[argument 7; litteral](str){\n}<LSEP>[argument 8; litteral](str){ - Newly assigned FAD & LAD are: }<LEND>[argument 9; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){newStartEndTime_extinct}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){newStartEndTime_extinct}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newSamplingTimes_all}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){sliceTime}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){newSamplingTimes_all}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){newSamplingTimes_all}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Sampling times for taxa are be...}<LSEP>[argument 1; litteral](str){ rescale modern time to zer...}<LSEP>[argument 2; litteral](str){ - Old sampling dates are: }<LEND>[argument 3; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){ }<LEND>[argument 4; litteral](str){\n}<LSEP>[argument 5; litteral](str){ - sliceTime is: }<LSEP>[](symbol){sliceTime}<LSEP>[argument 7; litteral](str){\n}<LSEP>[argument 8; litteral](str){ - Newly assigned sampling dat...}<LEND>[argument 9; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){newSamplingTimes_all}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){newSamplingTimes_all}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modernTime}<LSEP>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){isAlive}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){sliceTime}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modernTime}<LSEP>[](symbol){sliceTime}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){whichExtant}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){nLive}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichExtant}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){liveSampled}<LEND>[call](){}<LSEP>[](symbol){as.logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbinom}<LSEP>[](symbol){nLive}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){modern.samp.prob}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){whichSampled}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichExtant}<LSEP>[](symbol){liveSampled}<LEND>[statement 17; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){whichSampled}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){modernTime}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){fossilRecord}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){fossilRecordSimulation}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){fossilRecord}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){fossilRecord}<LEND>[assign](){<-}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){checkResult}<LEND>[call](){}<LSEP>[](symbol){checkFossilRecord}<LSEP>[](symbol){fossilRecord}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){checkNegDates}<LEND>[call](){}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LSEP>[](symbol){fossilRecord}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaConvert}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxaConvert}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fossilRecord}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxaConvert}<LEND>[assign](){<-}<LSEP>[](symbol){fossilTaxa2fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilTaxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fossilRecord}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){fossilTaxa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){numeric}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fossilRecord}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fossilTaxa}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){fossilRecord}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){fossilRecordSimulation}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){fossilRecord}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){checkResult}<LEND>[call](){}<LSEP>[](symbol){checkFossilRecord}<LSEP>[](symbol){fossilRecord}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){checkNegDates}<LEND>[call](){}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LSEP>[](symbol){fossilRecord}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){fossilRecord}<LEND>[assign](){<-}<LSEP>[](symbol){fossilRecord2fossilRanges}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){merge.cryptic}<LSEP>[](symbol){ranges.only}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){checkResult}<LEND>[call](){}<LSEP>[](symbol){checkFossilRecord}<LSEP>[](symbol){fossilRecord}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){checkNegDates}<LEND>[call](){}<LSEP>[](symbol){checkRecordForNoDatePastZero}<LSEP>[](symbol){fossilRecord}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sampData}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sampOcc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sampOcc}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fossilRecord}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){merge.cryptic}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxonIDs}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cryptIDs}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonIDs}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cryptIDs}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonIDs}<LSEP>[](symbol){i}<LEND>[](symbol){cryptIDs}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){sampling data for taxa is not ...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){ranges.only}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ranges}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){max}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){min}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){ranges}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sampOcc}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){ranges}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){FAD}<LSEP>[argument 1; litteral](str){LAD}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){result}<LSEP>[](symbol){ranges}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[](symbol){sampOcc}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){checkFossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fossilRecord}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){fossilRecord}<LSEP>[argument 1; litteral](str){fossilRecordSimulation}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fossilRecord object is not of ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fossilRecord}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fossilRecord object is empty?!}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fossilRecord object has taxon ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fossilRecord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fossilRecord object has taxon ...}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](logical){TRUE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){make_durationFreqCont}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeData}<LSEP>[](symbol){groups}<LSEP>[](symbol){drop.extant}<LSEP>[](symbol){threshold}<LSEP>[](symbol){tol}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){timeData}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData not of matrix or data...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){naDroppers}<LEND>[call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){naDroppers}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){naDroppers}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){naDroppers}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){number of rows in groups isn't...}<LEND>[argument 1; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){after taxa listed with NA in t...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){modernTest}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){timeData}<LSEP>[](symbol){tol}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){modernTest}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){modDroppers}<LEND>[call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){tol}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modDroppers}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){drop.extant}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){modernTest}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modDroppers}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){number of rows in groups isn't...}<LEND>[argument 1; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){after modern taxa are dropped}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData is not in time relati...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeData <0 ?}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){dur}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dur}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){dur}<LSEP>[](symbol){threshold}<LEND>[litteral](real){0.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){parnames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){q}<LSEP>[argument 1; litteral](str){r}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups2}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dur}<LEND>[argument 2; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups2}<LSEP>[](symbol){groups}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of rows in groups isn't...}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){groups2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parnames}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parnames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups2}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){.}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){groups2}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){ngroup}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groupings}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){breakNames}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parnames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){lowerBound}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.001000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){upperBound}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){parbounds}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){lowerBound}<LSEP>[](symbol){upperBound}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){logL}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){par}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of input parameters is ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){logLsum}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngroup}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){breakNames}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parnew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LSEP>[](symbol){selector}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){breaknew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){selector}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){r}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dur1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dur}<LSEP>[](symbol){selector}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ft}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dur1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LSEP>[](symbol){q}<LEND>[argument 2; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dur1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LSEP>[](symbol){q}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){logLsum}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ft}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){logLsum}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){res}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){logL}<LEND>[call](){}<LSEP>[](symbol){make_paleotreeFunc}<LSEP>[](symbol){logL}<LSEP>[](symbol){parnames}<LSEP>[](symbol){parbounds}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){logL}<LEND>[assign](){<-}<LSEP>[](symbol){make_durationFreqDisc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LSEP>[](symbol){groups}<LSEP>[](symbol){drop.extant}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LSEP>[](symbol){timeList}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){timeData}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeList}<LSEP>[](symbol){timeData}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modernTest}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){modernTest}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){modernTest}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one modern interval ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modInt}<LEND>[call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){modernTest}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newInt}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){newInt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one interval stretch...}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){modDroppers}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){modInt}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modDroppers}<LEND>[](symbol){}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){drop.extant}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){modernTest}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){modDroppers}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){number of rows in groups isn't...}<LEND>[argument 1; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){after modern taxa are dropped}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sapply}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){modInt}<LEND>[true branch; block](){}<LSEP>[](symbol){newInt}<LEND>[false branch; block](){}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){naDroppers}<LEND>[call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){naDroppers}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){naDroppers}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){naDroppers}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){number of rows in groups isn't...}<LEND>[argument 1; control flow](){if}<LSEP>[](symbol){drop.extant}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){after taxa listed with NA in t...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData / timeList[[2]] not i...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList <0 ?}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some of these interval numbers...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){dur}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){parnames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){q}<LSEP>[argument 1; litteral](str){R}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groups}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups2}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dur}<LEND>[argument 2; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groups2}<LSEP>[](symbol){groups}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groups2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of rows in groups isn't...}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){groups2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parnames}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parnames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groups2}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){.}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){groups2}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){ngroup}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){groupings}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){breakNames}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){parnames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){lowerBound}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.001000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){upperBound}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upperBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){R}<LEND>[litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){parbounds}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){lowerBound}<LSEP>[](symbol){upperBound}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){logL}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){par}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of input parameters is ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){logLsum}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngroup}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selector}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){breakNames}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parnew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LSEP>[](symbol){selector}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){breaknew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){selector}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){q}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){R}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parnew}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaknew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){R}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dur1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dur}<LSEP>[](symbol){selector}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){TMax}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dur1}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){Ti}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){TMax}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){Ti}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){t}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[](symbol){dur1}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){PDT}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){Rex}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){TMax}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){ft}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){Ti}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){t}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PDT}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){t}<LSEP>[](symbol){TMax}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){R}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Rex}<LSEP>[](symbol){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Ti}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){t}<LSEP>[](symbol){TMax}<LEND>[](symbol){t}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){R}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Ti}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){t}<LSEP>[](symbol){TMax}<LEND>[](symbol){t}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ft}<LEND>[call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){ft}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ft}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){logLsum}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){N}<LSEP>[](symbol){ft}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){ft}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){logLsum}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){res}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){logL}<LEND>[call](){}<LSEP>[](symbol){make_paleotreeFunc}<LSEP>[](symbol){logL}<LSEP>[](symbol){parnames}<LSEP>[](symbol){parbounds}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){logL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){obtainDatedPosteriorTreesMrB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){runFile}<LSEP>[](symbol){nRuns}<LSEP>[](symbol){burnin}<LSEP>[](symbol){outputTrees}<LSEP>[](symbol){labelPostProb}<LSEP>[](symbol){getFixedTimes}<LSEP>[](symbol){getRootAges}<LSEP>[](symbol){originalNexusFile}<LSEP>[](symbol){file}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){outputTrees}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){outputTrees must be of length 1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){outputTrees}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){all}<LSEP>[argument 1; litteral](str){MCCT}<LSEP>[argument 2; litteral](str){MAPosteriori}<LSEP>[argument 3; litteral](str){MAPriori}<LSEP>[argument 4; litteral](str){MaxLikelihood}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){outputTrees}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){outputTrees must be one of 'al...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){outputTrees}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If numeric, outputTrees must b...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){burnin}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){burnin}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){burnin must be a value between...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){getRootAges}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){getFixedTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Root ages cannot be set for ou...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){getRootAges}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){file}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Root ages cannot be set when f...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){runPath}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){runFile}<LSEP>[argument 1; litteral](str){\\.run}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){runPath}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unable to parse the runPath co...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){runPath}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){runPath}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){treeFiles}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nRuns}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){read.nexus}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){runPath}<LSEP>[argument 1; litteral](str){.run}<LSEP>[](symbol){x}<LSEP>[argument 3; litteral](str){.t}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){parFiles}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nRuns}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){read.table}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){runPath}<LSEP>[argument 1; litteral](str){.run}<LSEP>[](symbol){x}<LSEP>[argument 3; litteral](str){.p}<LEND>[](symbol){T}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 11; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nRuns}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){treeFiles}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parFiles}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Parameter data and tree data n...}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){getFixedTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){originalNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){endNex}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){\\.nex$}<LSEP>[](symbol){runPath}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){endNex}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){originalNexusFile}<LSEP>[](symbol){runPath}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){originalNexusFile}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){runPath}<LSEP>[argument 1; litteral](str){.nex}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){fixedTable}<LEND>[call](){}<LSEP>[](symbol){getMrBFixedAgesFromNexus}<LSEP>[](symbol){originalNexusFile}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){fixedTable}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){getRootAges}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No fixed ages found for obtain...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fixedTable}<LSEP>[litteral](NULL){NULL}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){sampleStart}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){treeFiles}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){burnin}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){treeFilesBurn}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){treeFiles}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){startSamp}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[](symbol){burnin}<LEND>[statement 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){startSamp}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){parFilesBurn}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){parFiles}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){startSamp}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[](symbol){burnin}<LEND>[statement 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){startSamp}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[](symbol){}<LEND>[statement 16; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nRuns}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){treeFilesBurn}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parFilesBurn}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Parameter data and tree data n...}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){rescaleMrBTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){phy}<LSEP>[](symbol){rate}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){phy}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){phy}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rate}<LSEP>[](symbol){clockrate}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){phy}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){rescaledTrees}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nRuns}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){treeFilesBurn}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rescaleMrBTree}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){treeFilesBurn}<LSEP>[](symbol){x}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parFilesBurn}<LSEP>[](symbol){x}<LEND>[](symbol){y}<LSEP>[](symbol){}<LEND>[statement 19; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nRuns}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rescaledTrees}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rescaledTrees}<LSEP>[](symbol){i}<LEND>[](symbol){j}<LEND>[](symbol){LnPr}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parFilesBurn}<LSEP>[](symbol){i}<LEND>[](symbol){j}<LSEP>[](symbol){}<LEND>[](symbol){LnPr}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rescaledTrees}<LSEP>[](symbol){i}<LEND>[](symbol){j}<LEND>[](symbol){LnL}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parFilesBurn}<LSEP>[](symbol){i}<LEND>[](symbol){j}<LSEP>[](symbol){}<LEND>[](symbol){LnL}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){lumpTrees}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){rescaledTrees}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){lumpTrees}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){multiPhylo}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){lumpTrees}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](str){all}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LSEP>[](symbol){lumpTrees}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){outTree}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){lumpTrees}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](str){MAPriori}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){LnPr}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){lumpTrees}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){LnPr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichMaxPrior}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){LnPr}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){LnPr}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichMaxPrior}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Multiple trees found with iden...}<LSEP>[argument 1; litteral](str){May suggest overly flat priors...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichMaxPrior}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichMaxPrior}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lumpTrees}<LSEP>[](symbol){whichMaxPrior}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){outTree}<LSEP>[](symbol){lumpTrees}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](str){MaxLikelihood}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){LnL}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){lumpTrees}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){LnL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichMaxLikelihood}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){LnL}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){LnL}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichMaxLikelihood}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Multiple trees found with iden...}<LSEP>[argument 1; litteral](str){May suggest overly flat likeli...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichMaxLikelihood}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichMaxLikelihood}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){LnL}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){All log likelihood values are ...}<LSEP>[argument 1; litteral](str){Posterior probability is thus ...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lumpTrees}<LSEP>[](symbol){whichMaxLikelihood}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){outTree}<LSEP>[](symbol){lumpTrees}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](str){MAPosteriori}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){LnL}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){lumpTrees}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){LnL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){LnPr}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){lumpTrees}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){LnPr}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){LnPost}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){LnPr}<LSEP>[](symbol){LnL}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){whichMaxPosterior}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){LnPost}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){LnPost}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichMaxPosterior}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Multiple trees found with iden...}<LSEP>[argument 1; litteral](str){May suggest overly flat priors...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichMaxPosterior}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichMaxPosterior}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){LnL}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){All log likelihood values are ...}<LSEP>[argument 1; litteral](str){Posterior probability is thus ...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lumpTrees}<LSEP>[](symbol){whichMaxPosterior}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){outTree}<LSEP>[](symbol){lumpTrees}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](str){MCCT}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){phangorn}<LSEP>[](symbol){maxCladeCred}<LEND>[](symbol){lumpTrees}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){outTree}<LSEP>[](symbol){lumpTrees}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){outputTrees}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){outputTrees}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lumpTrees}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Numeric value for outputTrees (}<LSEP>[](symbol){outputTrees}<LSEP>[argument 2; litteral](str){) greater than the total numbe...}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lumpTrees}<LEND>[argument 4; litteral](str){)}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichOutput}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lumpTrees}<LEND>[](symbol){outputTrees}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lumpTrees}<LSEP>[](symbol){whichOutput}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){labelPostProb}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){outputTrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){outTree}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){lumpTrees}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){getPosteriorProbabiities}<LSEP>[](symbol){outTree}<LSEP>[](symbol){lumpTrees}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){file}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){write.nexus}<LSEP>[](symbol){outTree}<LSEP>[](symbol){file}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){fixedTable}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){You may need to know which tip...}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){in order to assign absolute da...}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){fixedTable}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){fixedTable}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){outTree}<LSEP>[argument 1; litteral](str){fixedTable}<LEND>[](symbol){fixedTable}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){outTree}<LSEP>[argument 1; litteral](str){multiPhylo}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){setRootAges}<LSEP>[](symbol){outTree}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outTree}<LEND>[call](){}<LSEP>[](symbol){setRootAge}<LSEP>[](symbol){outTree}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){outTree}<LEND>[assign](){<-}<LSEP>[](symbol){getPosteriorProbabiities}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){postBurninTrees}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cladeFreq}<LEND>[call](){}<LSEP>[](symbol){prop.clades}<LSEP>[](symbol){tree}<LSEP>[](symbol){postBurninTrees}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){postProbs}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){cladeFreq}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){postBurninTrees}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){node.label}<LEND>[](symbol){postProbs}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){taxonSortPBDBocc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){rank}<LSEP>[](symbol){onlyFormal}<LSEP>[](symbol){cleanUncertain}<LSEP>[](symbol){cleanResoValues}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){translatePBDBocc}<LSEP>[](symbol){data}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){primary_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){genus}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){need to add 'show = c('phylo',...}<LSEP>[argument 1; litteral](str){ pbdb_occurrences query\n *or*...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rank}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of rank must be 1}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){species}<LSEP>[argument 1; litteral](str){genus}<LSEP>[argument 2; litteral](str){family}<LSEP>[argument 3; litteral](str){order}<LSEP>[argument 4; litteral](str){class}<LSEP>[argument 5; litteral](str){phylum}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){rank}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){rank must be one of 'species',...}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){}<LEND>[litteral](logical){NA}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LSEP>[argument 1; litteral](str){species}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){cleanUncertain}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){species_reso}<LEND>[](symbol){cleanResoValues}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichFormal}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){accepted_rank}<LEND>[](symbol){rank}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxonVar}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){accepted_name}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaNames}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonVar}<LSEP>[](symbol){whichFormal}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){taxaNames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaNames}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){sortedOcc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxonVar}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sortedOcc}<LEND>[](symbol){taxaNames}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){onlyFormal}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxonVar2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){primary_name}<LSEP>[argument 1; litteral](str){species_name}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxonVar2}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){taxonVar2}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){paste}<LSEP>[argument 3; litteral](str){ }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){stillUseful}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){whichFormal}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){identified_rank}<LEND>[](symbol){rank}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaNames2}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonVar2}<LSEP>[](symbol){stillUseful}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){taxaNames2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames2}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){taxaNames2}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaNames2}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){sortedOcc2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaNames2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxonVar2}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sortedOcc2}<LEND>[](symbol){taxaNames2}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){share1}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaNames2}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){share2}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaNames2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaNames}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOccU}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sortedOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOccU}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share2}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOcc2U}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sortedOcc2}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share2}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOcc2U}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){share1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shared}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){share1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sortedOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sortedOcc2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaNames2}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){shared}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){share1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shared}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){sortedOcc}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){sortedOccU}<LSEP>[](symbol){sortedOcc2U}<LSEP>[](symbol){shared}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){cleanUncertain}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){primary_reso}<LEND>[](symbol){cleanResoValues}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxonVar}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){rank}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaNames}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){taxonVar}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaNames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaNames}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sortedOcc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxonVar}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sortedOcc}<LEND>[](symbol){taxaNames}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){onlyFormal}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxonVar2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){primary_name}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stillUseful}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxonVar}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){identified_rank}<LEND>[](symbol){rank}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaNames2}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonVar2}<LSEP>[](symbol){stillUseful}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaNames2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames2}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaNames2}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sortedOcc2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){taxaNames2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxonVar2}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sortedOcc2}<LEND>[](symbol){taxaNames2}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){share1}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaNames2}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){share2}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaNames2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaNames}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOccU}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sortedOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOccU}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share2}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOcc2U}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sortedOcc2}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){share2}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sortedOcc2U}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){share1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shared}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){share1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sortedOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sortedOcc2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaNames2}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){shared}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaNames}<LSEP>[](symbol){share1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shared}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){sortedOcc}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){sortedOccU}<LSEP>[](symbol){sortedOcc2U}<LSEP>[](symbol){shared}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){sortedOcc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sortedOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sortedOcc}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){sortedOcc}<LEND>[assign](){<-}<LSEP>[](symbol){translatePBDBocc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){taxon_name}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){taxon_name}<LEND>[litteral](str){identified_name}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){taxon_no}<LEND>[litteral](str){identified_no}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){taxon_rank}<LEND>[litteral](str){identified_rank}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){matched_name}<LEND>[litteral](str){accepted_name}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){matched_no}<LEND>[litteral](str){accepted_no}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){matched_rank}<LEND>[litteral](str){accepted_rank}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){genus_name}<LEND>[litteral](str){primary_name}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){genus_reso}<LEND>[litteral](str){primary_reso}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){tna}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){mna}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){tna}<LSEP>[argument 1; litteral](str){rnk}<LSEP>[argument 2; litteral](str){tid}<LSEP>[argument 3; litteral](str){mna}<LSEP>[argument 4; litteral](str){mra}<LSEP>[argument 5; litteral](str){mid}<LSEP>[argument 6; litteral](str){idt}<LSEP>[argument 7; litteral](str){ids}<LSEP>[argument 8; litteral](str){gnl}<LSEP>[argument 9; litteral](str){fml}<LSEP>[argument 10; litteral](str){odl}<LSEP>[argument 11; litteral](str){cll}<LSEP>[argument 12; litteral](str){phl}<LSEP>[argument 13; litteral](str){rst}<LSEP>[argument 14; litteral](str){rss}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not all fields founds for comp...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){tna}<LEND>[litteral](str){identified_name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){tid}<LEND>[litteral](str){identified_no}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){rnk}<LEND>[litteral](str){identified_rank}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){mna}<LEND>[litteral](str){accepted_name}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){mid}<LEND>[litteral](str){accepted_no}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){mra}<LEND>[litteral](str){accepted_rank}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){idt}<LEND>[litteral](str){primary_name}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){ids}<LEND>[litteral](str){species_name}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){rss}<LEND>[litteral](str){primary_reso}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){rst}<LEND>[litteral](str){species_reso}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){gnl}<LEND>[litteral](str){genus}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){fml}<LEND>[litteral](str){family}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){odl}<LEND>[litteral](str){order}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){cll}<LEND>[litteral](str){class}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){phl}<LEND>[litteral](str){phylum}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){idn}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){idn}<LSEP>[argument 1; litteral](str){idr}<LSEP>[argument 2; litteral](str){iid}<LSEP>[argument 3; litteral](str){tna}<LSEP>[argument 4; litteral](str){rnk}<LSEP>[argument 5; litteral](str){tid}<LSEP>[argument 6; litteral](str){idg}<LSEP>[argument 7; litteral](str){ids}<LSEP>[argument 8; litteral](str){gnl}<LSEP>[argument 9; litteral](str){fml}<LSEP>[argument 10; litteral](str){odl}<LSEP>[argument 11; litteral](str){cll}<LSEP>[argument 12; litteral](str){phl}<LSEP>[argument 13; litteral](str){rsg}<LSEP>[argument 14; litteral](str){rss}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not all fields founds for comp...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){idn}<LEND>[litteral](str){identified_name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){iid}<LEND>[litteral](str){identified_no}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){idr}<LEND>[litteral](str){identified_rank}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){tna}<LEND>[litteral](str){accepted_name}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){tid}<LEND>[litteral](str){accepted_no}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){rnk}<LEND>[litteral](str){accepted_rank}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){idg}<LEND>[litteral](str){primary_name}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){ids}<LEND>[litteral](str){species_name}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){rss}<LEND>[litteral](str){primary_reso}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){rsg}<LEND>[litteral](str){species_reso}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){gnl}<LEND>[litteral](str){genus}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){fml}<LEND>[litteral](str){family}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){odl}<LEND>[litteral](str){order}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){cll}<LEND>[litteral](str){class}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](str){phl}<LEND>[litteral](str){phylum}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxRankPBDB}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){subspecies}<LSEP>[argument 1; litteral](str){species}<LSEP>[argument 2; litteral](str){subgenus}<LSEP>[argument 3; litteral](str){genus}<LSEP>[argument 4; litteral](str){subtribe}<LSEP>[argument 5; litteral](str){tribe}<LSEP>[argument 6; litteral](str){subfamily}<LSEP>[argument 7; litteral](str){family}<LSEP>[argument 8; litteral](str){superfamily}<LSEP>[argument 9; litteral](str){infraorder}<LSEP>[argument 10; litteral](str){suborder}<LSEP>[argument 11; litteral](str){order}<LSEP>[argument 12; litteral](str){superorder}<LSEP>[argument 13; litteral](str){infraclass}<LSEP>[argument 14; litteral](str){subclass}<LSEP>[argument 15; litteral](str){class}<LSEP>[argument 16; litteral](str){superclass}<LSEP>[argument 17; litteral](str){subphylum}<LSEP>[argument 18; litteral](str){phylum}<LSEP>[argument 19; litteral](str){superphylum}<LSEP>[argument 20; litteral](str){subkingdom}<LSEP>[argument 21; litteral](str){kingdom}<LSEP>[argument 22; litteral](str){unranked clade}<LSEP>[argument 23; litteral](str){informal}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxRankCOM}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){26.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){identified_rank}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){identified_rank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxRankPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxRankCOM}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){accepted_rank}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){accepted_rank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxRankPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxRankCOM}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){data}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){taxa2cladogram}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){drop.cryptic}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){testParentChild}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxaData anc-desc relationship...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tlabs}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxaData}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){desc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){ndesc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){desc}<LSEP>[](symbol){length}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){rank}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ndesc}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ndesc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){NA}<LEND>[statement 8; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){rank}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rank}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){desc}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){comp}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ndesc}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){lab}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lab}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tlabs}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comp}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 13; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){comp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tpot}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){comp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tpot2}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rank}<LSEP>[](symbol){tpot}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tpick}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){tpot}<LSEP>[](symbol){tpot2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dlab}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lab}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){desc}<LSEP>[](symbol){tpick}<LEND>[argument 1; litteral](str){,}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lab}<LSEP>[](symbol){tpick}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){(}<LSEP>[](symbol){dlab}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tlabs}<LSEP>[](symbol){tpick}<LEND>[argument 3; litteral](str){)}<LSEP>[argument 4; litteral](str){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comp}<LSEP>[](symbol){tpick}<LEND>[litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lab}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){;}<LSEP>[argument 2; litteral](str){}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){read.tree}<LSEP>[](symbol){tree1}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){cleanNewPhylo}<LSEP>[](symbol){tree2}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){drop.cryptic}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tlabs}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){tree2}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree2}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree2}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){treeContradiction}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree2}<LSEP>[](symbol){rescale}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree1}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree1 is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree2}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree2 is not of class phylo}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){setdiff}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree2}<LEND>[argument 1; call](){}<LSEP>[](symbol){setdiff}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Trees do not contain same numb...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree2}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Trees contain less than one ti...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nUnshared}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree2}<LEND>[argument 1; litteral](str){number}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){part1}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){part2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nContra1}<LEND>[call](){}<LSEP>[](symbol){nContradiction}<LSEP>[](symbol){part1}<LSEP>[](symbol){part2}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){nContra2}<LEND>[call](){}<LSEP>[](symbol){nContradiction}<LSEP>[](symbol){part2}<LSEP>[](symbol){part1}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nContra1}<LSEP>[](symbol){nContra2}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){rescale}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nPossNodes}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){nPossNodes}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){testContradiction}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){namesA}<LSEP>[](symbol){namesB}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchA}<LEND>[call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){namesA}<LSEP>[](symbol){namesB}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){matchB}<LEND>[call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){namesB}<LSEP>[](symbol){namesA}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){matchB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){matchA}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){matchB}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](logical){FALSE}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){nContradiction}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){partA}<LSEP>[](symbol){partB}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){partContra}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){partA}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){partB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){testContradiction}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){partContra}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){compareNodeAges}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree2}<LSEP>[](symbol){dropUnshared}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree1}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree1 is not of class phylo}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree1orig}<LSEP>[](symbol){tree1}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree2}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree2}<LSEP>[argument 1; litteral](str){multiPhylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree2 is not of class phylo or...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){trees2}<LSEP>[](symbol){tree2}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){trees2}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){tree2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){trees2}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){multiPhylo}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){trees2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){matchMat}<LSEP>[litteral](NULL){NULL}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trees2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){trees2}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree1orig}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){matches1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){matches1}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){No shared taxa between tree2 a...}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){]]!}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tipmatch}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){matches1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){mtimeA}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree1}<LEND>[](symbol){matches1}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){mtimeB}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree2}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){tipmatch}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){ntime1}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree1}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){ntime2}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree2}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){mtime1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime1}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){tipmatch}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){mtime2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime2}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){tipmatch}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mtimeA}<LSEP>[](symbol){mtime1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntime1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.time}<LEND>[](symbol){ntime1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ntime1}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){ntime1}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ntime1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){tree1$root.time is less than t...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntime1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ntime1}<LEND>[](symbol){ntime1}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mtimeB}<LSEP>[](symbol){mtime2}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntime2}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){root.time}<LEND>[](symbol){ntime2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ntime2}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){ntime2}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ntime2}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree2[}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){]$root.time is less than total...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntime2}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ntime2}<LEND>[](symbol){ntime2}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){clades1}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){clades2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){matches}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){clades1}<LSEP>[](symbol){clades2}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){cladesMatches}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clades2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matches}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){matches}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matches}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){matches}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cladesMatches}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){cladesMatches}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){ages1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime1}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){matches}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){ages2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime2}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matches}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){matches}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){age_diff}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ages1}<LSEP>[](symbol){ages2}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){age_diff}<LEND>[litteral](NULL){NULL}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){cladesMatches}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){cladesMatches}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){,}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){matchMat}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){age_diff}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){matchMat}<LEND>[](symbol){cladesMatches}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){currMatches}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){cladesMatches}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){matchMat}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){matchMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){matchMat}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){currMatches}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){currMatches}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matchMat}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){currMatches}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){age_diff}<LSEP>[](symbol){j}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matchMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){age_diff}<LSEP>[](symbol){j}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){matchMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cladesMatches}<LSEP>[](symbol){j}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){dropUnshared}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matchMat}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){matchMat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trees2}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trees2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matchMat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){matchMat}<LEND>[litteral](NULL){NULL}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){matchMat}<LEND>[assign](){<-}<LSEP>[](symbol){compareTermBranches}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree2}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree1}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree1 is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree2}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree2 is not of class phylo}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){term1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){term1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){term1}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){term2}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree2}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){term2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){term2}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree2}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){term2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){term2}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tip.label}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){term_diff}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){term2}<LSEP>[](symbol){term1}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){term_diff}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){term_diff}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){equation2function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){equation}<LSEP>[](symbol){envir}<LSEP>[](symbol){notName}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){equation}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){equation}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){equation}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){equation}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){cannot coerce equation to a st...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){equation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){equation is not a string of le...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){argNames}<LEND>[call](){}<LSEP>[](symbol){all.vars}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){notName}<LSEP>[argument 1; litteral](str){~}<LEND>[](symbol){equation}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){argNames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){argNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){argNames}<LSEP>[](symbol){notName}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){args}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){bquote}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){argNames}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){args}<LEND>[](symbol){argNames}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){newFun}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LSEP>[body; block](){}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){formals}<LSEP>[](symbol){newFun}<LEND>[](symbol){args}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){body}<LSEP>[](symbol){newFun}<LEND>[call](){}<LSEP>[](symbol){parse}<LSEP>[](symbol){equation}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){environment}<LSEP>[](symbol){newFun}<LEND>[](symbol){envir}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newFun}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){taxicDivCont}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeData}<LSEP>[](symbol){int.length}<LSEP>[](symbol){int.times}<LSEP>[](symbol){plot}<LSEP>[](symbol){plotLogRich}<LSEP>[](symbol){timelims}<LSEP>[](symbol){drop.cryptic}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tblen}<LSEP>[](symbol){int.length}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){timeData}<LEND>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){drop.cryptic}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeDataF}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 2; litteral](real){3.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeDataL}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 2; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){timeDataF}<LSEP>[](symbol){timeDataL}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){timeData}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData not of matrix or data...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData is not in time relati...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeData <0 ?}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){FAD}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){LAD}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){int.times}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tblen}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){LAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tblen}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tblen}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){midtimes}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tblen}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tblen}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){midtimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){FAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.end}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){LAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.start}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){int.start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.end}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){10000.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){div1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){div}<LSEP>[](symbol){div}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){plotLogRich}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){div1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){div1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){div1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](str){y}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 6; litteral](str){Time (Before Present)}<LSEP>[argument 7; litteral](str){taxic Richness (Log Scale)}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){div1}<LSEP>[argument 2; litteral](str){l}<LEND>[argument 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 5; litteral](str){Time (Before Present)}<LSEP>[argument 6; litteral](str){Taxic Richness}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LSEP>[](symbol){div}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){taxicDivDisc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeList}<LSEP>[](symbol){int.times}<LSEP>[](symbol){drop.singletons}<LSEP>[](symbol){plot}<LSEP>[](symbol){plotLogRich}<LSEP>[](symbol){timelims}<LSEP>[](symbol){extant.adjust}<LSEP>[](symbol){split.int}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not of matrix or...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not of matrix or...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){intMat}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){drop.singletons}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[](symbol){extant.adjust}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){intMat}<LSEP>[](symbol){is.numeric}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some values in the interval ti...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intMat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not in intervals...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[1]] <0 ?}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not in intervals...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[2]] <0 ?}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){Fint}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){Lint}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){FAD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){Fint}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){LAD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){Lint}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){int.times}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){avg_dur}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.bounds}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){intMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){intMat}<LEND>[](symbol){avg_dur}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){intMat}<LEND>[](symbol){avg_dur}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.bounds}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.bounds}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.bounds}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){intMat}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.bounds}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){int.bounds}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.bounds}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){intMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){intMat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){mean}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){split.int}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){splinters}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){intMat}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mustSplit}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){int.times}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){splinters}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){y}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){mustSplit}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){mustSplit}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){splitter}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splinters}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){splinters}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){y}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LSEP>[](symbol){splitter}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){mustSplit}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){midtimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){FAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.end}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){LAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.start}<LSEP>[](symbol){x}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){int.start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.end}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){10000.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){div1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){div}<LSEP>[](symbol){div}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){plotLogRich}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){div1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){div1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){div1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](str){y}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 6; litteral](str){Time (Before Present)}<LSEP>[argument 7; litteral](str){Taxic Richness (Log Scale)}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){div1}<LSEP>[argument 2; litteral](str){l}<LEND>[argument 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 5; litteral](str){Time (Before Present)}<LSEP>[argument 6; litteral](str){Taxic Richness}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LSEP>[](symbol){div}<LEND>[statement 21; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){phyloDiv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){int.length}<LSEP>[](symbol){int.times}<LSEP>[](symbol){plot}<LSEP>[](symbol){plotLogRich}<LSEP>[](symbol){drop.ZLB}<LSEP>[](symbol){timelims}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tree}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){ttree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ttree is not of class phylo}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tblen}<LSEP>[](symbol){int.length}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){drop.ZLB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttree}<LEND>[call](){}<LSEP>[](symbol){dropZLB}<LSEP>[](symbol){ttree}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){savetree}<LSEP>[](symbol){ttree}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){is.binary.phylo}<LEND>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.rooted}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttree}<LEND>[call](){}<LSEP>[](symbol){multi2di}<LSEP>[](symbol){ttree}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ntime}<LEND>[](symbol){ntime}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[](symbol){ntime}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){ntime}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ntime}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree$root.time is less than to...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){int.times}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){tblen}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tblen}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tblen}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){midtimes}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tblen}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tblen}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){LAD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){FAD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ntime}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){midtimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){FAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.end}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){LAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.start}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){int.start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.end}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){10000.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){div1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){div}<LSEP>[](symbol){div}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 3; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){parOrig}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 5; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){savetree}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 7; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 8; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){plotLogRich}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){div1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){div1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){div1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](str){l}<LSEP>[argument 3; litteral](str){y}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 6; litteral](str){Time (Before Present)}<LSEP>[argument 7; litteral](str){Lineage Richness (Log Scale)}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LSEP>[](symbol){div1}<LSEP>[argument 2; litteral](str){l}<LEND>[argument 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 5; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){div1}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 6; litteral](str){Time (Before Present)}<LSEP>[argument 7; litteral](str){Lineage Richness}<LEND>[statement 10; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){parOrig}<LEND>[statement 11; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LSEP>[](symbol){div}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){make_paleotreeFunc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){parnames}<LSEP>[](symbol){parbounds}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){paleotreeFunc}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){f}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){value}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){parnames}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){value}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in parnames replacement}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){value}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicated names in parnames r...}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){parnames}<LEND>[](symbol){parnames}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){parbounds}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parbounds}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parbounds needs to be a list c...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){lower}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parbounds}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new lower parbounds ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){lower}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in lower parbounds r...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){upper}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parbounds}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){upper}<LEND>[](symbol){np}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of new upper parbounds ...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){upper}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NA values in upper parbounds r...}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parbounds}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parbounds}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){parnames}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[](symbol){parbounds}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){np}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parnames}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){f}<LEND>[assign](){<-}<LSEP>[](symbol){constrainParsePaleo}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){names.lhs}<LSEP>[](symbol){names.rhs}<LSEP>[](symbol){extra}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){formula}<LEND>[call](){}<LSEP>[](symbol){as.formula}<LSEP>[](symbol){formula}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){formula}<LEND>[argument 1; litteral](integer){3}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Invalid formula}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){formula}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){formula}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.name}<LSEP>[](symbol){lhs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Invalid target on LHS of formula}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){lhs.is.target}<LEND>[call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){lhs}<LEND>[](symbol){names.lhs}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.language}<LSEP>[](symbol){rhs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vars}<LEND>[call](){}<LSEP>[](symbol){all.vars}<LSEP>[](symbol){rhs}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ok}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){vars}<LSEP>[](symbol){names.rhs}<LEND>[argument 1; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vars}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){vars}<LSEP>[](symbol){extra}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){ok}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vars}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){e}<LEND>[call](){}<LSEP>[](symbol){parent.frame}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){exists}<LSEP>[](symbol){vars}<LSEP>[](symbol){e}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){get}<LSEP>[](symbol){vars}<LSEP>[](symbol){e}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ok}<LSEP>[litteral](logical){TRUE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){ok}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Invalid RHS of formula:\n\t}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){rhs}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){lhs}<LEND>[](symbol){vars}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){LHS cannot appear in RHS}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){rhs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){RHS must be expression, variab...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){lhs}<LSEP>[](symbol){rhs}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](str){lhs.is.target}<LEND>[](symbol){lhs.is.target}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){expandConstrainForm}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){nparcat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){formula}<LEND>[call](){}<LSEP>[](symbol){as.formula}<LSEP>[](symbol){formula}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){formula}<LEND>[argument 1; litteral](integer){3}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Invalid formula}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){formula}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){formula}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.name}<LSEP>[](symbol){lhs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Invalid target on LHS of formula}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.name}<LSEP>[](symbol){rhs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Can't have more than single, n...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){all.vars}<LSEP>[](symbol){lhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){all.vars}<LSEP>[](symbol){rhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lhs}<LEND>[](symbol){nparcat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){formula LHS doesn't have right...}<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LSEP>[](symbol){formula}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rhs}<LEND>[](symbol){nparcat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){formula RHS doesn't have right...}<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LSEP>[](symbol){formula}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){lhsAll}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lhs}<LSEP>[argument 1; litteral](str){all}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){rhsAll}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rhs}<LSEP>[argument 1; litteral](str){all}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){lhsMatch}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lhs}<LSEP>[argument 1; litteral](str){match}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){rhsMatch}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rhs}<LSEP>[argument 1; litteral](str){match}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){expand.grid}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nparcat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lhsAll}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lhs}<LSEP>[](symbol){x}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){expand.grid}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nparcat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhsAll}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rhs}<LSEP>[](symbol){x}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){rhs}<LSEP>[](symbol){lhs}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){lhsMatch}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){rhsMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){lhsMatch}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){rhsMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){'match' statements aren't symm...}<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LSEP>[](symbol){formula}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){replaceList}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){lhsMatch}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breakNames}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lhs}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){replaceMatch}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lhs}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){replaceMatch}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){replaceList}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){replaceList}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){replaceMatch}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lhs}<LSEP>[](symbol){replaceList}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){lhs}<LSEP>[](symbol){unique}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){lhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){rhs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){rhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){y}<LSEP>[](symbol){as.character}<LEND>[argument 1; litteral](str){.}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){lhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){lhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){x}<LSEP>[](symbol){as.character}<LEND>[argument 1; litteral](str){.}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lhs}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rhs}<LSEP>[](symbol){x}<LEND>[](symbol){y}<LSEP>[argument 2; litteral](str){ ~ }<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plotPhyloPicTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){maxAgeDepth}<LSEP>[](symbol){depthAxisPhylo}<LSEP>[](symbol){colorAxisPhylo}<LSEP>[](symbol){addTaxonStratDurations}<LSEP>[](symbol){taxaStratRanges}<LSEP>[](symbol){stratDurationBoxWidth}<LSEP>[](symbol){sizeScale}<LSEP>[](symbol){removeSurroundingMargin}<LSEP>[](symbol){orientation}<LSEP>[](symbol){resetGrPar}<LSEP>[](symbol){taxaColor}<LSEP>[](symbol){transparency}<LSEP>[](symbol){cacheDir}<LSEP>[](symbol){cacheImage}<LSEP>[](symbol){noiseThreshold}<LSEP>[](symbol){rescalePNG}<LSEP>[](symbol){trimPNG}<LSEP>[](symbol){colorGradient}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oldPar}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){reservedPlotArgs}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){direction}<LSEP>[argument 1; litteral](str){show.tip.label}<LSEP>[argument 2; litteral](str){no.margin}<LSEP>[argument 3; litteral](str){plot}<LSEP>[argument 4; litteral](str){xlim}<LSEP>[argument 5; litteral](str){ylim}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dotArgNames}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){reservedPlotArgs}<LSEP>[](symbol){dotArgNames}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchingReserved}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){reservedPlotArgs}<LSEP>[](symbol){dotArgNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){reservedPlotArgs}<LSEP>[](symbol){dotArgNames}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){matchingReserved}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dotArgNames}<LSEP>[](symbol){matchingReserved}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){arguments '}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){matchingReserved}<LSEP>[argument 1; litteral](str){' & '}<LEND>[argument 2; litteral](str){' are reserved and cannot be d...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){orientation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){argument orientation must be a...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){only orientation values of "u...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){checkRes}<LEND>[call](){}<LSEP>[](symbol){checkRootTime}<LSEP>[](symbol){tree}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){addTaxonStratDurations}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){addTaxonStratDurations is inap...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){taxaStratRanges}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){addTaxonStratDurations = TRUE,...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ranges}<LEND>[call](){}<LSEP>[](symbol){getSortedMinMaxStratRanges}<LSEP>[](symbol){tree}<LSEP>[](symbol){taxaStratRanges}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ranges}<LSEP>[litteral](NULL){NULL}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){maxAgeDepth}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){maxAgeLim}<LSEP>[litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){maxAgeLim}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){maxAgeDepth}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){maxAgeDepth}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){maxAgeDepth must be a numeric ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){maxAgeDepth provided but input...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){maxAgeLim}<LSEP>[](symbol){maxAgeDepth}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ranges}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){minAgeLim}<LSEP>[litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){furthestTipDist}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){minAgeLim}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[](symbol){furthestTipDist}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){minAgeLim}<LEND>[call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ranges}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){maxAgeLim}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){minAgeLim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ageLimInput}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ageLimInput}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){maxAgeLim}<LSEP>[](symbol){minAgeLim}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ageLimInput}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){maxAgeLim}<LSEP>[](symbol){minAgeLim}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rangesRescaled}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[](symbol){ranges}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlimInput}<LSEP>[](symbol){ageLimInput}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ylimInput}<LSEP>[litteral](NULL){NULL}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlimInput}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ylimInput}<LSEP>[](symbol){ageLimInput}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){phylopicIDsPBDB}<LEND>[call](){}<LSEP>[](symbol){getPhyloPicIDNumFromPBDB}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){tree}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){taxaColor}<LEND>[call](){}<LSEP>[](symbol){matchTaxaColor}<LSEP>[](symbol){taxaColor}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){transparency}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){depthAxisPhylo}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){depthAxisPhylo is TRUE but tre...}<LSEP>[argument 1; litteral](str){\nWhy do you want to plot a ph...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){removeSurroundingMargin}<LSEP>[](symbol){depthAxisPhylo}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){removeSurroundingMargin}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.500000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){2.500000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){outPlot}<LEND>[call](){}<LSEP>[](symbol){plot.phylo}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){xlimInput}<LSEP>[](symbol){ylimInput}<LSEP>[](symbol){orientation}<LSEP>[](symbol){removeSurroundingMargin}<LSEP>[argument 6; litteral](logical){FALSE}<LSEP>[](symbol){...}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){devAspRatio}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.size}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.size}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){new_xlim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outPlot}<LSEP>[](symbol){x.lim}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outPlot}<LSEP>[](symbol){x.lim}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){new_ylim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outPlot}<LSEP>[](symbol){y.lim}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outPlot}<LSEP>[](symbol){y.lim}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){plotSizeX}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){plotSizeY}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){OneUserCoordUnitX_in_InchesX}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.size}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){plotSizeX}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){OneUserCoordUnitY_in_InchesY}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.size}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){plotSizeY}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){OneUserCoordUnitY_in_UserCoordUnitX}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){OneUserCoordUnitY_in_InchesY}<LSEP>[](symbol){OneUserCoordUnitX_in_InchesX}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){OneUserCoordUnitX_in_UserCoordUnitY}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){OneUserCoordUnitX_in_InchesX}<LSEP>[](symbol){OneUserCoordUnitY_in_InchesY}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){extraMargin}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){OneUserCoordUnitY_in_UserCoordUnitX}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sizeScale}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){devAspRatio}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){extraMargin}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){extraMargin}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){OneUserCoordUnitX_in_UserCoordUnitY}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sizeScale}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){devAspRatio}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new_ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){extraMargin}<LEND>[statement 30; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 31; call](){}<LSEP>[](symbol){plot.phylo}<LSEP>[](symbol){tree}<LSEP>[](symbol){new_xlim}<LSEP>[](symbol){new_ylim}<LSEP>[](symbol){orientation}<LSEP>[argument 4; litteral](logical){FALSE}<LSEP>[](symbol){removeSurroundingMargin}<LSEP>[](symbol){...}<LEND>[statement 32; control flow](){if}<LSEP>[](symbol){depthAxisPhylo}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){axisPhylo}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){colorAxisPhylo}<LSEP>[](symbol){colorAxisPhylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){axisPhylo}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){colorAxisPhylo}<LSEP>[](symbol){colorAxisPhylo}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){lastPP}<LEND>[call](){}<LSEP>[](symbol){get}<LSEP>[argument 0; litteral](str){last_plot.phylo}<LSEP>[](symbol){.PlotPhyloEnv}<LEND>[statement 34; control flow](){if}<LSEP>[](symbol){addTaxonStratDurations}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newXY}<LEND>[call](){}<LSEP>[](symbol){plotTaxonStratDurations}<LSEP>[](symbol){rangesRescaled}<LSEP>[](symbol){orientation}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lastPP}<LSEP>[](symbol){xx}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lastPP}<LSEP>[](symbol){yy}<LEND>[](symbol){stratDurationBoxWidth}<LSEP>[](symbol){taxaColor}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newXY}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lastPP}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lastPP}<LSEP>[](symbol){yy}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){plotDimensions}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 36; assign](){<-}<LSEP>[](symbol){plotSizeX}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){plotDimensions}<LSEP>[](symbol){xmax}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){plotDimensions}<LSEP>[](symbol){xmin}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){plotSizeY}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){plotDimensions}<LSEP>[](symbol){ymax}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){plotDimensions}<LSEP>[](symbol){ymin}<LEND>[statement 38; assign](){<-}<LSEP>[](symbol){plotAspRatio}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){plotSizeX}<LSEP>[](symbol){plotSizeY}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){plotAspRatio}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){devAspRatio}<LEND>[statement 40; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){rightwards}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){offsetPic}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){plotDimensions}<LSEP>[](symbol){xmax}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){newXY}<LSEP>[](symbol){XX}<LEND>[statement 41; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){orientation}<LSEP>[argument 1; litteral](str){upwards}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){offsetPic}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){plotDimensions}<LSEP>[](symbol){ymax}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){newXY}<LSEP>[](symbol){YY}<LEND>[statement 42; assign](){<-}<LSEP>[](symbol){offsetPic}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){offsetPic}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 43; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lastPP}<LSEP>[](symbol){Ntip}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){getPhyloPicPNG}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){phylopicIDsPBDB}<LSEP>[](symbol){i}<LEND>[](symbol){cacheDir}<LSEP>[](symbol){cacheImage}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaColor}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){colorGradientTaxon}<LSEP>[](symbol){colorGradient}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){colorGradientTaxon}<LSEP>[litteral](str){trueMonochrome}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){picPNG}<LEND>[call](){}<LSEP>[](symbol){prepPhyloPic}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){noiseThreshold}<LSEP>[](symbol){rescalePNG}<LSEP>[](symbol){trimPNG}<LSEP>[](symbol){colorGradientTaxon}<LSEP>[argument 5; litteral](logical){FALSE}<LEND>[statement 3; call](){}<LSEP>[](symbol){plotSinglePhyloPic}<LSEP>[](symbol){picPNG}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){newXY}<LSEP>[](symbol){XX}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){newXY}<LSEP>[](symbol){YY}<LEND>[](symbol){offsetPic}<LSEP>[](symbol){orientation}<LSEP>[](symbol){plotAspRatio}<LSEP>[](symbol){sizeScale}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaColor}<LSEP>[](symbol){i}<LEND>[statement 44; assign](){<-}<LSEP>[](symbol){modPhyloPlotInfo}<LSEP>[](symbol){lastPP}<LEND>[statement 45; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){modPhyloPlotInfo}<LSEP>[](symbol){savedPar}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 46; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){modPhyloPlotInfo}<LSEP>[](symbol){newXY}<LEND>[](symbol){newXY}<LEND>[statement 47; control flow](){if}<LSEP>[](symbol){resetGrPar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){oldPar}<LEND>[statement 48; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){modPhyloPlotInfo}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){taxa2phylo}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){obs_time}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaDataNew}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){obs_time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obs_time}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_time}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newAnc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataNew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){newAnc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataNew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){newAnc}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ancestor IDs cannot be reassig...}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataNew}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){taxaDataNew}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot coerce input table so t...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){isRoot}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){isRoot}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){isRoot}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Multiple taxa listed as an app...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){isRoot}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No taxa are listed as an appar...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Root taxon (ancestor listed as...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaData1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){testParentChild}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){input anc-desc relationships a...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Last occurrences appear to occ...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Duplicated values of taxon ID'...}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){tabulate}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){ }<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){obs_time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obs}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obs}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){obs_time}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){obsOutRange}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){obs_time}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_time}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_time}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_time}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){obsOutRange}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){ERROR: Given obs_time are outs...}<LSEP>[argument 1; litteral](str){\n If cryptic taxa, perhaps yo...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData1}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){obs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Number of observations are not...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){fake_taxa}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){obs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData1}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs}<LSEP>[](symbol){x}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs}<LSEP>[](symbol){x}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fake_taxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){fake_taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData1}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){taxaData2}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){taxaData1}<LSEP>[](symbol){fake_taxa}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ntaxa}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData2}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){desc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){births2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){desc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){3.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){desc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){desc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){desc}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){desc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){births2}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){rank}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){births2}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){random}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){numeric}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){births}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){desc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){3.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){events}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){desc}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){desc}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){births}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){births}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){nseg}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){times}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){seg_labs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nseg}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nseg}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){seg_labs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){seg_labs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){taxa_anc}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){ntaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){seg_labs}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){events}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData2}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){moms2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){seg_labs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){moms}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa_anc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moms2}<LSEP>[](symbol){x}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){lengths}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){times}<LSEP>[](symbol){diff}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){term}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){seg_labs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){moms}<LEND>[](symbol){x}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){edgeD}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){seg_labs}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){moms}<LEND>[argument 2; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){lengths}<LEND>[](symbol){term}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){MRCA}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){id}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){<}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){anc}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){edgeD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){MRCA}<LEND>[](symbol){}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData1}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 31; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgeD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){droppers}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxaData1}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){ndesc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 34; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ndesc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){epick}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ndesc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){epick}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){epick}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){epick}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){edesc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){epick}<LSEP>[](symbol){id}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){edgeD}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edesc}<LSEP>[](symbol){id}<LEND>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){newe}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edesc}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){epick}<LSEP>[](symbol){anc}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){epick}<LSEP>[](symbol){brlen}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edesc}<LSEP>[](symbol){brlen}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edesc}<LSEP>[](symbol){term}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){epick}<LSEP>[](symbol){id}<LEND>[](symbol){}<LEND>[](symbol){newe}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ndesc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){id}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){anc}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){ndesc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){id}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){anc}<LEND>[statement 36; assign](){<-}<LSEP>[](symbol){e_fix}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 37; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e_fix}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){term}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){term}<LEND>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fake_taxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[statement 38; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e_fix}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){term}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){term}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){term}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){ea_fix}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){anc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){MRCA}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e_fix}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){id}<LEND>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){term}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 40; assign](){<-}<LSEP>[](symbol){tlabs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxaData1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){obs}<LEND>[statement 41; assign](){<-}<LSEP>[](symbol){edgf}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){ea_fix}<LSEP>[](symbol){e_fix}<LEND>[statement 42; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){edgf}<LEND>[litteral](NULL){NULL}<LEND>[statement 43; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){edgf}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NAs introduced into edge matrix?}<LEND>[statement 44; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){testParentChild}<LSEP>[](symbol){edgf}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){produced edge matrix is incons...}<LEND>[statement 45; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){edgf}<LSEP>[](symbol){tlabs}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeD}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgf}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 46; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){tree1}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){phylo}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){tree1}<LEND>[statement 47; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){cleanNewPhylo}<LSEP>[](symbol){tree1}<LEND>[statement 48; assign](){<-}<LSEP>[](symbol){first_obs_time}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){obs}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 49; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){first_obs_time}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 50; assign](){<-}<LSEP>[](symbol){rootOffset}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 51; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){rootOffset}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[](symbol){rootOffset}<LEND>[statement 52; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 53; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){dateTaxonTreePBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){minBranchLen}<LSEP>[](symbol){tipTaxonDateUsed}<LSEP>[](symbol){dropZeroOccurrenceTaxa}<LSEP>[](symbol){plotTree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){lastapp_min_ma}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){a data table of PBDB variables...}<LSEP>[argument 1; litteral](str){ must be provided either directly}<LSEP>[argument 2; litteral](str){or as a taxaDataPBDB element o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lastAppTimes}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){lastapp_min_ma}<LSEP>[argument 1; litteral](str){lastapp_max_ma}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){firstAppTimes}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstapp_min_ma}<LSEP>[argument 1; litteral](str){firstapp_max_ma}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaDataPBDB_orig}<LSEP>[](symbol){taxaDataPBDB}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){node.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){No node labels found - is this...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){combData}<LSEP>[](symbol){taxaDataPBDB}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeNames}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){node.label}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nodeNames}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){nodeNames}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nodeNamesNoMatch}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nodeNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){taxon_name}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){nodeNamesNoMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeNames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeNames}<LSEP>[](symbol){nodeNamesNoMatch}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nodeNames}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){nodeNames}<LSEP>[argument 1; litteral](str){,}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){apiAddressNodes}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data1.2/...}<LSEP>[](symbol){nodeNames}<LSEP>[argument 2; litteral](str){&show=app,parent}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nodeData}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){apiAddressNodes}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sharedColNames}<LEND>[call](){}<LSEP>[](symbol){intersect}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){nodeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){taxaDataReduced}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[](symbol){sharedColNames}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nodeDataReduced}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeData}<LSEP>[](symbol){}<LSEP>[](symbol){sharedColNames}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){combData}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){taxaDataReduced}<LSEP>[](symbol){nodeDataReduced}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){appData}<LEND>[call](){}<LSEP>[](symbol){processTaxonAppData}<LSEP>[](symbol){combData}<LSEP>[](symbol){dropZeroOccurrenceTaxa}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){dropTips}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){tip.label}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){appData}<LSEP>[](symbol){taxon_name}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){dropTips}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){The following tips did not hav...}<LSEP>[argument 1; litteral](str){ appearance times and were dro...}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){dropTips}<LEND>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxaTree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){taxaTree}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){dropTips}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){node.label}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeChildren}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){taxaTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nodeMaxAges}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){taxaTree}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchedChildren}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){nodeChildren}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){appData}<LSEP>[](symbol){taxon_name}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){maxChildAges}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){appData}<LSEP>[](symbol){firstapp_max_ma}<LEND>[](symbol){matchedChildren}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeMaxAges}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){maxChildAges}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeMaxAges}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){appData}<LSEP>[](symbol){firstapp_max_ma}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){node.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){appData}<LSEP>[](symbol){taxon_name}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tipMatches}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){appData}<LSEP>[](symbol){taxon_name}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){fourDateRanges}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){appData}<LSEP>[](symbol){tipMatches}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){firstAppTimes}<LSEP>[](symbol){lastAppTimes}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tipTaxonDateUsed}<LSEP>[argument 1; litteral](str){deepestAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipAges}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fourDateRanges}<LSEP>[](symbol){firstapp_max_ma}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tipTaxonDateUsed}<LSEP>[argument 1; litteral](str){shallowestAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipAges}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fourDateRanges}<LSEP>[](symbol){lastapp_min_ma}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){allAges}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){tipAges}<LSEP>[](symbol){nodeMaxAges}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){taxaNAapps}<LEND>[call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){allAges}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){taxaNAapps}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){namesAllAges}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){node.label}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){noappNames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){namesAllAges}<LSEP>[](symbol){taxaNAapps}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){noappNames}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){noappNames}<LSEP>[argument 1; litteral](str){,\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Some ages contain NAs: \n}<LSEP>[](symbol){noappNames}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){datedTree}<LEND>[call](){}<LSEP>[](symbol){nodeDates2branchLengths}<LSEP>[](symbol){allAges}<LSEP>[](symbol){taxaTree}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){minBranchLen}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){datedTree}<LEND>[call](){}<LSEP>[](symbol){minBranchLength}<LSEP>[](symbol){datedTree}<LSEP>[](symbol){minBranchLen}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){datedTree}<LEND>[call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){datedTree}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){plotName}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Dated Phylogeny (}<LSEP>[](symbol){minBranchLen}<LSEP>[argument 2; litteral](str){ Minimum Branch Length)}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){plotName}<LSEP>[litteral](str){Dated Phylogeny}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){checkRootTimeRes}<LEND>[call](){}<LSEP>[](symbol){checkRootTime}<LSEP>[](symbol){datedTree}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){plotTree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){datedTree}<LSEP>[](symbol){plotName}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 1; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fourDateRanges}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaTree}<LSEP>[](symbol){tip.label}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){datedTree}<LSEP>[](symbol){tipTaxonFourDateRanges}<LEND>[](symbol){fourDateRanges}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){datedTree}<LSEP>[](symbol){ranges.used}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fourDateRanges}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstapp_max_ma}<LSEP>[argument 1; litteral](str){lastapp_min_ma}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){datedTree}<LSEP>[](symbol){ranges.used}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){FAD}<LSEP>[argument 1; litteral](str){LAD}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){datedTree}<LSEP>[](symbol){taxaDataPBDB}<LEND>[](symbol){taxaDataPBDB_orig}<LEND>[statement 25; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){datedTree}<LEND>[assign](){<-}<LSEP>[](symbol){processTaxonAppData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dataPBDB}<LSEP>[](symbol){dropZeroOccurrenceTaxa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lastAppTimes}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){lastapp_min_ma}<LSEP>[argument 1; litteral](str){lastapp_max_ma}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){firstAppTimes}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstapp_min_ma}<LSEP>[argument 1; litteral](str){firstapp_max_ma}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){isExtant}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataPBDB}<LSEP>[](symbol){is_extant}<LEND>[argument 1; litteral](str){extant}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){isExtinct}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataPBDB}<LSEP>[](symbol){is_extant}<LEND>[argument 1; litteral](str){extinct}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){hasZeroOcc}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataPBDB}<LSEP>[](symbol){n_occs}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){isExtinctAndZeroOcc}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){hasZeroOcc}<LSEP>[](symbol){isExtinct}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){hasNAFirstApps}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataPBDB}<LSEP>[](symbol){}<LSEP>[](symbol){firstAppTimes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){isExtant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataPBDB}<LSEP>[](symbol){isExtant}<LSEP>[](symbol){lastAppTimes}<LEND>[litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){isExtant}<LSEP>[](symbol){hasNAFirstApps}<LEND>[](symbol){firstAppTimes}<LEND>[litteral](real){0.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){isExtinctAndZeroOcc}<LEND>[](symbol){dropZeroOccurrenceTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dataPBDB}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){isExtinctAndZeroOcc}<LEND>[](symbol){}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){dataPBDB}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){sProb2sRate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){R}<LSEP>[](symbol){int.length}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){R}<LEND>[](symbol){int.length}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){sRate2sProb}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){int.length}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[](symbol){int.length}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){pqsRate2sProb}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){int.length}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dt}<LSEP>[](symbol){int.length}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PDbt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LEND>[](symbol){dt}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){PDbL}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){PDFt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){dt}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){PDFL}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NbNFL}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){dt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){term1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){term2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){dt}<LEND>[](symbol){p}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){term3}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){terms}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){term1}<LSEP>[](symbol){term2}<LEND>[](symbol){term3}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){NbNFL}<LEND>[](symbol){p}<LEND>[](symbol){terms}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NbNFL}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){term1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){term2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[](symbol){dt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){term3}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){dt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){terms}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){term1}<LSEP>[](symbol){term2}<LEND>[](symbol){term3}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){NbNFL}<LEND>[](symbol){terms}<LEND>[](symbol){res}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){Pbt}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){PbL}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){PFt}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){dt}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PFL}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){dt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){PFL}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){dt}<LEND>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){PDbt}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[](symbol){Pbt}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){PDbL}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[](symbol){PbL}<LEND>[argument 2; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){PDFt}<LSEP>[](symbol){p}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[](symbol){PFt}<LEND>[argument 3; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){PDFL}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){dt}<LEND>[](symbol){PFL}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[litteral](NULL){NULL}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){qsProb2Comp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){R}<LSEP>[](symbol){q}<LSEP>[](symbol){p}<LSEP>[](symbol){mode}<LSEP>[](symbol){nrep}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){budding}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){bifurcating}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){p}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Origination rate (p) not given...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){anagenesis}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){p}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Rate of pseudo-speciation / an...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){t}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nrep}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){R}<LEND>[](symbol){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){Pd}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){res}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[litteral](NULL){NULL}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){qsRate2Comp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){q}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LSEP>[](symbol){q}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plotOccData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){occList}<LSEP>[](symbol){groupLabel}<LSEP>[](symbol){occColors}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){xlims}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groupLabel}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){groupLabel}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){groupLabel must be length = 1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){occColors}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){occColors}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){occList}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){occColors must be the same len...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){occList}<LEND>[call](){}<LSEP>[](symbol){pullOccListData}<LSEP>[](symbol){occList}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sumOcc}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){nrow}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){occList}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){occList}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){max}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){occList}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){occList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlims}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){max}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){min}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xlimMod}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlims}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlims}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.010000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xlims}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlims}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){xlimMod}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlims}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){xlimMod}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){plotMainTitle}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){groupLabel}<LEND>[argument 1; litteral](str){Age Uncertainty of Occurrence ...}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Age Uncertainty of Occurrence ...}<LSEP>[](symbol){groupLabel}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){origPar}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 9; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){n}<LEND>[statement 10; call](){}<LSEP>[](symbol){plot}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](str){n}<LSEP>[](symbol){xlims}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){occList}<LSEP>[](symbol){nrow}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){occList}<LEND>[argument 5; litteral](str){}<LSEP>[argument 6; litteral](str){Time (Ma)}<LSEP>[](symbol){plotMainTitle}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){occColors}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){occColors}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){occList}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lineWidth}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lineWidth}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.020000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){sumOcc}<LEND>[argument 1; litteral](real){3.200000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lineWidth}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){lineWidth}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){lineWidth}<LSEP>[argument 2; litteral](real){0.010000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){count}<LSEP>[litteral](real){1.000000}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){occList}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){occList}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){occList}<LSEP>[](symbol){i}<LEND>[](symbol){j}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){count}<LSEP>[](symbol){count}<LEND>[](symbol){lineWidth}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){occColors}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 15; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){origPar}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){occList}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){reverseList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){list}<LSEP>[](symbol){simplify}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){list}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not all lists equally long}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){list1}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){list}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){list1}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){list}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){simplify}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){list1}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){list}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){list1}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){parseNexusFile}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){origNexusFile}<LSEP>[](symbol){asIs}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphNexusAsIs}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[](symbol){origNexusFile}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){asIs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphNexus}<LEND>[call](){}<LSEP>[](symbol){scan}<LSEP>[](symbol){origNexusFile}<LEND>[argument 1; call](){}<LSEP>[](symbol){character}<LEND>[argument 2; litteral](str){\n}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](str){[}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntaxLine}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[](symbol){morphNexus}<LSEP>[argument 1; litteral](str){\\bNTAX}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ntaxLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one line containing ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ntaxLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No line containing 'NTAX' foun...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){oldNtax}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){(.+?)(ntax\\s*\\=\\s*)(\\d+)(.+)}<LSEP>[argument 1; litteral](str){\\3}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LSEP>[](symbol){ntaxLine}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ntaxLineFirst}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){(.+?)(ntax\\s*\\=\\s*)(\\d+)(.+)}<LSEP>[argument 1; litteral](str){\\1\\2}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LSEP>[](symbol){ntaxLine}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ntaxLineLast}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){(.+?)(ntax\\s*\\=\\s*)(\\d+)(.+)}<LSEP>[argument 1; litteral](str){\\4}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LSEP>[](symbol){ntaxLine}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){matrixLine}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[](symbol){morphNexus}<LSEP>[argument 1; litteral](str){\\bMATRIX}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){matrixLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one line containing ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){matrixLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No line containing 'MATRIX' fo...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){matrixEnd}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){matrixLine}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){matrixLine}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; litteral](str){;}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){matrixEnd}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot find semicolon on line ...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){headerOne}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){ntaxLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){headerTwo}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){ntaxLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){matrixLine}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){footer}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){;}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){matrixEnd}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){morphNexus}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){taxonLines}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){morphNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){matrixLine}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){matrixEnd}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){taxonLines}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){;}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){taxonLines}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){taxonLines}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonLines}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){taxonLines}<LSEP>[argument 1; litteral](str){}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){taxonLines}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){\t}<LSEP>[argument 1; litteral](str){ }<LSEP>[](symbol){taxonLines}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxonLines}<LEND>[](symbol){oldNtax}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of apparent lines i...}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){taxonData}<LEND>[call](){}<LSEP>[](symbol){regmatches}<LSEP>[](symbol){taxonLines}<LEND>[argument 1; call](){}<LSEP>[](symbol){regexpr}<LSEP>[argument 0; litteral](str){ }<LSEP>[](symbol){taxonLines}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){taxonNames}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxonData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){z}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){charData}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxonData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){z}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){remakeDataBlockFun}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){newTaxaTable}<LSEP>[](symbol){taxonNames}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origMatch}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newTaxaTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxonNames}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){origMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){more than one match of taxon n...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){origMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No match for original taxon na...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newData}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newTaxaTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){charData}<LSEP>[](symbol){origMatch}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){newTaxonBlock}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){newData}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){ }<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){newNtaxValue}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newTaxaTable}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){newNtaxLine}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){ntaxLineFirst}<LSEP>[argument 1; litteral](str){ }<LSEP>[](symbol){newNtaxValue}<LSEP>[argument 3; litteral](str){ }<LSEP>[](symbol){ntaxLineLast}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){newBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){headerOne}<LSEP>[](symbol){newNtaxLine}<LSEP>[](symbol){headerTwo}<LSEP>[argument 3; litteral](str){}<LSEP>[](symbol){newTaxonBlock}<LSEP>[argument 5; litteral](str){}<LSEP>[](symbol){footer}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newBlock}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxonNames}<LSEP>[](symbol){remakeDataBlockFun}<LSEP>[](symbol){morphNexusAsIs}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){morphNexusAsIs}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){probAnc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){R}<LSEP>[](symbol){mode}<LSEP>[](symbol){analysis}<LSEP>[](symbol){Mmax}<LSEP>[](symbol){nrep}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){budding}<LSEP>[argument 1; litteral](str){bifurcating}<LSEP>[argument 2; litteral](str){anagenesis}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mode not designated, must be '...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){anagenesis}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){p will be treated as the rate ...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){analysis}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){directDesc}<LSEP>[argument 1; litteral](str){indirectDesc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Analysis type not designated, ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nrep}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Nrep is less than zero?}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){analysis}<LSEP>[argument 1; litteral](str){directDesc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pp}<LEND>[call](){}<LSEP>[](symbol){qsProb2Comp}<LSEP>[](symbol){R}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){mode}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){budding}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PN}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LSEP>[](symbol){Ni}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){Ti}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){Ti}<LEND>[](symbol){Ni}<LEND>[argument 1; call](){}<LSEP>[](symbol){factorial}<LSEP>[](symbol){Ni}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){maxN}<LSEP>[litteral](real){100.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){bifurcating}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PN}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LSEP>[](symbol){Ni}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){maxN}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){anagenesis}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Ti}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[](symbol){Ti}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){PN}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){Ti}<LSEP>[](symbol){Ni}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){Ni}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){maxN}<LSEP>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){t}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nrep}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Nres}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){N}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){maxN}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Nres}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){PN}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){t}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Pp}<LEND>[](symbol){N}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){R}<LEND>[](symbol){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){Pd}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){t}<LEND>[](symbol){Pp}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){Nres}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){analysis}<LSEP>[argument 1; litteral](str){indirectDesc}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){budding}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){bifurcating}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Indirect Descendant formulae a...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Qm}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){M}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){factorial}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){M}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){M}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){factorial}<LSEP>[](symbol){M}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){x}<LSEP>[](symbol){M}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){M}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Pp}<LEND>[call](){}<LSEP>[](symbol){qsProb2Comp}<LSEP>[](symbol){R}<LSEP>[](symbol){q}<LSEP>[argument 2; litteral](str){budding}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){M}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Mmax}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){M}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){Qm}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){M}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Pp}<LEND>[](symbol){M}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mode}<LSEP>[argument 1; litteral](str){anagenesis}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Pp}<LEND>[call](){}<LSEP>[](symbol){qsProb2Comp}<LSEP>[](symbol){R}<LSEP>[](symbol){q}<LSEP>[argument 2; litteral](str){anagenesis}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){QmStar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){M}<LSEP>[](symbol){T}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){firstTerm}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){t}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){T}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){firstTerm}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[](symbol){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){M}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){factorial}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){M}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){secondTerm}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){T}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LEND>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){M}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){factorial}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){M}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){firstTerm}<LEND>[](symbol){secondTerm}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){T}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nrep}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Tres}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){M}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Mmax}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Tres}<LSEP>[](symbol){M}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){QmStar}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){M}<LSEP>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){Pp}<LEND>[](symbol){M}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){T}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){Tres}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){res}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Input parameters and nrep prod...}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){May want to decrease nrep to s...}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){res}<LEND>[litteral](real){0.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){res}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[litteral](NULL){NULL}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Treat result with caution: if ...}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Values higher than 0.5 result ...}<LEND>[statement 2; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){See documentation.}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){writeSimpleSumtNexus}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){directory}<LSEP>[](symbol){origNexus}<LSEP>[](symbol){outputNexus}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){files}<LEND>[call](){}<LSEP>[](symbol){list.files}<LSEP>[](symbol){directory}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){paths}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){directory}<LSEP>[argument 1; litteral](str){//}<LSEP>[](symbol){files}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){treeFiles}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){files}<LEND>[argument 1; call](){}<LSEP>[](symbol){grep}<LSEP>[](symbol){files}<LSEP>[argument 1; litteral](str){run..t}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){inputs}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){.run..t}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){treeFiles}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){inputs}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){.tree.}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){inputs}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){bayesBlock}<LSEP>[litteral](str){#NEXUS}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){inputs}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexus}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origNex}<LEND>[call](){}<LSEP>[](symbol){scan}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inputs}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){character}<LSEP>[argument 2; litteral](str){\n}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origNex}<LEND>[call](){}<LSEP>[](symbol){scan}<LSEP>[](symbol){origNexus}<LSEP>[argument 1; litteral](str){character}<LSEP>[argument 2; litteral](str){\n}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cropNex}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){origNex}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){grep}<LSEP>[](symbol){origNex}<LSEP>[argument 1; litteral](str){mcmcp}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cropNex}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cropNex}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){grep}<LSEP>[](symbol){cropNex}<LSEP>[argument 1; litteral](str){log start}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sumtLine}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){sumt filename = }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inputs}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){ outputname = }<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inputs}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){.simple}<LEND>[argument 4; litteral](str){ conformat = simple;}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){bayesBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bayesBlock}<LSEP>[](symbol){cropNex}<LSEP>[](symbol){sumtLine}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](str){end;}<LSEP>[argument 5; litteral](str){}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){cropNex}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cropNex}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){grep}<LSEP>[](symbol){cropNex}<LSEP>[argument 1; litteral](str){log start}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){inputs}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sumtLine}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){sumt filename = }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inputs}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){ outputname = }<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inputs}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){.simple}<LEND>[argument 4; litteral](str){ conformat = simple;}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){bayesBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bayesBlock}<LSEP>[](symbol){cropNex}<LSEP>[](symbol){sumtLine}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](str){end;}<LSEP>[argument 5; litteral](str){}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outputNexus}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){write}<LSEP>[](symbol){bayesBlock}<LSEP>[](symbol){outputNexus}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){bayesBlock}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){binTimeData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeData}<LSEP>[](symbol){int.length}<LSEP>[](symbol){start}<LSEP>[](symbol){int.times}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data?}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData is not in time relati...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeData <0 ?}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){int.times}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){start}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){start}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){timeData}<LEND>[](symbol){int.length}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Error:Start<max(timeData)?}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){end}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){timeData}<LEND>[](symbol){int.length}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){int.length}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){bins}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){start}<LSEP>[](symbol){end}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.length}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){bins}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){bins}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){0.000000}<LSEP>[](symbol){bins}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){fads}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){bins}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){lads}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){bins}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bins}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bins}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fads}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bins}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lads}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bins}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bins}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bins}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bins}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bins}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){fads}<LSEP>[](symbol){lads}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){int.durs}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){int.durs}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some input time intervals have...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){int.durs}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){Fint}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){int.times}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){Lint}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){int.times}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Fint}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Lint}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){taxon.times}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){Fint}<LSEP>[](symbol){Lint}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxon.times}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){taxon.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxon.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){taxon.times}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[](symbol){}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){new.order}<LEND>[call](){}<LSEP>[](symbol){rank}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxon.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new.order}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxon.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxon.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new.order}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxon.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){int.times}<LSEP>[](symbol){taxon.times}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){dropZLB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){drop_e}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){drop_t}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){drop_e}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){drop_t}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){drop_t}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){fixRootTime}<LSEP>[](symbol){tree}<LSEP>[](symbol){tree1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){tree1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](logical){NA}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){dropExtinct}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){tol}<LSEP>[](symbol){ignore.root.time}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){No tree$root.time: Assuming la...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dnode}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dnode}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){dnode}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){ignore.root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dnode}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){all tips are extinct based on ...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dnode}<LSEP>[](symbol){tol}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dnode}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Less than 2 tips are extant on...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){stree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){droppers}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stree}<LEND>[call](){}<LSEP>[](symbol){fixRootTime}<LSEP>[](symbol){tree}<LSEP>[](symbol){stree}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){stree}<LEND>[assign](){<-}<LSEP>[](symbol){dropExtant}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){tol}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: no tree$root.time! As...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dnode}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dnode}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){dnode}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dnode}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){all tips are extinct based on ...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dnode}<LSEP>[](symbol){tol}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dnode}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Less than 2 tips extinct on th...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){stree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){droppers}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stree}<LEND>[call](){}<LSEP>[](symbol){fixRootTime}<LSEP>[](symbol){tree}<LSEP>[](symbol){stree}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){stree}<LEND>[assign](){<-}<LSEP>[](symbol){addTermBranchLength}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){addtime}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){branchSel}<LEND>[call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newBrLen}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){branchSel}<LEND>[](symbol){addtime}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){newBrLen}<LEND>[](symbol){newBrLen}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree has negative branch lengths!}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[](symbol){addtime}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}<LEND>[assign](){<-}<LSEP>[](symbol){dropPaleoTip}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){fixRootTime}<LSEP>[](symbol){tree}<LSEP>[](symbol){tree1}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree1}<LEND>[assign](){<-}<LSEP>[](symbol){bindPaleoTip}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){tipLabel}<LSEP>[](symbol){nodeAttach}<LSEP>[](symbol){tipAge}<LSEP>[](symbol){edgeLength}<LSEP>[](symbol){positionBelow}<LSEP>[](symbol){noNegativeEdgeLength}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipLabel}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){tipLabel}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){tipLabel}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){cannot coerce tipLabel to a st...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tipLabel}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){A string of length = 1 is need...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){positionBelow}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){bindTipPaleo does not accept n...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeAttach}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){positionBelow}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.edge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.edge}<LEND>[](symbol){positionBelow}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.edge}<LEND>[](symbol){positionBelow}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.edge}<LEND>[](symbol){positionBelow}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){positionBelow}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){nodeAttach}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){positionBelow cannot be greate...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){No tree$root.time given; Setti...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){bindTipPaleo is for trees with...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){edgeLength}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tipAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeHeight}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[](symbol){nodeAttach}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){modNodeHeight}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nodeHeight}<LSEP>[](symbol){positionBelow}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newLength}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[](symbol){tipAge}<LEND>[](symbol){modNodeHeight}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){newLength}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){noNegativeEdgeLength}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Negative edge length created d...}<LSEP>[argument 1; litteral](str){ older than age of nodeAttach ...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Warning: negative edge length ...}<LSEP>[argument 1; litteral](str){ older than age of nodeAttach ...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){either tipAge or edgeLength mu...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tipAge}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){both tipAge or edgeLength cann...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newLength}<LSEP>[](symbol){edgeLength}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){newLength}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){noNegativeEdgeLength}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Negative edgeLength given ?!}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){bind.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){tipLabel}<LSEP>[](symbol){nodeAttach}<LSEP>[](symbol){positionBelow}<LSEP>[](symbol){newLength}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeAttach}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){positionBelow}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.time}<LEND>[](symbol){positionBelow}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.edge}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.edge}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){root.edge}<LEND>[litteral](NULL){NULL}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree1}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){timePaleoPhy}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeData}<LSEP>[](symbol){type}<LSEP>[](symbol){vartime}<LSEP>[](symbol){ntrees}<LSEP>[](symbol){randres}<LSEP>[](symbol){timeres}<LSEP>[](symbol){add.term}<LSEP>[](symbol){inc.term.adj}<LSEP>[](symbol){dateTreatment}<LSEP>[](symbol){node.mins}<LSEP>[](symbol){noisyDrop}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){timeData}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData not of matrix or data...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree tip labels are not a char...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ntrees<1}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstLast}<LSEP>[argument 1; litteral](str){minMax}<LSEP>[argument 2; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dateTreatment must be one of '...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){allowedTypesTPP}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){basic}<LSEP>[argument 1; litteral](str){mbl}<LSEP>[argument 2; litteral](str){equal}<LSEP>[argument 3; litteral](str){equal_paleotree_legacy}<LSEP>[argument 4; litteral](str){equal_date.phylo_legacy}<LSEP>[argument 5; litteral](str){aba}<LSEP>[argument 6; litteral](str){zlba}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[](symbol){allowedTypesTPP}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){type must be one of the types ...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){add.term}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Inconsistent arguments: random...}<LSEP>[argument 1; litteral](str){ so add.term must be true for ...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){add.term}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Inconsistent arguments: random...}<LSEP>[argument 1; litteral](str){ so there are effectively no t...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){randres}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){firstLast}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Time-scale more trees without ...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){randres}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Do not interpret a si...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Do not interpret a si...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Do not interpret a si...}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){randres}<LSEP>[](symbol){timeres}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Inconsistent arguments:\n}<LSEP>[argument 1; litteral](str){ You cannot randomly resolve p...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){add.term}<LEND>[](symbol){inc.term.adj}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Inconsistent arguments:\n}<LSEP>[argument 1; litteral](str){ Terminal ranges cannot be use...}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){basic}<LEND>[](symbol){inc.term.adj}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Inconsistent arguments:\n}<LSEP>[argument 1; litteral](str){Terminal range adjustment of b...}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){originalInputTree}<LSEP>[](symbol){tree}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Absolutely NO valid taxa share...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){noisyDrop}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Warning: Following taxa droppe...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){droppers}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){droppers}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Absolutely NO valid taxa share...}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 2; litteral](real){1.000000}<LEND>[litteral](logical){NA}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData is not in time relati...}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate taxa in timeList[[2]]}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate tip taxon names in t...}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Odd irreconcilable mismatch be...}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){rmtree}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){savetree}<LSEP>[](symbol){tree}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){saveTD}<LSEP>[](symbol){timeData}<LEND>[statement 28; control flow](){for}<LSEP>[](symbol){ntr}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntrees}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LSEP>[](symbol){savetree}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){is.binary.phylo}<LEND>[](symbol){savetree}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.rooted}<LSEP>[](symbol){savetree}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){randres}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){multi2di}<LSEP>[](symbol){savetree}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){timeres}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){timeLadderTree}<LSEP>[](symbol){savetree}<LSEP>[](symbol){timeData}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){saveTD}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){saveTD}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree}<LEND>[](symbol){x}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 2; litteral](real){1.000000}<LEND>[](symbol){ntime}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){savetree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){node.mins must be same length ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){node.mins not compatible with ...}<LSEP>[argument 1; litteral](str){Drop unshared taxa and recalcu...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){is.binary.phylo}<LEND>[](symbol){originalInputTree}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.rooted}<LSEP>[](symbol){tree}<LEND>[](symbol){randres}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origDesc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){originalInputTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){originalInputTree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){treeDesc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){node_changes}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){origDesc}<LSEP>[](symbol){treeDesc}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){node.mins1}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node.mins1}<LSEP>[](symbol){node_changes}<LEND>[](symbol){node.mins}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){node.mins1}<LSEP>[](symbol){node.mins}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ntime}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){desc_all}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){tree}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){all}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){desc_nodes}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){desc_all}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){desc_all}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){node_times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node.mins1}<LSEP>[](symbol){desc_nodes}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_times}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){node_times}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal_paleotree_legacy}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){vartime}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){vartime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tree}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){ttree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){x}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){add.term}<LSEP>[](symbol){inc.term.adj}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obs_ranges}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){term_id}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){term_add}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){term_id}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_ranges}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){new_edge_length_with_term}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[](symbol){term_add}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[](symbol){new_edge_length_with_term}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){aba}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){vartime}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No All Branch Additive Value G...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){vartime}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){zlba}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){vartime}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No Branch Additive Value Given!}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){new_edge_lengths}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){0.000100}<LEND>[](symbol){vartime}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){0.000100}<LEND>[](symbol){new_edge_lengths}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){mbl}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){vartime}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No Minimum Branch Length Value...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ttree}<LEND>[call](){}<LSEP>[](symbol){minBranchLength}<LSEP>[](symbol){ttree}<LSEP>[](symbol){vartime}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal_paleotree_legacy}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal_date.phylo_legacy}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zbr}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LEND>[argument 0; call](){}<LSEP>[](symbol){unitLengthTree}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal_paleotree_legacy}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zbr}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){equal_date.phylo_legacy}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zbr}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){zbr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zbr}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){zbr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zbr}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zbr}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){vartime}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){The equal method requires edge...}<LSEP>[argument 1; litteral](str){ This expectation is current n...}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){zbr}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mom}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){mom}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){mom}<LEND>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brs}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){brs}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){mom}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mom}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){mom}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brs}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){brs}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){mom}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){totbl}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){brs}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brs}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brs}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){totbl}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){brs}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){brs}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){ttree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){x}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){add.term}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){inc.term.adj}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obs_ranges}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){term_id}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){term_add}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){term_id}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs_ranges}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){new_term_edge_lengths}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[](symbol){term_add}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[](symbol){new_term_edge_lengths}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){add.term}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){latestAge}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tip.label}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){latestAge}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){latestAge}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tip.label}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){latestAge}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[statement 17; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parOrig}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.500000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 2; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){ttree}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 5; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 6; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){parOrig}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[](symbol){ntr}<LEND>[](symbol){ttree}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 30; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ttrees}<LEND>[assign](){<-}<LSEP>[](symbol){bin_timePaleoPhy}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeList}<LSEP>[](symbol){type}<LSEP>[](symbol){vartime}<LSEP>[](symbol){ntrees}<LSEP>[](symbol){nonstoch.bin}<LSEP>[](symbol){randres}<LSEP>[](symbol){timeres}<LSEP>[](symbol){sites}<LSEP>[](symbol){point.occur}<LSEP>[](symbol){add.term}<LSEP>[](symbol){inc.term.adj}<LSEP>[](symbol){dateTreatment}<LSEP>[](symbol){node.mins}<LSEP>[](symbol){noisyDrop}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not of matrix or...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not of matrix or...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){nonstoch.bin}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Do not interpret a si...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ntrees<1}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[](symbol){point.occur}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Inconsistent arguments, point....}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstLast}<LSEP>[argument 1; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dateTreatment must be one of '...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){randres}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Do not interpret a si...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){randres}<LSEP>[](symbol){timeres}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Inconsistent arguments: You ca...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[](symbol){point.occur}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Inconsistent arguments, point....}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Absolutely NO valid taxa share...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){noisyDrop}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Warning: Following taxa droppe...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){droppers}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){droppers}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Less than two valid taxa share...}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 2; litteral](real){1.000000}<LEND>[litteral](logical){NA}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){node.mins not compatible with ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){node.mins must be same length ...}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){notTree}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){notTree}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){noisyDrop}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Warning: Following taxa droppe...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){notTree}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some taxa in timeList not incl...}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Both timeList[[1]] and timeLis...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unexpected NAs in timeList}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unexpected character-type data...}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not in intervals...}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[1]] <0 ?}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not in intervals...}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[2]] <0 ?}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate taxa in timeList[[2]]}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate tip taxon names in t...}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Odd irreconcilable mismatch be...}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){point.occur}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){point.occur = TRUE but some ta...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sites}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 2; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sites}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){rmtree}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){siteTime}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){sites}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 29; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){go}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sites}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){go}<LSEP>[](symbol){}<LEND>[statement 30; control flow](){for}<LSEP>[](symbol){ntrb}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntrees}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){nonstoch.bin}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bad_sites}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){siteDates}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){siteTime}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bad_sites}<LEND>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LSEP>[](symbol){bad_sites}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LSEP>[](symbol){bad_sites}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){bad_sites}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){suppressMessages}<LEND>[argument 0; call](){}<LSEP>[](symbol){timePaleoPhy}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeData}<LSEP>[](symbol){type}<LSEP>[](symbol){vartime}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[](symbol){randres}<LSEP>[](symbol){timeres}<LSEP>[](symbol){add.term}<LSEP>[](symbol){inc.term.adj}<LSEP>[](symbol){dateTreatment}<LSEP>[](symbol){node.mins}<LSEP>[](symbol){plot}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){FAD}<LSEP>[argument 1; litteral](str){LAD}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){ranges.used}<LEND>[](symbol){timeData}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[](symbol){ntrb}<LEND>[](symbol){tree1}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 32; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ttrees}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){unitLengthTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){horizonSampRate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){durations}<LSEP>[](symbol){nCollections}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sampOcc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No input data supplied!}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){sampOcc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){sampOcc is supplied but in't a...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sampOcc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampOcc}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){sampOcc}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nCollections}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){length}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){durations}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){max}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){sampOcc}<LSEP>[](symbol){min}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){durations}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nCollections}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sampOcc}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){durations and nCollections are...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Input data lacks names, assuming }<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Attempting to reorder duration...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nCollections}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){durations}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matches}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nCollections}<LEND>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){matches}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nCollections}<LSEP>[](symbol){matches}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Name matches between durations...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Multiple matches of names on d...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){durations and nCollections do ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){names still not matching after...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nCollections}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){durations and nCollections hav...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sampRate}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nCollections}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){nCollections}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sampRate}<LEND>[litteral](str){sampRate}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){sampRate}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){fixRootTime}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){treeOrig}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){testConsistentDepth}<LSEP>[](symbol){fixingMethod}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){treeOrig}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){treeOrig is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){treeNew}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){treeNew is not of class phylo}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeOrig}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ERROR: treeOrig passed to fixR...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxaNewNM}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){tip.label}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeOrig}<LSEP>[](symbol){tip.label}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaNewNM}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){taxa:}<LSEP>[](symbol){taxaNewNM}<LSEP>[argument 2; litteral](str){are present in treeNew but not...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fixingMethod}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fixingMethod must be length 1}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){fixingMethod}<LSEP>[argument 1; litteral](str){matchCladeTransferNodeAge}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){fixingMethod}<LSEP>[argument 1; litteral](str){rescaleUsingTipToRootDist}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fixingMethod must be one of "...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fixingMethod}<LSEP>[argument 1; litteral](str){matchCladeTransferNodeAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dates}<LEND>[call](){}<LSEP>[](symbol){dateNodes}<LSEP>[](symbol){treeOrig}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](real){0.001000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){treeDesc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){treeOrig}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeOrig}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){allNewTaxa}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){treeDesc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){tip.label}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){allNewTaxa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nUnshared}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){treeDesc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){tip.label}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){matchRootNew}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){allNewTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nUnshared}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nUnshared}<LSEP>[](symbol){allNewTaxa}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matchRootNew}<LEND>[call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){allNewTaxa}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){matchRootNew}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More than one node contains th...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){matchRootNew}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No nodes match the new tree's ...}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dates}<LSEP>[](symbol){matchRootNew}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fixingMethod}<LSEP>[argument 1; litteral](str){rescaleUsingTipToRootDist}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){orig_dist}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){treeOrig}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){tip.label}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeOrig}<LSEP>[](symbol){tip.label}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){new_dist}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){treeNew}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeNew}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeOrig}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){orig_dist}<LSEP>[](symbol){new_dist}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){testConsistentDepth}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkRootTime}<LSEP>[](symbol){treeNew}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){treeNew}<LEND>[assign](){<-}<LSEP>[](symbol){checkRootTime}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){stopIfFail}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){stopIfFail}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Max tip-to-root tree depth (}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 2; litteral](str){) is greater than root age(}<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 4; litteral](str){), so tips are in the future}<LSEP>[argument 5; litteral](str){\nSomething has probably gone ...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Max tip-to-root tree depth (}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 2; litteral](str){) is greater than root age(}<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 4; litteral](str){), so tips are in the future}<LSEP>[argument 5; litteral](str){\nSomething has probably gone ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LSEP>[litteral](logical){FALSE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){constrainParPaleo}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){formulae}<LSEP>[](symbol){names}<LSEP>[](symbol){extra}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bounds}<LEND>[call](){}<LSEP>[](symbol){parbounds}<LSEP>[](symbol){f}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){paleotreeFunc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Given function does not appear...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){constrained}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){formulae}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){formulae}<LEND>[](symbol){formulae}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){origfunction}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rels}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){names.lhs}<LEND>[assign](){<-}<LSEP>[](symbol){names.rhs}<LSEP>[](symbol){names}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){formulae}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){formulae}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){breakTerms}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){formulae}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){all.vars}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){needExpand}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){breakTerms}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){match}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){all}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){needExpand}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){breakNames}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){names}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nparcat}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){breakNames}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newFormulae}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){needExpand}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newFormulae}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){newFormulae}<LEND>[argument 1; call](){}<LSEP>[](symbol){expandConstrainForm}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){formulae}<LSEP>[](symbol){i}<LEND>[](symbol){breakNames}<LSEP>[](symbol){nparcat}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){formulae}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){formulae}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){needExpand}<LEND>[](symbol){newFormulae}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){formulae}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){formulae}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){formula}<LSEP>[](symbol){formulae}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){constrainParsePaleo}<LSEP>[](symbol){formula}<LSEP>[](symbol){names.lhs}<LSEP>[](symbol){names.rhs}<LSEP>[](symbol){extra}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](str){lhs.is.target}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){try}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){rels}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](str){try-error}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){Error parsing constraint with ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rels}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lhs.txt}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){rels}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){lhs.txt}<LEND>[argument 1; call](){}<LSEP>[](symbol){all.vars}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){lhs (%s) is in an expression a...}<LSEP>[](symbol){lhs.txt}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){names.lhs}<LEND>[call](){}<LSEP>[](symbol){setdiff}<LSEP>[](symbol){names.lhs}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LSEP>[](symbol){all.vars}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){names.rhs}<LEND>[call](){}<LSEP>[](symbol){setdiff}<LSEP>[](symbol){names.rhs}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rels}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){rels}<LEND>[argument 1; call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){relsIsPar}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rels}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){rels}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){relsIsPar}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){termBound}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){relsIsPar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){bounds}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){relsBound}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){relsIsPar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){bounds}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){relsBound}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){termBound}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){relsBound}<LSEP>[](symbol){termBound}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){noMatch}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){termBound}<LSEP>[](symbol){relsBound}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){all}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){noMatch}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](str){~}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){relsIsPar}<LEND>[](symbol){noMatch}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Upper and Lower bounds do not ...}<LSEP>[](symbol){noMatch}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){rels}<LSEP>[](symbol){as.character}<LEND>[](symbol){extra}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){final}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){extra}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){i}<LEND>[](symbol){names.rhs}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){npar}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){final}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){bounds}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){bounds}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){final}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){names}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){free}<LEND>[call](){}<LSEP>[](symbol){setdiff}<LSEP>[](symbol){names.rhs}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rels}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){free.i}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){free}<LSEP>[](symbol){names}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){free.j}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){free}<LSEP>[](symbol){final}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){target.i}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rels}<LEND>[](symbol){names}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){pars.out}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){names}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pars.out}<LEND>[](symbol){names}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){g}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){pars}<LSEP>[](symbol){...}<LSEP>[](symbol){pars.only}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){pars}<LEND>[](symbol){npar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){Incorrect parameter length: ex...}<LSEP>[](symbol){npar}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){pars}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pars.out}<LSEP>[](symbol){free.i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pars}<LSEP>[](symbol){free.j}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){e}<LEND>[call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.list}<LSEP>[](symbol){pars}<LEND>[](symbol){final}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pars.out}<LSEP>[](symbol){target.i}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){rels}<LSEP>[](symbol){eval}<LSEP>[](symbol){e}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){pars.only}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){pars.out}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){f}<LSEP>[](symbol){pars.out}<LSEP>[](symbol){...}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](str){class}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){constrained}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){f}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](str){parnames}<LEND>[](symbol){final}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](str){parbounds}<LEND>[](symbol){bounds}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](str){formulae}<LEND>[](symbol){formulae}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](str){extra}<LEND>[](symbol){extra}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](str){origfunction}<LEND>[](symbol){f}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){g}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){degradeTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){prop_collapse}<LSEP>[](symbol){nCollapse}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){leave.zlb}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nCollapse}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){prop_collapse}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){One of either 'prop_collapse' ...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nCollapse}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nCollapse}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){nCollapse must be greater than 1}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){prop_collapse}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prop_collapse}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){prop_collapse must be less than 1}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nCollapse}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){prop_collapse}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Providing both 'prop_collapse'...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nCollapse}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nCollapse}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){prop_collapse}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){edge}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){node.depth}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){sample}<LSEP>[](symbol){edge}<LSEP>[](symbol){nCollapse}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){node_pdesc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree}<LEND>[](symbol){length}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){edge_pdesc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_pdesc}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){edge}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){edge_prob}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){edge_pdesc}<LSEP>[](symbol){node.depth}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){edge_prob}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){edge_prob}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){edge_prob}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){sample}<LSEP>[](symbol){edge}<LSEP>[](symbol){nCollapse}<LSEP>[](symbol){edge_prob}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){leave.zlb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){cedge}<LEND>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){tree}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){cedge}<LEND>[litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){di2multi}<LSEP>[](symbol){tree}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){tree}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}<LEND>[assign](){<-}<LSEP>[](symbol){collapseNodes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){nodeID}<LSEP>[](symbol){collapseType}<LSEP>[](symbol){leave.zlb}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nodeID}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nodeID}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){some nodeID values outside the...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nodeID}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Some nodeID values in...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){collapseType}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){collapseType must be a single ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){collapseType}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){forward}<LSEP>[argument 1; litteral](str){backward}<LSEP>[argument 2; litteral](str){clade}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){collapseType must be either 'f...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){collapseType}<LSEP>[argument 1; litteral](str){backward}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){nodeID}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){collapseType}<LSEP>[argument 1; litteral](str){forward}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){nodeID}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){collapseType}<LSEP>[argument 1; litteral](str){clade}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){descNodes}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nodeID}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){tree}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](str){all}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){descNodes}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){leave.zlb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){cedge}<LEND>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){tree}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){cedge}<LEND>[litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){di2multi}<LSEP>[](symbol){tree}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){tree}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){simTermTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ntaxa}<LSEP>[](symbol){sumRate}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){deadTree}<LSEP>[](symbol){ntaxa}<LSEP>[](symbol){sumRate}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){termEdge}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){taxonDurations}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){termEdge}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nodeDist}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){taxonLADs}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeDist}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){taxonFADs}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){taxonLADs}<LSEP>[](symbol){taxonDurations}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){taxonRanges}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){taxonFADs}<LSEP>[](symbol){taxonLADs}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxonRanges}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){termEdge}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxonRanges}<LSEP>[](symbol){tree}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){simTermTaxaAdvanced}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){mintaxa}<LSEP>[](symbol){maxtaxa}<LSEP>[](symbol){mintime}<LSEP>[](symbol){maxtime}<LSEP>[](symbol){minExtant}<LSEP>[](symbol){maxExtant}<LSEP>[](symbol){min.cond}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){record}<LEND>[call](){}<LSEP>[](symbol){simFossilRecord}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){mintaxa}<LSEP>[](symbol){maxtaxa}<LEND>[argument 5; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){mintime}<LSEP>[](symbol){maxtime}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){minExtant}<LSEP>[](symbol){maxExtant}<LEND>[argument 7; litteral](real){0.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LSEP>[argument 11; litteral](real){1.000000}<LEND>[argument 12; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 13; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[argument 14; litteral](real){0.010000}<LSEP>[argument 15; litteral](str){withExtantOnly}<LSEP>[argument 16; litteral](logical){FALSE}<LSEP>[argument 17; litteral](logical){TRUE}<LSEP>[argument 18; litteral](logical){FALSE}<LSEP>[argument 19; litteral](logical){FALSE}<LSEP>[argument 20; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){fossilRecord2fossilTaxa}<LSEP>[](symbol){record}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){dropZLB}<LEND>[argument 0; call](){}<LSEP>[](symbol){taxa2phylo}<LSEP>[](symbol){taxa}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ntaxa}<LEND>[call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){termEdge}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntaxa}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){termNodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){termEdge}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){taxonDurations}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){termEdge}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){nodeDist}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){taxonLADs}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeDist}<LSEP>[](symbol){termNodes}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){taxonFADs}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){taxonLADs}<LSEP>[](symbol){taxonDurations}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){taxonRanges}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){taxonFADs}<LSEP>[](symbol){taxonLADs}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxonRanges}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){termNodes}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){taxonRanges}<LSEP>[](symbol){tree}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){trueTermTaxaTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){TermTaxaRes}<LSEP>[](symbol){time.obs}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxR}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){TermTaxaRes}<LSEP>[](symbol){taxonRanges}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nameMatch}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){time.obs}<LEND>[argument 1; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxR}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){nameMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ERROR: names on time.obs and i...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeObsOutsideRanges}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){time.obs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){time.obs}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){time.obs}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxR}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nameMatch}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){time.obs}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxR}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nameMatch}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){timeObsOutsideRanges}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ERROR: Given time.obs are outs...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){TermTaxaRes}<LSEP>[](symbol){tree}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){newDurations}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxR}<LSEP>[](symbol){nameMatch}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){time.obs}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){time.obs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ERROR: No taxon names on obser...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){tipMatch}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){time.obs}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){dropTaxa}<LEND>[call](){}<LSEP>[](symbol){character}<LEND>[statement 10; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newDur}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newDurations}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipMatch}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){newDur}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){i}<LEND>[](symbol){newDur}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){New duration longer than origi...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){i}<LEND>[](symbol){newDur}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dropTaxa}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){dropTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){i}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){treeNoDrop}<LSEP>[](symbol){tree1}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dropTaxa}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree1}<LSEP>[](symbol){dropTaxa}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){fixRootTime}<LSEP>[](symbol){treeNoDrop}<LSEP>[](symbol){tree1}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree1}<LEND>[assign](){<-}<LSEP>[](symbol){deadTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ntaxa}<LSEP>[](symbol){sumRate}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){rtree}<LEND>[](symbol){ntaxa}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rexp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){ntaxa}<LSEP>[](symbol){ntaxa}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){sumRate}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){200.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){minCharChange}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree}<LSEP>[](symbol){randomMax}<LSEP>[](symbol){maxParsimony}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){type}<LSEP>[](symbol){cost}<LSEP>[](symbol){printMinResult}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){dropAmbiguity}<LSEP>[](symbol){polySymbol}<LSEP>[](symbol){contrast}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ancMat}<LEND>[call](){}<LSEP>[](symbol){ancPropStateMat}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){type}<LSEP>[](symbol){cost}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxSol}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){ancMat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nSol}<LEND>[call](){}<LSEP>[](symbol){prod}<LSEP>[](symbol){taxSol}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){charN}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){ancMat}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nSol}<LSEP>[](symbol){randomMax}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){solMat}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){ancMat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){charN}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){randomMax}<LSEP>[](symbol){T}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){noChange}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxSol}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){solMat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){noChange}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){charN}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ancMat}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){solMat}<LEND>[](symbol){noChange}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nSol}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){taxSol}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){changers}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxSol}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LSEP>[](symbol){changers}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){solMat2}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){charN}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ancMat}<LSEP>[](symbol){j}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){solMat}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){solMat1}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){solMat2}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){solMat2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){solMat1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){solMat1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){solMat2}<LSEP>[](symbol){k}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){solMat1}<LEND>[litteral](NULL){NULL}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){solMat1}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){solMat}<LEND>[](symbol){j}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){solMat}<LSEP>[](symbol){solMat1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){solMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){solMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){solMat}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){solUnq}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){solMat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){solUnq}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nSol}<LSEP>[](symbol){randomMax}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){solDup}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){solMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){solMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){solMat}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){solMat}<LSEP>[](symbol){}<LSEP>[](symbol){y}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){solMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){solMat}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){solDup}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Not all solutions are unique, ...}<LSEP>[argument 1; litteral](str){ despite random permutations n...}<LSEP>[argument 2; litteral](str){Please investigate or contact ...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){edgeSol}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){solMat}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){solMat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xSol}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){solMat}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeSol}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xSol}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){xSol}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xSol}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){xSol}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tranMat}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){charN}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){charN}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){solMat}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tranMat}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){anc.}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){ancMat}<LEND>[argument 2; litteral](str){}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tranMat}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){desc.}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){ancMat}<LEND>[argument 2; litteral](str){}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){sumTran}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){solMat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgeTran}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeSol}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tranMat1}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){charN}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){charN}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeTran}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeTran}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){y}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tranMat}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[](symbol){tranMat1}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){tranMat1}<LEND>[litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sumTran}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){tranMat1}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nSol}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){maxPars}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tranMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tranMat}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){edgeSol}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeSol}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){maxPars}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sumTran}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){sumTran}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){maxParsimony}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){solMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){solMat}<LSEP>[](symbol){}<LSEP>[](symbol){maxPars}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tranMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tranMat}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){maxPars}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sumTran}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sumTran}<LSEP>[](symbol){maxPars}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){tranSumChange}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tranMat}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tranMat}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){y}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){upper.tri}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){x}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tranSumChange}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Gains}<LSEP>[argument 1; litteral](str){NoChanges}<LSEP>[argument 2; litteral](str){Losses}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){minTran}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tranMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){min}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){funcMess}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){nSol}<LSEP>[argument 1; litteral](str){ potential solutions under }<LSEP>[](symbol){type}<LSEP>[argument 3; litteral](str){, }<LEND>[argument 4; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){maxPars}<LEND>[argument 5; litteral](str){ most parsimonious solutions f...}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nSol}<LSEP>[](symbol){randomMax}<LEND>[argument 1; litteral](str){Solutions sampled stochastically}<LSEP>[argument 2; litteral](str){Solutions exhaustively checked}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){printMinResult}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){maxPars}<LEND>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){funcMess}<LSEP>[](symbol){sumTran}<LSEP>[](symbol){tranMat}<LSEP>[](symbol){minTran}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){funcMess}<LSEP>[](symbol){sumTran}<LSEP>[](symbol){minTran}<LEND>[statement 20; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){funcMess}<LSEP>[](symbol){sumTran}<LSEP>[](symbol){minTran}<LSEP>[](symbol){edgeSol}<LSEP>[](symbol){tranMat}<LSEP>[](symbol){tranSumChange}<LEND>[assign](){<-}<LSEP>[](symbol){ancPropStateMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){type}<LSEP>[](symbol){cost}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){dropAmbiguity}<LSEP>[](symbol){polySymbol}<LSEP>[](symbol){contrast}<LSEP>[](symbol){returnContrast}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){saveNames}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){trait}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){trait}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[](symbol){saveNames}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){trait}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){trait}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){trait must be vector of state ...}<LSEP>[argument 1; litteral](str){ a single character, that can ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.logical}<LSEP>[](symbol){orderedChar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){orderedChar must be a logical ...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){orderedChar}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){orderedChar must be a single l...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){ACCTRAN}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){cost}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){cost matrix is inapplicable if...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){ACCTRAN}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.binary}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be fully resolved if...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){orderedChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){cost}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot treat character as orde...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){polySymbol}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){polySymbol must be length 1, m...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trait}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){names(trait) missing and lengt...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){names(trait) missing \n}<LSEP>[argument 1; litteral](str){trait values will be assigned ...}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){dropAmbiguity}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){isAmbig}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){trait}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichAmbig}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[](symbol){isAmbig}<LEND>[statement 2; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){dropping following taxa with a...}<LSEP>[](symbol){whichAmbig}<LSEP>[argument 2; litteral](str){\n }<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){trait}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){trait}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){isAmbig}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){whichAmbig}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Too few non-ambiguous taxa rem...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){contrast}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){contrast supplied, thus ignori...}<LSEP>[argument 1; litteral](str){ indicated in arguments ambitu...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anyPoly}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){trait}<LEND>[](symbol){grepl}<LSEP>[](symbol){polySymbol}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){anyPoly}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){contrast}<LEND>[call](){}<LSEP>[](symbol){buildContrastPoly}<LSEP>[](symbol){trait}<LSEP>[](symbol){polySymbol}<LSEP>[](symbol){ambiguity}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){contrast}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){unqState}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){trait}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){isAmbigState}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqState}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){trueStates}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unqState}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){isAmbigState}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){trueStates}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){contrast}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){char1}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){trait}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){char1}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){trait}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){char1}<LEND>[call](){}<LSEP>[](symbol){phyDat}<LSEP>[](symbol){char1}<LSEP>[argument 1; litteral](str){USER}<LSEP>[](symbol){trueStates}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){contrast}<LSEP>[argument 5; litteral](logical){FALSE}<LEND>[statement 17; control flow](){if}<LSEP>[](symbol){orderedChar}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){cost}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Do not give cost matrix if you...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nStates}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trueStates}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cost}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[](symbol){nStates}<LSEP>[](symbol){nStates}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nStates}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nStates}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cost}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){cost}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){cost}<LEND>[](symbol){trueStates}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){anc1}<LEND>[call](){}<LSEP>[](symbol){ancestral.pars}<LSEP>[](symbol){tree}<LSEP>[](symbol){char1}<LSEP>[](symbol){type}<LSEP>[](symbol){cost}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){anc1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Ancestral reconstruction retur...}<LSEP>[argument 1; litteral](str){ is empty, check arguments inv...}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){contrastTable}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){anc1}<LSEP>[argument 1; litteral](str){contrast}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){contrastTable}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){anc1}<LSEP>[argument 1; litteral](str){allLevels}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){anc1}<LSEP>[argument 1; litteral](str){levels}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){anc2}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){anc1}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){anc1}<LSEP>[argument 1; litteral](str){levels}<LEND>[](symbol){T}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){anc2}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){anc2}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){anc2}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ancestral state matrix has wro...}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){anc2}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){anc1}<LEND>[](symbol){levels}<LEND>[statement 26; control flow](){if}<LSEP>[](symbol){returnContrast}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[](symbol){contrastTable}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[](symbol){anc2}<LEND>[statement 27; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){buildContrastPoly}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){trait}<LSEP>[](symbol){polySymbol}<LSEP>[](symbol){ambiguity}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){unqState}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){trait}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){containPoly}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqState}<LSEP>[](symbol){grepl}<LSEP>[](symbol){polySymbol}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){isAmbig}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){unqState}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){trueStates}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unqState}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){containPoly}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){isAmbig}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){polyState}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unqState}<LSEP>[](symbol){containPoly}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){polyStateBr}<LEND>[call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){polyState}<LSEP>[](symbol){polySymbol}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){uniquePolyTrueStates}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){polyStateBr}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){trueStates}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){trueStates}<LSEP>[](symbol){uniquePolyTrueStates}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){nTrue}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){trueStates}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){contrastTrue}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){nTrue}<LSEP>[](symbol){nTrue}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){contrastTrue}<LEND>[litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){contrastTrue}<LEND>[](symbol){trueStates}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){rowNamesGo}<LSEP>[](symbol){trueStates}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ambiguity}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){contrastAmbig}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ambiguity}<LEND>[](symbol){nTrue}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rowNamesGo}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){rowNamesGo}<LSEP>[](symbol){ambiguity}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){contrastAmbig}<LSEP>[litteral](NULL){NULL}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){polyMatch}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){polyStateBr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){x}<LSEP>[](symbol){trueStates}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){nPoly}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){polyState}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){contrastPoly}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){nPoly}<LSEP>[](symbol){nTrue}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){contrastPolyRaw}<LEND>[call](){}<LSEP>[](symbol){numeric}<LSEP>[](symbol){nTrue}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nPoly}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newContrast}<LSEP>[](symbol){contrastPolyRaw}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newContrast}<LSEP>[](symbol){polyMatch}<LEND>[litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){contrastPoly}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[](symbol){newContrast}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){rowNamesGo}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){rowNamesGo}<LSEP>[](symbol){polyState}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){contrast}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){contrastTrue}<LSEP>[](symbol){contrastAmbig}<LSEP>[](symbol){contrastPoly}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){contrast}<LEND>[](symbol){rowNamesGo}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){contrast}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){resolveTreeChar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){trait}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){stateBias}<LSEP>[](symbol){iterative}<LSEP>[](symbol){cost}<LSEP>[](symbol){ambiguity}<LSEP>[](symbol){dropAmbiguity}<LSEP>[](symbol){polySymbol}<LSEP>[](symbol){contrast}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Input tree is fully resolved??}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){stateBias}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){orderedChar}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stateBias}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){primitive}<LSEP>[argument 1; litteral](str){derived}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){For 'orderedChar' analyses, st...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){stateBias cannot be used in an...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.logical}<LSEP>[](symbol){iterative}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){iterative must be a logical cl...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){iterative}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){iterative must be a single log...}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){iterative}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){continueRes}<LSEP>[litteral](logical){TRUE}<LEND>[statement 2; control flow](){while}<LSEP>[](symbol){continueRes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){resolveTreeCharMechanism}<LSEP>[](symbol){tree2}<LSEP>[](symbol){trait}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){stateBias}<LSEP>[argument 4; litteral](str){MPR}<LSEP>[](symbol){cost}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){is.binary.phylo}<LEND>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.rooted}<LSEP>[](symbol){tree1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){continueRes}<LSEP>[litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){continueRes}<LSEP>[litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tree1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){treeFinal}<LSEP>[](symbol){tree2}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){treeFinal}<LEND>[call](){}<LSEP>[](symbol){resolveTreeCharMechanism}<LSEP>[](symbol){tree}<LSEP>[](symbol){trait}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){stateBias}<LSEP>[argument 4; litteral](str){MPR}<LSEP>[](symbol){cost}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){treeFinal}<LEND>[assign](){<-}<LSEP>[](symbol){resolveTreeCharMechanism}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){trait}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){stateBias}<LSEP>[](symbol){type}<LSEP>[](symbol){cost}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeParts}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichPoly}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){polyParts}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeParts}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){whichPoly}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){polyParts}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){polyParts}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){whichPoly}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){polyParts}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){polyParts}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){polyParts}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxa mysteriously lost/added?}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){labelClades}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){chosen}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){labelClades}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){polyParts}<LSEP>[](symbol){i}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chosen}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot find a polytomy on the ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chosen}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Selected more than one polytom...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ancMat}<LEND>[call](){}<LSEP>[](symbol){ancPropStateMat}<LSEP>[](symbol){trait}<LSEP>[](symbol){tree1}<LSEP>[](symbol){orderedChar}<LSEP>[](symbol){type}<LSEP>[](symbol){cost}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){maxWt}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){ancMat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){x}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){maxWt}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Error in ancestral state recon...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){descChosen}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){chosen}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){stateBias}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeChar}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){maxWt}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){maxWt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[](symbol){descChosen}<LEND>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ancChar}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){maxWt}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){maxWt}<LEND>[](symbol){chosen}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){orderedChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stateBias}<LSEP>[argument 1; litteral](str){derived}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stateBias}<LSEP>[argument 1; litteral](str){primitive}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stateBias}<LSEP>[argument 1; litteral](str){derived}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeChar}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){maxWt}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){maxWt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[](symbol){descChosen}<LEND>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ancChar}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){maxWt}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){maxWt}<LEND>[](symbol){chosen}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stateBias}<LSEP>[argument 1; litteral](str){primitive}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeChar}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){maxWt}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){maxWt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[](symbol){descChosen}<LEND>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ancChar}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){maxWt}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){maxWt}<LEND>[](symbol){chosen}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Inconsistent orderedChar and s...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){foundStates}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ancChar}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){foundStates}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){groupings}<LSEP>[](symbol){length}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){k}<LSEP>[litteral](real){1.000000}<LEND>[statement 14; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){groupings}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){drop}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){groupings}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drop}<LSEP>[](symbol){k}<LEND>[litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dropFS}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){foundStates}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){drop}<LEND>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){m}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){dropFS}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){foundStates}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){groupings}<LSEP>[](symbol){k}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){drop}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){groupings}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){groupings}<LSEP>[](symbol){mean}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){groupAssign}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){foundStates}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){groupings}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){groupings}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){groupAssign}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nodeChar}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupAssign}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){groupAssign}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){ancChar}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupAssign}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){groupAssign}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeChar}<LSEP>[](symbol){ancChar}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodeChar}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){nodeChar}<LSEP>[](symbol){ancChar}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){bottom}<LSEP>[](symbol){chosen}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){newsie}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){orderedChar}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){chainUp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){groupings}<LSEP>[](symbol){ancChar}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){chainDown}<LEND>[call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){groupings}<LSEP>[](symbol){ancChar}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainUp}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){leveler}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chainUp}<LSEP>[](symbol){j}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){bottom}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeChar}<LSEP>[](symbol){leveler}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainDown}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgar}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bottom}<LSEP>[](symbol){newsie}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){savedBottom}<LSEP>[](symbol){newsie}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainUp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newsie}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){newsie}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainUp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgar}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bottom}<LSEP>[](symbol){newsie}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){bottom}<LSEP>[](symbol){newsie}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newsie}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){newsie}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){edgar}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainDown}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bottom}<LSEP>[](symbol){savedBottom}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newsie}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){newsie}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainDown}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){leveler}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){chainDown}<LSEP>[](symbol){j}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){bottom}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeChar}<LSEP>[](symbol){leveler}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){chainDown}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgar}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bottom}<LSEP>[](symbol){newsie}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){bottom}<LSEP>[](symbol){newsie}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newsie}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){newsie}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){edgar}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){edgeMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){edgeMat is not the right size ...}<LSEP>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){bottom}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeChar}<LSEP>[](symbol){ancChar}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){edgar}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){grouping}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){groupings}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){groupings}<LSEP>[](symbol){ancChar}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){grouping}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgeMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bottom}<LSEP>[](symbol){newsie}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){bottomG}<LSEP>[](symbol){newsie}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){leveler}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){grouping}<LSEP>[](symbol){j}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){edgar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){bottomG}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nodeChar}<LSEP>[](symbol){leveler}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){newsie}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){newsie}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){edgar}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){edgeMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){edgeMat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){tree2}<LSEP>[](symbol){tree1}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){chosen}<LEND>[](symbol){}<LEND>[](symbol){edgeMat}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){Nnode}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){Nnode}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){nodeChar}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){tree3}<LEND>[call](){}<LSEP>[](symbol){cleanNewPhylo}<LSEP>[](symbol){tree2}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree3}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Taxa loss/added somehow in fix...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Taxa loss/added somehow in fix...}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree3}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){treeFinal}<LEND>[call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree1}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){treeFinal}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){twoWayEcologyCluster}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xDist}<LSEP>[](symbol){yDist}<LSEP>[](symbol){propAbund}<LSEP>[](symbol){clustMethod}<LSEP>[](symbol){marginBetween}<LSEP>[](symbol){abundExpansion}<LSEP>[](symbol){cex.axisLabels}<LSEP>[](symbol){xAxisLabel}<LSEP>[](symbol){yAxisLabel}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xClust}<LEND>[call](){}<LSEP>[](symbol){hclust}<LSEP>[](symbol){xDist}<LSEP>[](symbol){clustMethod}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){yClust}<LEND>[call](){}<LSEP>[](symbol){hclust}<LSEP>[](symbol){yDist}<LSEP>[](symbol){clustMethod}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xPhylo}<LEND>[call](){}<LSEP>[](symbol){as.phylo}<LSEP>[](symbol){xClust}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xPhylo}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xPhylo}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){yPhylo}<LEND>[call](){}<LSEP>[](symbol){as.phylo}<LSEP>[](symbol){yClust}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){yPhylo}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){yPhylo}<LSEP>[](symbol){edge.length}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){propAbund}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){propAbund}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xClust}<LSEP>[](symbol){order}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){yClust}<LSEP>[](symbol){order}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){propScale}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){propAbund}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){propAbund}<LEND>[](symbol){abundExpansion}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){propAbund}<LEND>[call](){}<LSEP>[](symbol){strtrim}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){propAbund}<LEND>[argument 1; litteral](real){5.000000}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){propAbund}<LEND>[call](){}<LSEP>[](symbol){strtrim}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){propAbund}<LEND>[argument 1; litteral](real){5.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){oldPar}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 11; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[argument 1; litteral](real){5.000000}<LSEP>[](symbol){marginBetween}<LSEP>[](symbol){marginBetween}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){iSet}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){propAbund}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){jSet}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){propAbund}<LEND>[statement 15; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){propAbund}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){propAbund}<LEND>[argument 2; litteral](str){}<LSEP>[](symbol){xAxisLabel}<LSEP>[](symbol){yAxisLabel}<LSEP>[argument 5; litteral](str){n}<LSEP>[argument 6; litteral](logical){FALSE}<LEND>[statement 16; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){iSet}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LSEP>[](symbol){jSet}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){points}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){16.000000}<LSEP>[argument 3; litteral](str){black}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){propScale}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 17; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){iSet}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){propAbund}<LEND>[](symbol){cex.axisLabels}<LEND>[statement 18; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){jSet}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){0.100000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){propAbund}<LEND>[](symbol){cex.axisLabels}<LEND>[statement 19; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[](symbol){marginBetween}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 20; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){yPhylo}<LSEP>[argument 1; litteral](str){leftwards}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 21; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){axTicks}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 22; call](){}<LSEP>[](symbol){mtext}<LSEP>[argument 0; litteral](str){Height}<LSEP>[argument 1; litteral](real){0.800000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){2.500000}<LEND>[statement 23; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){5.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[](symbol){marginBetween}<LEND>[statement 24; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){xPhylo}<LSEP>[argument 1; litteral](str){downwards}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 25; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){axTicks}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 26; call](){}<LSEP>[](symbol){mtext}<LSEP>[argument 0; litteral](str){Height}<LSEP>[argument 1; litteral](real){0.800000}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.500000}<LEND>[statement 27; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 28; call](){}<LSEP>[](symbol){plot}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](str){n}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){legendScale}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){propAbund}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){propAbund}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){legendScale}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){legendScale}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){propAbund}<LEND>[](symbol){legendScale}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){legendScale}<LEND>[argument 2; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){propAbund}<LEND>[statement 31; call](){}<LSEP>[](symbol){legend}<LSEP>[argument 0; litteral](str){center}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){legendScale}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){abundExpansion}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){legendScale}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){legendScale}<LEND>[argument 3; litteral](real){16.000000}<LEND>[statement 32; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 33; call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){oldPar}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){createMrBayesConstraints}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){partial}<LSEP>[](symbol){file}<LSEP>[](symbol){includeIngroupConstraint}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){splits}<LEND>[call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){splits}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splits}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){splits}<LSEP>[](symbol){length}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){includes}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){splits}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){excludes}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){splits}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){includes}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){includes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){excludes}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){excludes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){partial}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){constraints}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){includes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){constraint node}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){ partial = }<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){includes}<LSEP>[](symbol){i}<LEND>[argument 4; litteral](str){ : }<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){excludes}<LSEP>[](symbol){i}<LEND>[argument 6; litteral](str){;}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){constraints}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){includes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){constraint node}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){ = }<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){includes}<LSEP>[](symbol){i}<LEND>[argument 4; litteral](str){;}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){constList}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){node}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){splits}<LEND>[argument 2; litteral](str){,}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){includeIngroupConstraint}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){prsetLine}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){prset topologypr = constraints(}<LSEP>[](symbol){constList}<LSEP>[argument 2; litteral](str){,ingroup);}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){prsetLine}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){prset topologypr = constraints(}<LSEP>[](symbol){constList}<LSEP>[argument 2; litteral](str){);}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){finalText}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){constraints}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){prsetLine}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){file}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){write}<LSEP>[](symbol){finalText}<LSEP>[](symbol){file}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalText}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rootSplit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tips}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){zz}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){zz}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){zz}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){zz}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tips}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){freqRat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){timeData}<LSEP>[](symbol){calcExtinction}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){timeData}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not in intervals...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[2]] <0 ?}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){durations}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){sumDur}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){durations}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){durations}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){durations}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){f1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sumDur}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sumDur}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){f3}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sumDur}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){freqRat}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){f2}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){f1}<LSEP>[](symbol){f3}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freqRat}<LEND>[litteral](str){freqRat}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){freqRat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Frequency distributio...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){freqRat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: Frequency distributio...}<LEND>[statement 13; control flow](){if}<LSEP>[](symbol){calcExtinction}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){logSD}<LEND>[call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sumDur}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){logSD}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){logSD}<LEND>[litteral](logical){NA}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){intseq}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){durations}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){reg}<LEND>[call](){}<LSEP>[](symbol){lm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){logSD}<LSEP>[](symbol){intseq}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){extRate}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){coefficients}<LSEP>[](symbol){reg}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){extRate}<LEND>[litteral](str){extRate}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){freqRat}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){freqRat}<LSEP>[](symbol){extRate}<LEND>[statement 14; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){durations}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){durations}<LEND>[argument 2; litteral](str){Duration (time-units)}<LSEP>[argument 3; litteral](str){}<LEND>[statement 15; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){freqRat}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){expandTaxonTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxonTree}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){collapse}<LSEP>[](symbol){keepBrLen}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){taxonTree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxonTree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxaData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){some values of taxonData missi...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){collapse}<LEND>[](symbol){keepBrLen}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: collapsed branch leng...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tree}<LSEP>[](symbol){taxonTree}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){keepBrLen}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){tree}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){taxaData}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tip}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){collapse}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){collapse}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){tip}<LEND>[litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cotaxa}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){taxaData}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){repTree}<LEND>[call](){}<LSEP>[](symbol){stree}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cotaxa}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){keepBrLen}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repTree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cotaxa}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repTree}<LSEP>[](symbol){edge.length}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cotaxa}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repTree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){cotaxa}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){bind.tree}<LSEP>[](symbol){tree}<LSEP>[](symbol){repTree}<LSEP>[](symbol){tip}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){keepBrLen}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){di2multi}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree1}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree1}<LEND>[call](){}<LSEP>[](symbol){cleanNewPhylo}<LSEP>[](symbol){tree1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree1}<LSEP>[](symbol){tree}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plot}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){taxonTree}<LEND>[statement 2; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){tree1}<LEND>[statement 3; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree1}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){timeSliceTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ttree}<LSEP>[](symbol){sliceTime}<LSEP>[](symbol){drop.extinct}<LSEP>[](symbol){tipLabels}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){ttree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ttree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Warning: no ttree$root.time! A...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tslice}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[](symbol){sliceTime}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dnode}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnode}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){tslice}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnode}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){tslice}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cedge}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){sliceTime is later than latest...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){propPartTree}<LEND>[call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){ttree}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cedge}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){desc}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cedge}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){desc}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){desctip}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){propPartTree}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){desc}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){droppers}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){desctip}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tipLabels}<LSEP>[argument 1; litteral](str){allDesc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){desctip}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){desctip}<LEND>[argument 1; litteral](str){;}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){stree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){ttree}<LSEP>[](symbol){droppers}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){dnode}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){stree}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnode}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){stree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){tslice}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){cnode_depth}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnode}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){stree}<LSEP>[](symbol){edge}<LEND>[](symbol){cedge}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){stree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){cedge}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tslice}<LSEP>[](symbol){cnode_depth}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){stree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[statement 15; control flow](){if}<LSEP>[](symbol){drop.extinct}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stree1}<LEND>[call](){}<LSEP>[](symbol){dropExtinct}<LSEP>[](symbol){stree}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){stree1}<LSEP>[](symbol){stree}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){ttree}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 3; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){stree1}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 5; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 17; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){stree1}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){createMrBayesTipDatingNexus}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){outgroupTaxa}<LSEP>[](symbol){treeConstraints}<LSEP>[](symbol){ageCalibrationType}<LSEP>[](symbol){whichAppearance}<LSEP>[](symbol){treeAgeOffset}<LSEP>[](symbol){minTreeAge}<LSEP>[](symbol){collapseUniform}<LSEP>[](symbol){anchorTaxon}<LSEP>[](symbol){newFile}<LSEP>[](symbol){origNexusFile}<LSEP>[](symbol){parseOriginalNexus}<LSEP>[](symbol){createEmptyMorphMat}<LSEP>[](symbol){orderedChars}<LSEP>[](symbol){morphModel}<LSEP>[](symbol){morphFiltered}<LSEP>[](symbol){runName}<LSEP>[](symbol){ngen}<LSEP>[](symbol){doNotRun}<LSEP>[](symbol){autoCloseMrB}<LSEP>[](symbol){cleanNames}<LSEP>[](symbol){printExecute}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){tipTimes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){why is tipTimes a list of not ...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outgroupTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){treeConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Either outgroupTaxa or treeCon...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outgroupTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){treeConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Only one of outgroupTaxa or tr...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){morphNexus}<LSEP>[litteral](NULL){NULL}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichAppearance}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstLast}<LSEP>[argument 1; litteral](str){rangeThrough}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){multOTU}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){parseOriginalNexus}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexusData}<LEND>[call](){}<LSEP>[](symbol){parseNexusFile}<LSEP>[](symbol){origNexusFile}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){remakeDataBlockFun}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){nexusData}<LSEP>[](symbol){remakeDataBlockFun}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){morphNexus}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){nexusData}<LSEP>[](symbol){morphNexusAsIs}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot use an option for multi...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){multOTU}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){parseOriginalNexus}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexusData}<LEND>[call](){}<LSEP>[](symbol){parseNexusFile}<LSEP>[](symbol){origNexusFile}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){morphNexus}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){nexusData}<LSEP>[](symbol){morphNexusAsIs}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexusData}<LEND>[call](){}<LSEP>[](symbol){parseNexusFile}<LSEP>[](symbol){origNexusFile}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){morphNexus}<LSEP>[](symbol){nexusData}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){orderedChars}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Morphological data in an origi...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexusData}<LSEP>[litteral](NULL){NULL}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichAppearance}<LSEP>[argument 1; litteral](str){rangeThrough}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){isTimeListSequential}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes must be a sequential ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaTipTimes}<LEND>[call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxaTipTimes}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){treeConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){treeConstraints}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){treeConstraints must be a phyl...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxaTree}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeConstraints}<LSEP>[](symbol){tip.label}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){missingTip}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaTipTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaTipTimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaTree}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){missingTree}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaTree}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaTipTimes}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){missingTip}<LSEP>[](symbol){missingTree}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Following taxa in tipTimes not...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){missingTip}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 2; litteral](str){\nFollowing taxa on treeConstr...}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){missingTree}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaTree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaTipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Somehow have taxa missing from...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){taxaTipTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){taxaTree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Nope, taxa in tipTimes and on ...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outgroupTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){missingOutgroup}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){outgroupTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){outgroupTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaTipTimes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){missingOutgroup}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Following outgroup taxa have n...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){missingOutgroup}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){parseOriginalNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexusTaxa}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){nexusData}<LSEP>[](symbol){taxonNames}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){missingTip}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaTipTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxaTipTimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){nexusTaxa}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){missingNexus}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nexusTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nexusTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){taxaTipTimes}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){missingTip}<LSEP>[](symbol){missingNexus}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Following taxa in tipTimes not...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){missingTip}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 2; litteral](str){\nFollowing taxa in NEXUS file...}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){missingNexus}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nexusTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxaTipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Somehow have taxa missing from...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){taxaTipTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){nexusTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Nope, taxa in tipTimes and in ...}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){morphModel}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){morphModel must be of length 1}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){morphModel}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){relaxed}<LSEP>[argument 1; litteral](str){strong}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){morphModel must be one 'relaxe...}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){morphModel}<LSEP>[argument 1; litteral](str){relaxed}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Why are you relaxing the morph...}<LSEP>[argument 1; litteral](str){\n I hope you know what you ...}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){ngen}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ngen must be type character; i...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){createEmptyMorphMat}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.logical}<LSEP>[](symbol){createEmptyMorphMat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){createEmpthyMorphMat must be ...}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){orderedChars}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){orderedChars}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){orderedChars}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){orderedChars should only have ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){orderedChars}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){orderedChars}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){orderedChars}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){orderedChars}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){orderedChars cannot be coerced...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){orderedChars}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){orderedChars}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){orderedChars is not a numeric ...}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){cleanTaxonNames}<LSEP>[](symbol){taxaTipTimes}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){cleanTaxonNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cleanTaxonNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some taxon names were identica...}<LEND>[statement 21; control flow](){if}<LSEP>[](symbol){cleanNames}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cleanTaxonNames}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){cleanTaxonNames}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){cleanTaxonNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cleanTaxonNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some taxon names were identica...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outgroupTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outgroupTaxa}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){outgroupTaxa}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){treeConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeConstraints}<LSEP>[](symbol){tip.label}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){treeConstraints}<LSEP>[](symbol){tip.label}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){parseOriginalNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nexusTaxa}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){nexusTaxa}<LEND>[statement 22; control flow](){if}<LSEP>[](symbol){multOTU}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichAppearance}<LSEP>[argument 1; litteral](str){rangeThrough}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes must be a timeList ob...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origName}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rawIntervals}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){intervalMatrix}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){rawIntervals}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newNames}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){origName}<LSEP>[argument 1; litteral](str){_}<LEND>[argument 2; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){intervalMatrix}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){newOTU}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){newNames}<LSEP>[](symbol){origName}<LSEP>[](symbol){intervalMatrix}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichAppearance}<LSEP>[argument 1; litteral](str){firstLast}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){tipTimes if not a timeList obj...}<LSEP>[argument 1; litteral](str){ indicating uncertainty bound...}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){tipTimes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origName}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){intervalMatrix}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newNames}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){origName}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){_Fint}<LSEP>[argument 1; litteral](str){_Lint}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){newOTU}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){newNames}<LSEP>[](symbol){origName}<LSEP>[](symbol){intervalMatrix}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origName}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rawIntervals}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){intervalMatrix}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){rawIntervals}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newNames}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){origName}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){_Fint}<LSEP>[argument 1; litteral](str){_Lint}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){newOTU}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){newNames}<LSEP>[](symbol){origName}<LSEP>[](symbol){intervalMatrix}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newOTU}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){treeConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){treeTaxaExpand}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){treeTaxaExpand}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){treeConstraints}<LEND>[call](){}<LSEP>[](symbol){expandTaxonTree}<LSEP>[](symbol){treeConstraints}<LSEP>[](symbol){treeTaxaExpand}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){outgroupTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newOutgroupOTU}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){outgroupTaxa}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){outgroupTaxa}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){newOutgroupOTU}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){parseOriginalNexus}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphNexus}<LEND>[call](){}<LSEP>[](symbol){remakeDataBlockFun}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){cleanTaxonNames}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){taxonnames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newOTU}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){whichAppearance}<LSEP>[litteral](str){first}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxonnames}<LSEP>[](symbol){cleanTaxonNames}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){origNexusFile}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){createEmptyMorphMat}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphNexus}<LEND>[call](){}<LSEP>[](symbol){makeEmptyMorphNexusMrB}<LSEP>[](symbol){taxonnames}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphNexus}<LSEP>[litteral](str){ }<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){morphNexus}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){A morphological nexus was neit...}<LSEP>[argument 1; litteral](str){ Please contact dwbapst@gmai...}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){runName}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){newFile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){runName}<LSEP>[litteral](str){new_run_paleotree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){runName}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){newFile}<LSEP>[argument 1; litteral](str){\\\\}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){runName}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){runName}<LSEP>[argument 1; litteral](str){/}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){logfileline}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){log start filename = "}<LSEP>[](symbol){runName}<LSEP>[argument 2; litteral](str){.out" replace;}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){outputNameLine}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Filename = "}<LSEP>[](symbol){runName}<LSEP>[argument 2; litteral](str){"}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){treeConstraints}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ingroupConstraint}<LEND>[call](){}<LSEP>[](symbol){makeIngroupConstraintMrB}<LSEP>[](symbol){outgroupTaxa}<LSEP>[](symbol){taxonnames}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){topologicalConstraints}<LSEP>[litteral](str){ }<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ingroupConstraint}<LSEP>[litteral](str){ }<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){topologicalConstraints}<LEND>[call](){}<LSEP>[](symbol){createMrBayesConstraints}<LSEP>[](symbol){treeConstraints}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](NULL){NULL}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){ageCalibrations}<LEND>[call](){}<LSEP>[](symbol){createMrBayesTipCalibrations}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){ageCalibrationType}<LSEP>[](symbol){whichAppearance}<LSEP>[](symbol){treeAgeOffset}<LSEP>[](symbol){minTreeAge}<LSEP>[](symbol){collapseUniform}<LSEP>[](symbol){anchorTaxon}<LSEP>[argument 7; litteral](NULL){NULL}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){MrBayesBlock}<LEND>[call](){}<LSEP>[](symbol){makeMrBayesBlock}<LSEP>[](symbol){logfileline}<LSEP>[](symbol){ingroupConstraint}<LSEP>[](symbol){ageCalibrations}<LSEP>[](symbol){topologicalConstraints}<LSEP>[](symbol){orderedChars}<LSEP>[](symbol){autoCloseMrB}<LSEP>[](symbol){morphModel}<LSEP>[](symbol){morphFiltered}<LSEP>[](symbol){ngen}<LSEP>[](symbol){doNotRun}<LSEP>[](symbol){outputNameLine}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){finalText}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){morphNexus}<LSEP>[](symbol){MrBayesBlock}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){newFile}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){write}<LSEP>[](symbol){finalText}<LSEP>[](symbol){newFile}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){printExecute}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Now go to MrBayes and paste in...}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Execute "}<LEND>[argument 1; call](){}<LSEP>[](symbol){normalizePath}<LSEP>[](symbol){newFile}<LEND>[argument 2; litteral](str){";}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalText}<LEND>[assign](){<-}<LSEP>[](symbol){makeIngroupConstraintMrB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){outgroupTaxa}<LSEP>[](symbol){allTaxa}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){outgroupTaxa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){outgroupTaxa must be of length...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){outgroupTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){outgroupTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){outgroupTaxa must be a vector ...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){allTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){allTaxa}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxon labels cannot be turned ...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){notPresent}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){outgroupTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){allTaxa}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){notPresent}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Following outgroup taxa not pr...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){outgroupTaxa}<LSEP>[](symbol){notPresent}<LEND>[argument 1; litteral](str){ }<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){inGroup}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){allTaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){allTaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LSEP>[](symbol){outgroupTaxa}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){inGroup}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Less than two taxa are in the ...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ingroupBlock}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){constraint ingroup = }<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){inGroup}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 2; litteral](str){;}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){ingroupBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){ingroupBlock}<LSEP>[argument 1; litteral](str){prset topologypr = constraints...}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ingroupBlock}<LEND>[assign](){<-}<LSEP>[](symbol){makeEmptyMorphNexusMrB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxonNames}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){taxonNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){taxonNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxon names not formatted corr...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nTaxa}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){taxonNames}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nTaxa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){vector of taxon names is zero-...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){headMat}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){#NEXUS}<LSEP>[argument 1; litteral](str){BEGIN DATA;}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){DIMENSIONS NTAX = }<LSEP>[](symbol){nTaxa}<LSEP>[argument 2; litteral](str){ NCHAR = 1;}<LEND>[argument 3; litteral](str){FORMAT DATATYPE = STANDARD GAP...}<LSEP>[argument 4; litteral](str){MATRIX}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){endMat}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){;}<LSEP>[argument 2; litteral](str){END;}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){bodyMat}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){taxonNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){ ?}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){finalMatBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){headMat}<LSEP>[](symbol){bodyMat}<LSEP>[](symbol){endMat}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){finalMatBlock}<LEND>[litteral](NULL){NULL}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalMatBlock}<LEND>[assign](){<-}<LSEP>[](symbol){makeMrBayesBlock}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){logBlock}<LSEP>[](symbol){ingroupBlock}<LSEP>[](symbol){ageBlock}<LSEP>[](symbol){orderedChars}<LSEP>[](symbol){autoCloseMrB}<LSEP>[](symbol){constraintBlock}<LSEP>[](symbol){morphModel}<LSEP>[](symbol){morphFiltered}<LSEP>[](symbol){ngen}<LSEP>[](symbol){doNotRun}<LSEP>[](symbol){outputNameLine}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){block1}<LSEP>[litteral](str){\nbegin mrbayes;\n\n[This bloc...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){autoCloseMrB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){block1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){block1}<LSEP>[argument 1; litteral](str){set autoclose = yes;\n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){block1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){block1}<LSEP>[argument 1; litteral](str){[set autoclose = yes;]\n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){block2}<LSEP>[litteral](str){\n[DATA]\n\n[edits to taxon or...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){block3}<LSEP>[litteral](str){\t\n[TOPOLOGICAL CONSTRAINTS F...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){orderedChars}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){orderedChars}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ }<LSEP>[argument 1; litteral](str){[ordered characters block]}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){ctype ordered: }<LSEP>[](symbol){orderedChars}<LSEP>[argument 2; litteral](str){;}<LEND>[argument 3; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){orderedChars}<LSEP>[litteral](str){}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){morphFiltered}<LSEP>[argument 1; litteral](str){parsInf}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){filteredType}<LSEP>[litteral](str){informative}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){morphFiltered}<LSEP>[argument 1; litteral](str){variable}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){filteredType}<LSEP>[litteral](str){variable}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){filteredType}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){morphFiltered must be one of '...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){morphModelBlock_Strong}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){\n\n[CHARACTER MODELS]\n\t\n[m...}<LSEP>[](symbol){filteredType}<LSEP>[argument 2; litteral](str){; [equal rate variation]\n\t\t...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){morphModelBlock_Relaxed}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){\n\n[CHARACTER MODELS]\n\t\n[m...}<LSEP>[](symbol){filteredType}<LSEP>[argument 2; litteral](str){; [equal rate variation]]\n\t\...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){block4}<LSEP>[litteral](str){\n[TIP AND TREE AGE CALIBRATIO...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){block5a}<LSEP>[litteral](str){\t\n[FOSSILIZED BIRTH DEATH MO...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){block5b}<LSEP>[litteral](str){ relburnin = yes burninfrac = ...}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){runBlock}<LSEP>[litteral](str){\t\n\n[RUN]\n\tmcmc;\n\tsump;\...}<LEND>[statement 14; control flow](){if}<LSEP>[](symbol){doNotRun}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){runBlock}<LSEP>[litteral](str){ }<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){morphModel}<LSEP>[argument 1; litteral](str){strong}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphModelBlock}<LSEP>[](symbol){morphModelBlock_Strong}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){morphModel}<LSEP>[argument 1; litteral](str){relaxed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){morphModelBlock}<LSEP>[](symbol){morphModelBlock_Relaxed}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){block5}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){block5a}<LSEP>[](symbol){ngen}<LSEP>[argument 2; litteral](str){ }<LSEP>[](symbol){outputNameLine}<LSEP>[](symbol){block5b}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){finalBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){block1}<LSEP>[](symbol){logBlock}<LSEP>[](symbol){block2}<LSEP>[](symbol){ingroupBlock}<LSEP>[](symbol){block3}<LSEP>[](symbol){constraintBlock}<LSEP>[](symbol){orderedChars}<LSEP>[](symbol){morphModelBlock}<LSEP>[](symbol){block4}<LSEP>[](symbol){ageBlock}<LSEP>[](symbol){block5}<LSEP>[](symbol){runBlock}<LSEP>[argument 12; litteral](str){ }<LSEP>[argument 13; litteral](str){end;}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalBlock}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cladogeneticTraitCont}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxa}<LSEP>[](symbol){rate}<LSEP>[](symbol){meanChange}<LSEP>[](symbol){rootTrait}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxa}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Ancestors have higher IDs than...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){anctaxa}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){traits}<LSEP>[](symbol){rootTrait}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxa}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxa}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){traits}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){traits}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){anctaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rnorm}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){meanChange}<LEND>[argument 2; call](){}<LSEP>[](symbol){sqrt}<LSEP>[](symbol){rate}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){traits}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){traits}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){anctaxa}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){traits}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxa}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){traits}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){createMrBayesTipCalibrations}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){ageCalibrationType}<LSEP>[](symbol){whichAppearance}<LSEP>[](symbol){treeAgeOffset}<LSEP>[](symbol){minTreeAge}<LSEP>[](symbol){collapseUniform}<LSEP>[](symbol){anchorTaxon}<LSEP>[](symbol){file}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){tipTimes}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){why is tipTimes a list of not ...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ageCalibrationType}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){argument ageCalibrationType mu...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){whichAppearance}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){argument whichAppearance must ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){whichAppearance}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){first}<LSEP>[argument 1; litteral](str){last}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){argument whichAppearance must ...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ageCalibrationType}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){fixedDateEarlier}<LSEP>[argument 1; litteral](str){fixedDateLatter}<LSEP>[argument 2; litteral](str){fixedDateRandom}<LSEP>[argument 3; litteral](str){uniformRange}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){argument ageCalibrationType mu...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){treeAgeOffset}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){treeAgeOffset must be of length 1}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){minTreeAge}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){minTreeAge}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){minTreeAge must be of length 1}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){timeList2fourDate}<LSEP>[](symbol){tipTimes}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes must be of type matri...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes2}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.numeric}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes2}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){tipTimes2}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes must have 1 or 2 or 4...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){taxonNames}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ageCalibrationType}<LSEP>[argument 1; litteral](str){fixedDateEarlier}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){You appear to be supplying a s...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){anchorTaxon}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){anchorTaxon must be of length 1}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.logical}<LSEP>[](symbol){anchorTaxon}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pickFix}<LSEP>[](symbol){anchorTaxon}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){anchorTaxon}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ageCalibrationType}<LSEP>[argument 1; litteral](str){uniformRange}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anchorTaxon}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNames}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anchorTaxon}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){anchorTaxon}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){anchorTaxon must be of type ch...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pickFix}<LSEP>[litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){anchorTaxon}<LSEP>[](symbol){taxonNames}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){anchorTaxon appears to be a ta...}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){tipTimes}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){tipTimes}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes not coercing to matri...}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes not coercing to four ...}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){tipTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tipTimes not coercing to type ...}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){misorderedTimes}<LEND>[call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000100}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){misorderedTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){dates in tipTimes do not appea...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){misorderedTimes}<LEND>[argument 1; litteral](str){ }<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){misorderedTimes}<LEND>[call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){misorderedTimes}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){dates in tipTimes do not appea...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){misorderedTimes}<LEND>[argument 1; litteral](str){ }<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichAppearance}<LSEP>[argument 1; litteral](str){first}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){whichAppearance}<LSEP>[argument 1; litteral](str){last}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){tipTimes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird data format for tipTimes}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ageCalibrationType}<LSEP>[argument 1; litteral](str){fixedDateEarlier}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeType}<LSEP>[litteral](str){fixed}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ageCalibrationType}<LSEP>[argument 1; litteral](str){fixedDateLatter}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeType}<LSEP>[litteral](str){fixed}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ageCalibrationType}<LSEP>[argument 1; litteral](str){fixedDateRandom}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tipTimes}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tipTimes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeType}<LSEP>[litteral](str){fixed}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ageCalibrationType}<LSEP>[argument 1; litteral](str){uniformRange}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeType}<LSEP>[litteral](str){uniform}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){timeType}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){fixed}<LSEP>[argument 1; litteral](str){uniform}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Problem when selecting ages. a...}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){timeType}<LSEP>[argument 1; litteral](str){fixed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dateBlock}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){tipTimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){calibrate }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){i}<LEND>[argument 2; litteral](str){ = fixed (}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){i}<LEND>[argument 4; litteral](str){);}<LEND>[statement 34; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){timeType}<LSEP>[argument 1; litteral](str){uniform}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){collapseUniform}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fixCollapse}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){tipTimes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fixCollapse}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){tipTimes}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){pickFix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){fixCollapse}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){anchorTaxon not user-defined, ...}<LSEP>[](symbol){anchorTaxon}<LSEP>[argument 2; litteral](str){ to be a fixed tip age}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixCollapse}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){anchorTaxon}<LEND>[litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){anchorTaxon}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixCollapse}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){anchorTaxon}<LEND>[litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dateBlock}<LEND>[call](){}<LSEP>[](symbol){character}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){tipTimes}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dateBlock}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixCollapse}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dateBlock}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){calibrate }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){i}<LEND>[argument 2; litteral](str){ = fixed (}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 4; litteral](str){);}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dateBlock}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){calibrate }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){i}<LEND>[argument 2; litteral](str){ = uniform (}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 4; litteral](str){, }<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipTimes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 6; litteral](str){);}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){fixCollapse}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fixedLine}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){[These taxa had fixed tip ages:}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tipTimes}<LEND>[](symbol){fixCollapse}<LEND>[argument 1; litteral](str){ }<LEND>[argument 2; litteral](str){]}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fixedLine}<LSEP>[litteral](str){ }<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dateBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){dateBlock}<LSEP>[](symbol){fixedLine}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){minTipAge}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){tipTimes}<LEND>[statement 36; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){minTreeAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){minTreeAge}<LSEP>[](symbol){minTipAge}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){minTreeAge}<LSEP>[argument 1; litteral](real){1.000100}<LEND>[](symbol){minTipAge}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){User given minTreeAge is young...}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){meanTreeAge}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){minTreeAge}<LSEP>[](symbol){treeAgeOffset}<LEND>[statement 38; assign](){<-}<LSEP>[](symbol){treeAgeBlock}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){prset treeagepr = offsetexp(}<LSEP>[](symbol){minTreeAge}<LSEP>[argument 2; litteral](str){, }<LSEP>[](symbol){meanTreeAge}<LSEP>[argument 4; litteral](str){);}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){finalBlock}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){dateBlock}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){treeAgeBlock}<LEND>[statement 40; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){file}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){write}<LSEP>[](symbol){finalBlock}<LSEP>[](symbol){file}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalBlock}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){minBranchLength}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){mbl}<LSEP>[](symbol){modifyRootAge}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){edge.length}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Tree has no edge lengths}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){timetree}<LSEP>[](symbol){tree}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){mbl}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mbl}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){mbl is a not a single numeric ...}<LEND>[statement 4; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){mbl}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){shortEdge}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nedge}<LSEP>[](symbol){timetree}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){mbl}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){shortLength}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){shortEdge}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){shortestLength}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){shortEdge}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){shortLength}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){shortLength}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mom}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){shortestLength}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mom}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){mom}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ancestors}<LSEP>[](symbol){timetree}<LSEP>[](symbol){mom}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){selNodes}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mom}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){debt}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mbl}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){debt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mom}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mom}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selNodes_mom}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mom}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){selNodes_child}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mom}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){selNodes_MC}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){selNodes_mom}<LSEP>[](symbol){selNodes_child}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){selNodes_MnotC}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){selNodes_mom}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){selNodes_child}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){small}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes_mom}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){mom_blen}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes_MC}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){maxMBLdiff}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mom_blen}<LSEP>[](symbol){mbl}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){maxMBLsmall}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mbl}<LSEP>[](symbol){small}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){debt}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){debt}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){maxMBLdiff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){maxMBLsmall}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){smallDiff}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){maxMBLdiff}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){debt}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes_MC}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mom_blen}<LSEP>[](symbol){maxMBLsmall}<LEND>[](symbol){smallDiff}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes_MnotC}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){selNodes_MnotC}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){debt}<LSEP>[](symbol){i}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){timetree}<LSEP>[](symbol){root.time}<LEND>[](symbol){modifyRootAge}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timetree}<LEND>[call](){}<LSEP>[](symbol){fixRootTime}<LSEP>[](symbol){timetree}<LSEP>[](symbol){tree}<LSEP>[argument 2; litteral](str){rescaleUsingTipToRootDist}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){timetree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){translatePBDBtaxa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){convertAccepted}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[argument 1; litteral](str){}<LEND>[litteral](logical){NA}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[argument 0; litteral](str){rnk}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){acn}<LEND>[litteral](str){accepted_name}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){snp}<LEND>[litteral](str){senpar_no}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){rnk}<LEND>[litteral](str){taxon_rank}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){nam}<LEND>[litteral](str){taxon_name}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){fml}<LEND>[litteral](str){family}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){odl}<LEND>[litteral](str){order}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){cll}<LEND>[litteral](str){class}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){phl}<LEND>[litteral](str){phylum}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){kgl}<LEND>[litteral](str){kingdom}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){par}<LEND>[litteral](str){parent_no}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){oid}<LEND>[litteral](str){taxon_no}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){taxRankPBDB}<LEND>[call](){}<LSEP>[](symbol){getTaxRankPBDB}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){taxRankCOM}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){26.000000}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){taxon_rank}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){taxon_rank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxRankPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxRankCOM}<LEND>[statement 14; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){compact vocab detected, releva...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){rank}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){rank}<LEND>[litteral](str){taxon_rank}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){convertAccepted}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){accepted_name}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nameFormal}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){accepted_name}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nameFormal}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){nameFormal}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){nameFormal}<LEND>[argument 2; litteral](str){taxon_name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_name}<LEND>[](symbol){nameFormal}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){taxNum}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){accepted_no}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxNum}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxNum}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxNum}<LEND>[argument 2; litteral](str){taxon_no}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_no}<LEND>[](symbol){taxNum}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; litteral](str){senpar_no}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parNum}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){senpar_no}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parNum}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){parNum}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){parNum}<LEND>[argument 2; litteral](str){parent_no}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaDataPBDB}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){parent_no}<LEND>[](symbol){parNum}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){taxaDataPBDB}<LEND>[assign](){<-}<LSEP>[](symbol){getTaxRankPBDB}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){subspecies}<LSEP>[argument 1; litteral](str){species}<LSEP>[argument 2; litteral](str){subgenus}<LSEP>[argument 3; litteral](str){genus}<LSEP>[argument 4; litteral](str){subtribe}<LSEP>[argument 5; litteral](str){tribe}<LSEP>[argument 6; litteral](str){subfamily}<LSEP>[argument 7; litteral](str){family}<LSEP>[argument 8; litteral](str){superfamily}<LSEP>[argument 9; litteral](str){infraorder}<LSEP>[argument 10; litteral](str){suborder}<LSEP>[argument 11; litteral](str){order}<LSEP>[argument 12; litteral](str){superorder}<LSEP>[argument 13; litteral](str){infraclass}<LSEP>[argument 14; litteral](str){subclass}<LSEP>[argument 15; litteral](str){class}<LSEP>[argument 16; litteral](str){superclass}<LSEP>[argument 17; litteral](str){subphylum}<LSEP>[argument 18; litteral](str){phylum}<LSEP>[argument 19; litteral](str){superphylum}<LSEP>[argument 20; litteral](str){subkingdom}<LSEP>[argument 21; litteral](str){kingdom}<LSEP>[argument 22; litteral](str){unranked clade}<LSEP>[argument 23; litteral](str){informal}<LEND>[assign](){<-}<LSEP>[](symbol){convertParentChildMatNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxID}<LSEP>[](symbol){parData}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxMatch}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){taxID}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){taxMatch}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newName}<LSEP>[litteral](str){NODE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newName}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[](symbol){taxMatch}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newName}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){newName}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newName}<LEND>[assign](){<-}<LSEP>[](symbol){queryMissingParents}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaID}<LSEP>[](symbol){APIversion}<LSEP>[](symbol){status}<LSEP>[](symbol){convertAccepted}<LSEP>[](symbol){stopIfSelfParent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){floatData}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data}<LSEP>[](symbol){APIversion}<LSEP>[argument 2; litteral](str){/taxa/list.txt?taxon_id=}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){taxaID}<LSEP>[argument 1; litteral](str){,}<LEND>[argument 4; litteral](str){&rel=exact&status=}<LSEP>[](symbol){status}<LSEP>[argument 6; litteral](str){&vocab=pbdb}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){floatData}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Current PBDB API would not ret...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){taxaID}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){floatData}<LEND>[call](){}<LSEP>[](symbol){translatePBDBtaxa}<LSEP>[](symbol){floatData}<LSEP>[](symbol){convertAccepted}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){floatData}<LEND>[call](){}<LSEP>[](symbol){parseParentPBDBData}<LSEP>[](symbol){floatData}<LSEP>[](symbol){stopIfSelfParent}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){floatData}<LEND>[assign](){<-}<LSEP>[](symbol){parseParentPBDBData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){parentData}<LSEP>[](symbol){stopIfSelfParent}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){parentData}<LEND>[argument 1; litteral](str){accepted_name}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){taxon_name}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parentData}<LSEP>[](symbol){accepted_name}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){taxon_name}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parentData}<LSEP>[](symbol){taxon_name}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){taxon_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parentData}<LSEP>[](symbol){parent_no}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parentData}<LSEP>[](symbol){taxon_no}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){result}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){stopIfSelfParent}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){fixSelfParents}<LSEP>[](symbol){result}<LSEP>[argument 1; litteral](str){stop}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){findNoParentMatch}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){parData}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){parent_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){fixSelfParents}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dataParents}<LSEP>[](symbol){approach}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){selfParents}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataParents}<LSEP>[](symbol){parent_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataParents}<LSEP>[](symbol){taxon_no}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){selfParents}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){approach}<LSEP>[argument 1; litteral](str){clean}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dataParents}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataParents}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){selfParents}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){approach}<LSEP>[argument 1; litteral](str){stop}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parMatch}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataParents}<LSEP>[](symbol){taxon_name}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dataParents}<LSEP>[](symbol){taxon_no}<LEND>[argument 3; litteral](str){)}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){parMatch}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parMatch}<LSEP>[](symbol){selfParents}<LEND>[argument 1; litteral](str){, }<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){The following taxa (with taxon...}<LSEP>[](symbol){parMatch}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){dataParents}<LEND>[assign](){<-}<LSEP>[](symbol){getAllParents}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){inputData}<LSEP>[](symbol){status}<LSEP>[](symbol){annotatedDuplicateNames}<LSEP>[](symbol){convertAccepted}<LSEP>[](symbol){stopIfSelfParent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parData}<LEND>[call](){}<LSEP>[](symbol){parseParentPBDBData}<LSEP>[](symbol){inputData}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){noParentMatch}<LEND>[call](){}<LSEP>[](symbol){findNoParentMatch}<LSEP>[](symbol){parData}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){floatingParentNumOld}<LSEP>[litteral](logical){NA}<LEND>[statement 3; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){noParentMatch}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){floatingParentNum}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){parent_no}<LEND>[](symbol){noParentMatch}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){floatingParentNumOld}<LSEP>[](symbol){floatingParentNum}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){convertAccepted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){convertAccepted}<LSEP>[litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dataUrlRef}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){http://paleobiodb.org/data}<LSEP>[argument 1; litteral](real){1.200000}<LSEP>[argument 2; litteral](str){/taxa/list.txt?taxon_id=}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){floatingParentNum}<LSEP>[argument 1; litteral](str){,}<LEND>[argument 4; litteral](str){&rel=exact&status=}<LSEP>[](symbol){status}<LSEP>[argument 6; litteral](str){&vocab=pbdb}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){dataNew}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){PBDB not returning single comm...}<LSEP>[argument 1; litteral](str){Following floating parent numb...}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){floatingParentNum}<LSEP>[argument 1; litteral](str){, }<LEND>[argument 3; litteral](str){\nThese were not resolved with...}<LSEP>[argument 4; litteral](str){\nCheck the following URL:\n}<LSEP>[](symbol){dataUrlRef}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){floatingParentNumOld}<LSEP>[](symbol){floatingParentNum}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dataNew}<LEND>[call](){}<LSEP>[](symbol){queryMissingParents}<LSEP>[](symbol){floatingParentNum}<LSEP>[](symbol){status}<LSEP>[](symbol){convertAccepted}<LSEP>[](symbol){stopIfSelfParent}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){parData}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){dataNew}<LSEP>[](symbol){parData}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){noParentMatch}<LEND>[call](){}<LSEP>[](symbol){findNoParentMatch}<LSEP>[](symbol){parData}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){parData}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){parData}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){parData}<LEND>[call](){}<LSEP>[](symbol){fixSelfParents}<LSEP>[](symbol){parData}<LSEP>[argument 1; litteral](str){clean}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){noParentMatch}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot find a single common an...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){parData}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){parData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parData}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){parData}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getAllParents added duplicate ...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parData}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getAllParents added duplicate ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Additional accepted parent tax...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){annotatedDuplicateNames}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[call](){}<LSEP>[](symbol){make.unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parData}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getAllParents added duplicate ...}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){parData}<LEND>[assign](){<-}<LSEP>[](symbol){getFloatAncPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){pcDat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){noChildren}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pcDat}<LSEP>[](symbol){parent_no}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pcDat}<LSEP>[](symbol){child_no}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pcDat}<LSEP>[](symbol){parent_no}<LEND>[](symbol){noChildren}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){constructParentChildMatrixPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){initPCmat}<LSEP>[](symbol){parData}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){initPCmat}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){initPCmat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){initPCmat}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){initPCmat}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){initial parent-child matrix ha...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newPCmat}<LSEP>[](symbol){initPCmat}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){floaters}<LEND>[call](){}<LSEP>[](symbol){getFloatAncPBDB}<LSEP>[](symbol){newPCmat}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){floaters}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){floaters}<LEND>[statement 4; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){floaters}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anchorMat}<LEND>[call](){}<LSEP>[](symbol){subsetParDataPBDB}<LSEP>[](symbol){floaters}<LSEP>[](symbol){parData}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newPCmat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){newPCmat}<LSEP>[](symbol){anchorMat}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newPCmat}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){newPCmat}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){newPCmat}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){newPCmat}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){annotated pcMat had duplicate ...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){floatersNew}<LEND>[call](){}<LSEP>[](symbol){getFloatAncPBDB}<LSEP>[](symbol){newPCmat}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){floatersNew}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){floaters}<LSEP>[](symbol){floatersNew}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Provided PBDB Dataset does not...}<LSEP>[argument 1; litteral](str){ monophyletic set of parent-c...}<LSEP>[argument 2; litteral](str){Multiple taxa appear to be lis...}<LSEP>[argument 3; litteral](str){ listed themselves so have no...}<LEND>[argument 4; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){floaters}<LSEP>[argument 1; litteral](str){, }<LEND>[argument 5; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){floaters}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[argument 1; litteral](str){, }<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){floaters}<LSEP>[](symbol){floatersNew}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){newPCmat}<LEND>[assign](){<-}<LSEP>[](symbol){subsetParDataPBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){subsetNum}<LSEP>[](symbol){parData}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){subsetNum}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){subsetNum}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some values of subsetNum are n...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){subsetRows}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){subsetNum}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){subsetRows}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){subsetRows}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){subsetRows}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){subsetRows}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){subsetRows}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){Total subsetRows:}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){subsetRows}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){Duplicates:}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dupSSR}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){subsetRows}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){subsetRows}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){subsetRows}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){subsetRows}<LEND>[statement 4; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){dupSSR}<LEND>[statement 5; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){Rows in Questions:}<LEND>[statement 6; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parData}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){dupSSR}<LEND>[](symbol){}<LEND>[statement 7; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Stop - the subset selected by ...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){subsetMat}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){parent_no}<LEND>[](symbol){subsetRows}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[](symbol){subsetRows}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){numSubset}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[](symbol){subsetRows}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){numSubset}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){numSubset}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){duplicatedValues}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){numSubset}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){numSubset}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){duplicatedRows}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){duplicatedValues}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){All Taxon Numbers:}<LEND>[statement 3; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){parData}<LSEP>[](symbol){taxon_no}<LEND>[statement 4; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){The Subset Taxon Numbers:}<LEND>[statement 5; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){numSubset}<LEND>[statement 6; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){The Rows of parData Containing...}<LEND>[statement 7; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parData}<LSEP>[](symbol){duplicatedRows}<LSEP>[](symbol){}<LEND>[statement 8; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getAllParents added duplicate ...}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){subsetMat}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){numSubset}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){subsetMat}<LEND>[assign](){<-}<LSEP>[](symbol){getLinneanTaxonTreePBDB}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LSEP>[](symbol){rankTaxon}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dataTransform}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){dataTransform}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.character}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){dataTransform}<LEND>[argument 1; litteral](str){family}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){taxaDataPBDB must be a taxonom...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tipSet}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Linnean taxon-tree option sele...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nDup}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){dataTransform}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](str){taxon_name}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){x}<LSEP>[argument 2; litteral](str){taxon_rank}<LEND>[](symbol){rankTaxon}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){nDup}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Duplicate taxa of selected rank: }<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){(}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){nDup}<LEND>[argument 2; litteral](str){) }<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){nDup}<LSEP>[argument 2; litteral](str){taxon_name}<LEND>[argument 4; litteral](str){, }<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dataTransform}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_rank}<LEND>[](symbol){rankTaxon}<LEND>[](symbol){}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){taxonFields}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){phylum}<LSEP>[argument 1; litteral](str){class}<LSEP>[argument 2; litteral](str){order}<LSEP>[argument 3; litteral](str){family}<LSEP>[argument 4; litteral](str){taxon_name}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){taxonData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[](symbol){taxonFields}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){taxonData}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){taxonData}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.character}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){taxonTable2taxonTree}<LSEP>[](symbol){taxonData}<LSEP>[](symbol){cleanTree}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){taxonTable}<LEND>[](symbol){taxonData}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}<LEND>[assign](){<-}<LSEP>[](symbol){parentChildPBDBOld}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LSEP>[](symbol){method}<LSEP>[](symbol){APIversion}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dataTransform}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){dataTransform}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.character}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxRankPBDB}<LEND>[call](){}<LSEP>[](symbol){getTaxRankPBDB}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rankID}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rank}<LSEP>[](symbol){taxRankPBDB}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){numTaxonRank}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_rank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxRankPBDB}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dataTransform}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){rankID}<LSEP>[](symbol){numTaxonRank}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){numTaxonRank}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_rank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){taxRankPBDB}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){taxonNameTable}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){accepted_name}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){parentFloat}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){parent_no}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){parentFloat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentFloat}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){parentFloat}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){taxonNameTable}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){parentFloat}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ID:}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){parentFloat}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){pcAll}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){parent_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataTransform}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_no}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcAll}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rankID}<LSEP>[](symbol){numTaxonRank}<LEND>[](symbol){}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){floaters}<LEND>[call](){}<LSEP>[](symbol){getFloatAncPBDB}<LSEP>[](symbol){pcMat}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){nCount}<LSEP>[litteral](real){0.000000}<LEND>[statement 14; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){floaters}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nCount}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nCount}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){anchors}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){floaters}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcAll}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){pcMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcAll}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){anchors}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){anchors}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){floatersNew}<LEND>[call](){}<LSEP>[](symbol){getFloatAncPBDB}<LSEP>[](symbol){pcMat}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){floatersNew}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){floaters}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){floatersNew}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){parentChildOldQueryPBDB}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){floatData}<LEND>[call](){}<LSEP>[](symbol){queryMissingParents}<LSEP>[](symbol){floatersNew}<LSEP>[](symbol){APIversion}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){whichUpdate}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){floatData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){taxon_no}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){replaceFloatName}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){floatData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){whichUpdate}<LEND>[argument 2; litteral](str){taxon_name}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){whichUpdate}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){whichUpdate}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){whichUpdate}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){whichUpdate}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){replaceFloatName}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){parentFloat}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){floatData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){parent_no}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){matchingFloat}<LEND>[call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){parentFloat}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){parentFloat}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){parentFloat}<LSEP>[](symbol){matchingFloat}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parentFloat}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){taxonNameTable}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){parentFloat}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ID:}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){parentFloat}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){newEntries}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){floatData}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){parent_no}<LSEP>[argument 1; litteral](str){taxon_no}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){pcMat}<LSEP>[](symbol){newEntries}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){pcAll}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){pcAll}<LSEP>[](symbol){newEntries}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){parentChildOldMergeRoot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){pcMat}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[argument 0; litteral](str){ArtificialRoot}<LSEP>[](symbol){floaters}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){taxonNameTable}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ArtificialRoot}<LSEP>[argument 1; litteral](str){ArtificialRoot}<LEND>[statement 2; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Multiple potential root-taxa a...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){floaters}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){floaters}<LEND>[call](){}<LSEP>[](symbol){getFloatAncPBDB}<LSEP>[](symbol){pcMat}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){floatersNew}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){floaters}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){floatersNew}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Provided PBDB Dataset does not...}<LSEP>[argument 1; litteral](str){ monophyletic set of parent-c...}<LSEP>[argument 2; litteral](str){Multiple taxa appear to be lis...}<LSEP>[argument 3; litteral](str){ listed themselves so have no...}<LEND>[argument 4; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){floaters}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](str){, }<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){floaters}<LSEP>[](symbol){floatersNew}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){pcMat}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pcMat}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.character}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){parentChild2taxonTree}<LSEP>[](symbol){pcMat}<LSEP>[](symbol){tipSet}<LSEP>[](symbol){cleanTree}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){node.label}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){node.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxonNameTable}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){parentChild}<LEND>[](symbol){pcMat}<LEND>[statement 20; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tree}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cal3TimePaleoPhy}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeData}<LSEP>[](symbol){brRate}<LSEP>[](symbol){extRate}<LSEP>[](symbol){sampRate}<LSEP>[](symbol){ntrees}<LSEP>[](symbol){anc.wt}<LSEP>[](symbol){node.mins}<LSEP>[](symbol){dateTreatment}<LSEP>[](symbol){FAD.only}<LSEP>[](symbol){adj.obs.wt}<LSEP>[](symbol){root.max}<LSEP>[](symbol){step.size}<LSEP>[](symbol){randres}<LSEP>[](symbol){noisyDrop}<LSEP>[](symbol){verboseWarnings}<LSEP>[](symbol){diagnosticMode}<LSEP>[](symbol){tolerance}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){timeData}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData not of matrix or data...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ntrees cannot be less than 1}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){verboseWarnings}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Do not interpret a single cal3...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstLast}<LSEP>[argument 1; litteral](str){minMax}<LSEP>[argument 2; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dateTreatment must be one of '...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[](symbol){FAD.only}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){FAD.only = TRUE is inapplicabl...}<LSEP>[argument 1; litteral](str){'randObs' assumes dates of obs...}<LSEP>[argument 2; litteral](str){ And thus there is no sensib...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[](symbol){FAD.only}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){FAD.only = TRUE is inapplicabl...}<LSEP>[argument 1; litteral](str){'minMax' assumes dates of obse...}<LSEP>[argument 2; litteral](str){ And thus taxa are not consi...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Absolutely NO valid taxa share...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){noisyDrop}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Warning: Following taxa droppe...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){droppers}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){droppers}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Less than two valid taxa share...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){whichDropperRows}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){whichDropperRows}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[litteral](logical){NA}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){node.mins not compatible with ...}<LSEP>[argument 1; litteral](str){Please drop taxa and check nod...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){node.mins must be same length ...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){timeData}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Weird NAs in Data??}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeData is not in time relati...}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate taxa in timeList[[2]]}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate tip taxon names in t...}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Odd irreconcilable mismatch be...}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sampRate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sampRate}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){sampRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sampRate}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sampRate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Sampling Rates Not Given For A...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){brRate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){brRate}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){brRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){brRate}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){brRate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Branching Rates Not Given For ...}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){extRate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){extRate}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){extRate}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){extRate}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){extRate}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Extinction Rates Not Given For...}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){anc.wt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anc.wt}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){anc.wt}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){anc.wt}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){anc.wt}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Ancestral Weights Not Given Fo...}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){Ps}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){pqr2Ps}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brRate}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){extRate}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampRate}<LSEP>[](symbol){x}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){Ps}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node.mins}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){locked_nodesOrig}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){node.mins}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){locked_nodesOrig}<LSEP>[litteral](logical){NA}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttree1}<LEND>[call](){}<LSEP>[](symbol){timePaleoPhy}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeData}<LSEP>[argument 2; litteral](str){basic}<LSEP>[argument 3; litteral](str){firstLast}<LSEP>[](symbol){node.mins}<LSEP>[argument 5; litteral](logical){FALSE}<LSEP>[argument 6; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ttree1}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){ttree1}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){rmtree}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){sampledLogLike}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 26; control flow](){for}<LSEP>[](symbol){ntr}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntrees}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[](symbol){FAD.only}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){FAD.only}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){timeData1}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){timeData1}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ttree1}<LEND>[call](){}<LSEP>[](symbol){timePaleoPhy}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeData1}<LSEP>[argument 2; litteral](str){basic}<LSEP>[argument 3; litteral](str){firstLast}<LSEP>[](symbol){node.mins}<LSEP>[argument 5; litteral](logical){FALSE}<LSEP>[argument 6; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){ttree1}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){ttree1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){timeData}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeData}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){randres}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){is.binary.phylo}<LEND>[](symbol){ttree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.rooted}<LSEP>[](symbol){ttree1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ktree}<LEND>[call](){}<LSEP>[](symbol){multi2di}<LSEP>[](symbol){ttree1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){locked_nodesOrig}<LSEP>[argument 1; litteral](logical){NA}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){origDesc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){ttree1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){treeDesc}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){ktree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){node_changes}<LEND>[call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){origDesc}<LSEP>[](symbol){treeDesc}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){locked_nodes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){node_changes}<LSEP>[](symbol){locked_nodesOrig}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){locked_nodes}<LSEP>[](symbol){locked_nodesOrig}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ktree}<LSEP>[](symbol){ttree1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){locked_nodes}<LSEP>[](symbol){locked_nodesOrig}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){anags}<LEND>[call](){}<LSEP>[](symbol){character}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){budds}<LEND>[call](){}<LSEP>[](symbol){character}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nAdjZip}<LSEP>[litteral](real){0.000000}<LEND>[statement 7; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nodes}<LEND>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){diagnosticMode}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){save_tree}<LSEP>[](symbol){ktree}<LEND>[statement 1; call](){}<LSEP>[](symbol){dev.new}<LEND>[statement 2; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){ktree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){node}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tipl}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tipd}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ttree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){tipl}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){tipl}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sampRate}<LSEP>[](symbol){tipl}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){brRate}<LSEP>[](symbol){tipl}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){extRate}<LSEP>[](symbol){tipl}<LEND>[argument 6; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Ps}<LSEP>[](symbol){tipl}<LEND>[argument 7; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){anc.wt}<LSEP>[](symbol){tipl}<LEND>[argument 8; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){tipl}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){node}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){min_zip}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){root.max}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){root.max}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){min_zip}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){node}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stem_len}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){node}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dnodes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){node}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){dlen}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){minlocked}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){locked_nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){node}<LSEP>[](symbol){locked_nodes}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dnodes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dSR}<LEND>[assign](){<-}<LSEP>[](symbol){drng}<LEND>[assign](){<-}<LSEP>[](symbol){dBR}<LEND>[assign](){<-}<LSEP>[](symbol){dER}<LEND>[assign](){<-}<LSEP>[](symbol){dPs}<LEND>[assign](){<-}<LSEP>[](symbol){danc.wt}<LEND>[assign](){<-}<LSEP>[](symbol){ddfLAD}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){dnodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dtips}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dearly}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dtips}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dtips}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dSR}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dSR}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dearly}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dBR}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dBR}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dearly}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dER}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dER}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dearly}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dPs}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dPs}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dearly}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){danc.wt}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){danc.wt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dearly}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ddfLAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ddfLAD}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dearly}<LSEP>[argument 2; litteral](real){9.000000}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drng}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){drng}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dtips}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){dtips}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dnode1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dlen}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){dlen}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){plin}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dlen}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[](symbol){stem_len}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drng}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[argument 3; litteral](logical){NA}<LSEP>[argument 4; litteral](real){0.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dlen}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[](symbol){stem_len}<LEND>[argument 6; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dlen}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drng}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[](symbol){stem_len}<LEND>[argument 7; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){danc.wt}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ddfLAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnode1}<LSEP>[](symbol){dnodes}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){plin}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){plin}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){plin}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){node}<LSEP>[argument 1; litteral](str){brl}<LSEP>[argument 2; litteral](str){rng}<LSEP>[argument 3; litteral](str){anc}<LSEP>[argument 4; litteral](str){tSpec}<LSEP>[argument 5; litteral](str){tFO}<LSEP>[argument 6; litteral](str){tLO}<LSEP>[argument 7; litteral](str){ancWt}<LSEP>[argument 8; litteral](str){diffLAD}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){add_nodes}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){dnodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dlen}<LSEP>[](symbol){stem_len}<LEND>[](symbol){drng}<LSEP>[](symbol){dSR}<LSEP>[](symbol){dBR}<LSEP>[](symbol){dER}<LSEP>[](symbol){dPs}<LSEP>[](symbol){danc.wt}<LSEP>[](symbol){ddfLAD}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){add_nodes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnodes}<LSEP>[](symbol){dnode1}<LEND>[](symbol){}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){add_nodes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dlen}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dnodes}<LSEP>[](symbol){dnode1}<LEND>[](symbol){}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){add_nodes}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){node}<LSEP>[argument 1; litteral](str){dstem}<LSEP>[argument 2; litteral](str){rng}<LSEP>[argument 3; litteral](str){SR}<LSEP>[argument 4; litteral](str){BR}<LSEP>[argument 5; litteral](str){ER}<LSEP>[argument 6; litteral](str){Ps}<LSEP>[argument 7; litteral](str){ancWt}<LSEP>[argument 8; litteral](str){diffLAD}<LEND>[statement 10; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){add_nodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zips}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){plin}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){min_zip}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){max_zip}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){minlocked}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){max_zip}<LSEP>[](symbol){stem_len}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){poss_zip}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){min_zip}<LSEP>[](symbol){max_zip}<LSEP>[](symbol){step.size}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){gap1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[](symbol){poss_zip}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){gap1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){gap1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){gap1}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){gap2}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){poss_zip}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){gapStem2zip}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[](symbol){poss_zip}<LEND>[](symbol){poss_zip}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){totalgap}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){gap1}<LSEP>[](symbol){gap2}<LEND>[](symbol){gapStem2zip}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){linDense}<LEND>[call](){}<LSEP>[](symbol){dgamma}<LSEP>[](symbol){totalgap}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){linDense}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){poss_zip}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){linDense}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[](symbol){linDense}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[argument 2; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[](symbol){step.size}<LEND>[](symbol){adj.obs.wt}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){9.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){adj_max}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){adj_zips}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[](symbol){step.size}<LEND>[](symbol){adj_max}<LSEP>[](symbol){step.size}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){gap1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[](symbol){adj_zips}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gap1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){gap1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){gap1}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){gap2}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){adj_zips}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){gapStem2zip}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[](symbol){adj_zips}<LEND>[](symbol){adj_zips}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){adj_totalgap}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){gap1}<LSEP>[](symbol){gap2}<LEND>[](symbol){gapStem2zip}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){adj_linDense}<LEND>[call](){}<LSEP>[](symbol){dgamma}<LSEP>[](symbol){adj_totalgap}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDense}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){linDense}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDense}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){linDense}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){adj_linDense}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nAdjZip}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nAdjZip}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){new_zip}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){linDense}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){poss_zip}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){zips}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){zips}<LSEP>[](symbol){new_zip}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){zips}<LEND>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zips}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zips}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zips}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zips}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){zips}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){linDensity}<LSEP>[argument 1; litteral](str){anc}<LSEP>[argument 2; litteral](str){tzip}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){zip_prob}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zips}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zip_prob}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){zip_prob}<LEND>[litteral](real){0.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){zip_prob}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zip_prob}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){zip_prob}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){zip_prob}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){zip_prob}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){zip_prob}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){ch_zip}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){zips}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){zip_prob}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){sampledLogLike}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){sampledLogLike}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zip_prob}<LSEP>[](symbol){ch_zip}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){ch_anc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zips}<LSEP>[](symbol){ch_zip}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){ch_tzip}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zips}<LSEP>[](symbol){ch_zip}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ch_anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){7.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ch_anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){7.000000}<LEND>[](symbol){ch_tzip}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anags}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){anags}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){ch_anc}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ch_anc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){6.000000}<LEND>[](symbol){ch_tzip}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){budds}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){budds}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){ch_anc}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){new_lin}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){ch_tzip}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){ch_anc}<LSEP>[](symbol){ch_tzip}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_nodes}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){9.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){plin}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){plin}<LSEP>[](symbol){new_lin}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){taxad_o}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){plin}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){7.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){7.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){new_anc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_o}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_o}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){taxad_n}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxad_o}<LEND>[](symbol){new_anc}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_o}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_n}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_n}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_n}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){taxad_n}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxad_o}<LEND>[argument 2; litteral](str){}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){subtree}<LEND>[call](){}<LSEP>[](symbol){taxa2phylo}<LSEP>[](symbol){taxad_n}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){matchSubTreeTaxaLab}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){subtree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){taxad_o}<LEND>[argument 2; litteral](str){}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){subtree}<LSEP>[](symbol){tip.label}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxad_o}<LSEP>[](symbol){matchSubTreeTaxaLab}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){new_stem}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plin}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){dnodes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dtip}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){subtree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){subclade}<LEND>[call](){}<LSEP>[](symbol){extract.clade}<LSEP>[](symbol){ktree}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){subtree}<LEND>[call](){}<LSEP>[](symbol){bind.tree}<LSEP>[](symbol){subtree}<LSEP>[](symbol){subclade}<LSEP>[](symbol){dtip}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){subtree}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){subtree}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){subtree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){dtip}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){i}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){node}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){drtips}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){prop.part}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){node}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tip_lab}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drtips}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){droptree}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LEND>[argument 0; call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){drtips}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){edgeLeadNew}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){droptree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){droptree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){tip_lab}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){droptree}<LSEP>[](symbol){edge.length}<LEND>[](symbol){edgeLeadNew}<LEND>[](symbol){new_stem}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){droptree}<LEND>[call](){}<LSEP>[](symbol){bind.tree}<LSEP>[](symbol){droptree}<LSEP>[](symbol){subtree}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){droptree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){tip_lab}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ktree1}<LSEP>[](symbol){droptree}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ktree1}<LSEP>[](symbol){subtree}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nodes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){d_o}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){d_n}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree1}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree1}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nodes1}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){d_o}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){d_n}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nodes1}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree1}<LEND>[](symbol){nodes1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){nodes1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes1}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth}<LSEP>[](symbol){ktree1}<LEND>[](symbol){nodes1}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){locked_nodes}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){d_ol}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LSEP>[](symbol){locked_nodes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){locked_nodes}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){d_ol}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){d_n}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){locked_nodes}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree1}<LEND>[](symbol){locked_nodes}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodes1}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 23; control flow](){if}<LSEP>[](symbol){diagnosticMode}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){save_tree}<LEND>[statement 2; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){ktree1}<LEND>[statement 3; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){ktree1}<LEND>[call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){ktree1}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){ktree}<LSEP>[](symbol){ktree1}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){nodes}<LSEP>[](symbol){nodes1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dlen1}<LEND>[call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){dlen}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dlen2}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dlen}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dnode1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dlen}<LSEP>[](symbol){dlen1}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dnode2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dnodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){dnodes}<LSEP>[](symbol){dnode1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){d2FADs}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){d2early}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){d2FADs}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){d2FADs}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){d2early}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){d2early}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sample}<LSEP>[](symbol){d2early}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){d2early}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){d2SR}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){4.000000}<LEND>[](symbol){d2early}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){d2BR}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){5.000000}<LEND>[](symbol){d2early}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){d2Ps}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){Descendants}<LSEP>[](symbol){ktree}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){7.000000}<LEND>[](symbol){d2early}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){d1rng}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](logical){NA}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){d2rng}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](logical){NA}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){d1ancWt}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){8.000000}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){d1diffLAD}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipd}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){9.000000}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){max_zip}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){d1ancWt}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){d1rng}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){d1rng}<LEND>[](symbol){dlen2}<LEND>[](symbol){dlen1}<LEND>[statement 15; control flow](){if}<LSEP>[](symbol){minlocked}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){max_zip}<LSEP>[litteral](real){0.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){poss_zip}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){min_zip}<LSEP>[](symbol){max_zip}<LSEP>[](symbol){step.size}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){gap1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){poss_zip}<LSEP>[](symbol){dlen1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){poss_zip}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){gap2}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dlen2}<LSEP>[](symbol){poss_zip}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){gapStem2zip}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){dlen1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){poss_zip}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){poss_zip}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){dlen1}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){totalgap}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){gap1}<LSEP>[](symbol){gap2}<LEND>[](symbol){gapStem2zip}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){linDense}<LEND>[call](){}<LSEP>[](symbol){dgamma}<LSEP>[](symbol){totalgap}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d2SR}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d2BR}<LSEP>[](symbol){d2Ps}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){linDensity}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){dlen1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){poss_zip}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d1ancWt}<LSEP>[](symbol){linDense}<LEND>[](symbol){linDense}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){adj.obs.wt}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){d1ancWt}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){d1diffLAD}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){d1rng}<LEND>[](symbol){step.size}<LEND>[](symbol){dlen2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){adj_max}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dlen2}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d1diffLAD}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){d1rng}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){adj_zips}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){d1rng}<LEND>[](symbol){step.size}<LEND>[](symbol){adj_max}<LSEP>[](symbol){step.size}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){gap1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){adj_zips}<LSEP>[](symbol){dlen1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){adj_zips}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gap2}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dlen2}<LSEP>[](symbol){adj_zips}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){gapStem2zip}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){dlen1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){adj_zips}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){adj_zips}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){stem_len}<LSEP>[](symbol){dlen1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){adj_totalgap}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){gap1}<LSEP>[](symbol){gap2}<LEND>[](symbol){gapStem2zip}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){adj_linDense}<LEND>[call](){}<LSEP>[](symbol){dgamma}<LSEP>[](symbol){totalgap}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d2SR}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d2BR}<LSEP>[](symbol){d2Ps}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDensity}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){linDensity}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDensity}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){linDensity}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){adj_linDense}<LSEP>[](symbol){d1ancWt}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){nAdjZip}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nAdjZip}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDensity}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){linDensity}<LEND>[litteral](real){0.000000}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){linDensity}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDensity}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){linDensity}<LEND>[litteral](real){1.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){linDensity1}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){linDensity}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){linDensity}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){ch_zip}<LEND>[call](){}<LSEP>[](symbol){sample}<LSEP>[](symbol){poss_zip}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){linDensity1}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){sampledLogLike}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){sampledLogLike}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linDensity1}<LSEP>[](symbol){ch_zip}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){new_dlen1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){ch_zip}<LSEP>[](symbol){dlen1}<LEND>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){ch_zip}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){new_dlen2}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dlen2}<LSEP>[](symbol){ch_zip}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){new_dlen1}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ch_zip}<LSEP>[](symbol){max_zip}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dlen1}<LSEP>[](symbol){d1rng}<LEND>[](symbol){dlen2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){anags}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){anags}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){dnode1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){new_dlen1}<LSEP>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){budds}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){budds}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){dnode1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){new_dlen1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d1rng}<LSEP>[](symbol){dlen1}<LEND>[](symbol){ch_zip}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){new_dlen1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){d1rng}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){new_dlen1}<LSEP>[](symbol){d1rng}<LEND>[](symbol){new_dlen1}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){new_dlen2}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){d2rng}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){new_dlen2}<LSEP>[](symbol){d2rng}<LEND>[](symbol){new_dlen2}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){node}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){node}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ch_zip}<LSEP>[](symbol){min_zip}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnode1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){new_dlen1}<LEND>[statement 35; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){dnode2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){new_dlen2}<LEND>[statement 36; control flow](){if}<LSEP>[](symbol){diagnosticMode}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){node}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ch_zip}<LSEP>[](symbol){min_zip}<LEND>[](symbol){new_dlen1}<LSEP>[](symbol){new_dlen2}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nodes}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){ktree}<LEND>[call](){}<LSEP>[](symbol){reorder}<LEND>[argument 0; call](){}<LSEP>[](symbol){collapse.singles}<LSEP>[](symbol){ktree}<LEND>[argument 1; litteral](str){cladewise}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[litteral](NULL){NULL}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){budd.tips}<LEND>[litteral](NULL){NULL}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){anag.tips}<LEND>[litteral](NULL){NULL}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){anag.tips}<LEND>[](symbol){anags}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){budd.tips}<LEND>[](symbol){budds}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){nAdjZip}<LEND>[](symbol){nAdjZip}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){sampledLogLike}<LEND>[](symbol){sampledLogLike}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){sumLogLike}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sampledLogLike}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){root.time}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){timeData1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){timeDataUsed}<LEND>[](symbol){timeData1}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){tipdiffs}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){test1}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tipdiffs}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){tolerance}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){test2}<LEND>[call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ktree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){ktree}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){timeData1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){test2}<LSEP>[litteral](logical){TRUE}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){test1}<LSEP>[](symbol){test2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){test}<LEND>[litteral](str){passed}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){tipdiffs}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ktree_test_messsage}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Tip age tests failed: \n}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LSEP>[](symbol){test1}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){Tip dates returned are differe...}<LEND>[argument 2; call](){}<LSEP>[](symbol){ifelse}<LSEP>[](symbol){test2}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){Order of tip dates disagrees w...}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){test}<LEND>[](symbol){ktree_test_messsage}<LEND>[statement 3; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Warning: Terminal tips imprope...}<LSEP>[argument 1; litteral](str){ cause unknown. Use output wit...}<LSEP>[](symbol){ktree_test_messsage}<LEND>[statement 26; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parOrig}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.500000}<LSEP>[argument 1; litteral](real){2.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){2.500000}<LEND>[statement 2; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){}<LEND>[statement 3; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){ttree1}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 5; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 6; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){ladderize}<LSEP>[](symbol){ktree}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 7; call](){}<LSEP>[](symbol){axisPhylo}<LEND>[statement 8; call](){}<LSEP>[](symbol){layout}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 9; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){parOrig}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ktree}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[](symbol){ntr}<LEND>[](symbol){ktree}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 28; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ttrees}<LEND>[assign](){<-}<LSEP>[](symbol){bin_cal3TimePaleoPhy}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeList}<LSEP>[](symbol){brRate}<LSEP>[](symbol){extRate}<LSEP>[](symbol){sampRate}<LSEP>[](symbol){ntrees}<LSEP>[](symbol){anc.wt}<LSEP>[](symbol){node.mins}<LSEP>[](symbol){dateTreatment}<LSEP>[](symbol){FAD.only}<LSEP>[](symbol){sites}<LSEP>[](symbol){point.occur}<LSEP>[](symbol){nonstoch.bin}<LSEP>[](symbol){adj.obs.wt}<LSEP>[](symbol){root.max}<LSEP>[](symbol){step.size}<LSEP>[](symbol){randres}<LSEP>[](symbol){noisyDrop}<LSEP>[](symbol){verboseWarnings}<LSEP>[](symbol){tolerance}<LSEP>[](symbol){diagnosticMode}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree is not of class phylo}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not of matrix or...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){data.frame}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not of matrix or...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Instead of dateTreatment = 'mi...}<LSEP>[argument 1; litteral](str){ argument point.occur instead ...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){firstLast}<LSEP>[argument 1; litteral](str){randObs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dateTreatment must be one of '...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ntrees<1}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){randObs}<LEND>[](symbol){FAD.only}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){FAD.only = TRUE and dateTreatm...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dateTreatment}<LSEP>[argument 1; litteral](str){minMax}<LEND>[](symbol){FAD.only}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){FAD.only = TRUE and dateTreatm...}<LSEP>[argument 1; litteral](str){ are conflicting, as there are...}<LSEP>[argument 2; litteral](str){ as dates are simply point occ...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[](symbol){point.occur}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Inconsistent arguments, point....}<LSEP>[argument 1; litteral](str){\n Why not just make site assi...}<LSEP>[argument 2; litteral](str){ and last appearance the same ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){verboseWarnings}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Do not interpret a single cal3...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){nonstoch.bin}<LEND>[](symbol){verboseWarnings}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Do not interpret a single tree...}<LSEP>[argument 1; litteral](str){ are stochastically pulled fro...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){droppers}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Absolutely NO valid taxa share...}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){noisyDrop}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Warning: Following taxa droppe...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){droppers}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){drop.tip}<LSEP>[](symbol){tree}<LSEP>[](symbol){droppers}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tree}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Absolutely NO valid taxa share...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Less than two valid taxa share...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){whichNoMatch}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){whichNoMatch}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[litteral](logical){NA}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){droppers}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){node.mins not compatible with ...}<LSEP>[argument 1; litteral](str){ taxa are dropped; drop before...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){Nnode}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){node.mins}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){node.mins must be same length ...}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){notTree}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){notTree}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){noisyDrop}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Following taxa dropped from ti...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){notTree}<LSEP>[argument 1; litteral](str){, }<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Some taxa in timeList not incl...}<LSEP>[argument 1; litteral](str){ no automatic taxon drop if 's...}<LSEP>[argument 2; litteral](str){ Please remove from both sites...}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Both timeList[[1]] and timeLis...}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unexpected NAs in timeList}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unexpected character-type data...}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[1]] not in intervals...}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[1]] <0 ?}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){diff}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){timeList[[2]] not in intervals...}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Some dates in timeList[[2]] <0 ?}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate taxa in timeList[[2]]}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Duplicate tip taxon names in t...}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Odd irreconcilable mismatch be...}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sites}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){point.occur}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){point.occur = TRUE but some ta...}<LSEP>[argument 1; litteral](str){ and LADs listed in different ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sites}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[argument 2; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sites}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){rmtree}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){siteTime}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){sites}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 30; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){go}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sites}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){go}<LSEP>[](symbol){}<LEND>[statement 31; control flow](){for}<LSEP>[](symbol){ntrb}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntrees}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){nonstoch.bin}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bad_sites}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){sites}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){siteDates}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){siteTime}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bad_sites}<LEND>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LSEP>[](symbol){bad_sites}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LSEP>[](symbol){bad_sites}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){bad_sites}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){timeDataSampled}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteDates}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timeDataSampled}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){siteTime}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sites}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){timeDataSampled}<LEND>[call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){timeList}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tree2}<LEND>[call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){cal3TimePaleoPhy}<LSEP>[](symbol){tree}<LSEP>[](symbol){timeDataSampled}<LSEP>[](symbol){brRate}<LSEP>[](symbol){extRate}<LSEP>[](symbol){sampRate}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[](symbol){anc.wt}<LSEP>[](symbol){node.mins}<LSEP>[](symbol){adj.obs.wt}<LSEP>[](symbol){root.max}<LSEP>[](symbol){step.size}<LSEP>[](symbol){FAD.only}<LSEP>[](symbol){dateTreatment}<LSEP>[](symbol){randres}<LSEP>[](symbol){tolerance}<LSEP>[](symbol){diagnosticMode}<LSEP>[](symbol){verboseWarnings}<LSEP>[](symbol){plot}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){timeDataSampled}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){FAD}<LSEP>[argument 1; litteral](str){LAD}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){ranges.used}<LEND>[](symbol){timeDataSampled}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree2}<LSEP>[](symbol){edge.length}<LEND>[litteral](NULL){NULL}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[](symbol){ntrb}<LEND>[](symbol){tree2}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ntrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttrees}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ttrees}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 33; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ttrees}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){multiDiv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){int.length}<LSEP>[](symbol){plot}<LSEP>[](symbol){split.int}<LSEP>[](symbol){drop.ZLB}<LSEP>[](symbol){drop.cryptic}<LSEP>[](symbol){extant.adjust}<LSEP>[](symbol){plotLogRich}<LSEP>[](symbol){yAxisLims}<LSEP>[](symbol){timelims}<LSEP>[](symbol){int.times}<LSEP>[](symbol){plotMultCurves}<LSEP>[](symbol){multRainbow}<LSEP>[](symbol){divPalette}<LSEP>[](symbol){divLineType}<LSEP>[](symbol){main}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dataClassType}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){data}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){classType}<LSEP>[litteral](logical){NA}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){classType}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){list}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){classType}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){classType}<LSEP>[litteral](real){3.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){classType}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Data of unknown type - not a m...}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){classType}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){int.times}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tblen}<LSEP>[](symbol){int.length}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lims1}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){T}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lims1}<LSEP>[litteral](logical){NA}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){data}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){data}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[](symbol){extant.adjust}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lims2}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lims2}<LSEP>[litteral](logical){NA}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lims3}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ttree}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){data}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ntime}<LEND>[](symbol){ntime}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){node.depth.edgelength}<LSEP>[](symbol){ttree}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ntime}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ttree}<LSEP>[](symbol){root.time}<LEND>[](symbol){ntime}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lims3}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){lims3}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ntime}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ntime}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lims3}<LSEP>[litteral](logical){NA}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){end}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){lims1}<LSEP>[](symbol){lims2}<LSEP>[](symbol){lims3}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){start}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){lims1}<LSEP>[](symbol){lims2}<LSEP>[](symbol){lims3}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tblen}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){end}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tblen}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tblen}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){midtimes}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tblen}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){midtimes}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tblen}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){split.int}<LEND>[argument 1; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dataClassType}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){splinters}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mustSplit}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){int.times}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){splinters}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){y}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){mustSplit}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){mustSplit}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){splitter}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splinters}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splinters}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){y}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){splitter}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){splitter}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitter}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){splitter}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){splitter}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){splitter}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LSEP>[](symbol){mustSplit}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.times}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){int.times}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){midtimes}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){int.times}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){data}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataClassType}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){divs1}<LEND>[call](){}<LSEP>[](symbol){taxicDivCont}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){data}<LSEP>[](symbol){i}<LEND>[](symbol){int.times}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[](symbol){drop.cryptic}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){divs1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){div}<LSEP>[](symbol){divs1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataClassType}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){divs2}<LEND>[call](){}<LSEP>[](symbol){taxicDivDisc}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){data}<LSEP>[](symbol){i}<LEND>[](symbol){int.times}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){divs2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){div}<LSEP>[](symbol){divs2}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataClassType}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){divs3}<LEND>[call](){}<LSEP>[](symbol){phyloDiv}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){data}<LSEP>[](symbol){i}<LEND>[](symbol){int.times}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[](symbol){drop.ZLB}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){divs3}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs3}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){div}<LSEP>[](symbol){divs3}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){div}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){div}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){dataset}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){div}<LEND>[argument 2; litteral](str){}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){median}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){div}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){median}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){q1}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){div}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){quantile}<LSEP>[argument 3; litteral](real){0.025000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){q2}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){div}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){quantile}<LSEP>[argument 3; litteral](real){0.975000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){median.curve}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){median}<LSEP>[](symbol){q1}<LSEP>[](symbol){q2}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){int.times}<LSEP>[](symbol){div}<LSEP>[](symbol){median.curve}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plotMultiDiv}<LSEP>[](symbol){res}<LSEP>[](symbol){plotLogRich}<LSEP>[](symbol){timelims}<LSEP>[](symbol){yAxisLims}<LSEP>[](symbol){plotMultCurves}<LSEP>[](symbol){multRainbow}<LSEP>[](symbol){divPalette}<LSEP>[](symbol){divLineType}<LSEP>[](symbol){main}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){res}<LEND>[assign](){<-}<LSEP>[](symbol){plotMultiDiv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){results}<LSEP>[](symbol){plotLogRich}<LSEP>[](symbol){timelims}<LSEP>[](symbol){yAxisLims}<LSEP>[](symbol){plotMultCurves}<LSEP>[](symbol){multRainbow}<LSEP>[](symbol){divPalette}<LSEP>[](symbol){divLineType}<LSEP>[](symbol){main}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){timelims}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){if given, timelims should be a...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){yAxisLims}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){yAxisLims}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){if given, yAxisLims should be ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){plotLogRich}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){yAxisLims}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){if richness is plotted on a lo...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){int.start}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){int.end}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){int.start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){int.end}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){int.start}<LSEP>[](symbol){int.end}<LEND>[argument 1; litteral](real){10000.000000}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){plotMultCurves}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){main}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main}<LSEP>[litteral](str){Multiple Diversity Curves}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){divs}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){divs1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){divs}<LSEP>[](symbol){divs}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){plotLogRich}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){yAxisLims}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){divs1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){divs1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LSEP>[](symbol){yAxisLims}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](str){n}<LSEP>[](symbol){y_lim}<LSEP>[argument 4; litteral](str){y}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 7; litteral](str){Time (Before Present)}<LSEP>[argument 8; litteral](str){Log Lineage/Taxic Richness}<LSEP>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){yAxisLims}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){divs1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){divs1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LSEP>[](symbol){yAxisLims}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](str){n}<LSEP>[](symbol){y_lim}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 6; litteral](str){Time (Before Present)}<LSEP>[argument 7; litteral](str){Lineage/Taxic Richness}<LSEP>[](symbol){main}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){divPalette}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){multRainbow}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){divPalette}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){divs1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){divPalette}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){divs1}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){divLineType}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){divs1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){divLineType}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){divLineType}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){divs1}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){divs1}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divs1}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divPalette}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){divLineType}<LSEP>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){main}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main}<LSEP>[litteral](str){Median Diversity Curve}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mdiv}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){results}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mdiv1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){mdiv}<LSEP>[](symbol){mdiv}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){times1}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){times1}<LEND>[call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){times1}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){plotLogRich}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){2.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){3.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){yAxisLims}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){mdiv1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){mdiv1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LSEP>[](symbol){yAxisLims}<LEND>[statement 3; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](str){n}<LSEP>[](symbol){y_lim}<LSEP>[argument 4; litteral](str){y}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 7; litteral](str){Time (Before Present)}<LSEP>[argument 8; litteral](str){Log Lineage/Taxic Richness}<LSEP>[](symbol){main}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){yAxisLims}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){mdiv1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mdiv1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y_lim}<LSEP>[](symbol){yAxisLims}<LEND>[statement 1; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](str){n}<LSEP>[](symbol){y_lim}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){times1}<LEND>[false branch; block](){}<LSEP>[](symbol){timelims}<LEND>[argument 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){timelims}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){r}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){i}<LEND>[argument 6; litteral](str){Time (Before Present)}<LSEP>[argument 7; litteral](str){Lineage/Taxic Richness}<LSEP>[](symbol){main}<LEND>[statement 5; call](){}<LSEP>[](symbol){polygon}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](str){gray}<LSEP>[argument 3; litteral](logical){NA}<LEND>[statement 6; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){times1}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mdiv1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; litteral](real){3.000000}