{"comment":{"url":"https://api.github.com/repos/thijsjanzen/STEPCAM/comments/19103024","html_url":"https://github.com/thijsjanzen/STEPCAM/commit/3397674888e9ff85e578f207325d1a60f8a3ca4f#commitcomment-19103024","id":19103024,"user":{"login":"lintr-bot","id":10925265,"avatar_url":"https://avatars.githubusercontent.com/u/10925265?v=3","gravatar_id":"","url":"https://api.github.com/users/lintr-bot","html_url":"https://github.com/lintr-bot","followers_url":"https://api.github.com/users/lintr-bot/followers","following_url":"https://api.github.com/users/lintr-bot/following{/other_user}","gists_url":"https://api.github.com/users/lintr-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/lintr-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lintr-bot/subscriptions","organizations_url":"https://api.github.com/users/lintr-bot/orgs","repos_url":"https://api.github.com/users/lintr-bot/repos","events_url":"https://api.github.com/users/lintr-bot/events{/privacy}","received_events_url":"https://api.github.com/users/lintr-bot/received_events","type":"User","site_admin":false},"position":null,"line":null,"path":null,"commit_id":"3397674888e9ff85e578f207325d1a60f8a3ca4f","created_at":"2016-09-20T20:01:07Z","updated_at":"2016-09-20T20:01:07Z","body":"[R/ABC_SMC.R:2:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L2) *style:* **Variable and function names should be all lowercase.**\n```r\n​getRandomVals <- function(max_val)  {\n^~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:15:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L15) *style:* **Variable and function names should be all lowercase.**\n```r\n​getFromPrevious <- function(inds, ws, disps, filts, comps)  {\n^~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:22:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L22) *style:* **Variable and function names should be all lowercase.**\n```r\n​calculateWeight <- function(params, target, sigma,\n^~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:25:68:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L25) *style:* **Commas should always have a space after.**\n```r\n​  diff <- params[target] - cbind(disp_vals, filt_vals, comp_vals)[,target]\n                                                                   ^\n```\n[R/ABC_SMC.R:26:54:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L26) *style:* **Trailing whitespace is superfluous.**\n```r\n​  vals <- weights * dnorm(diff, mean = 0, sd = sigma)  \n                                                     ^~\n```\n[R/ABC_SMC.R:27:12:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L27) *style:* **Put spaces around all infix operators.**\n```r\n​  return( 1/sum(vals) )\n          ~^~\n```\n[R/ABC_SMC.R:31:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L31) *style:* **Variable and function names should be all lowercase.**\n```r\n​normalizeWeights <- function(x) {\n^~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:65:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L65) *style:* **Variable and function names should be all lowercase.**\n```r\n​calculateDistance <- function(rich, even, div, opt_diff, obs, sd_vals)  {\n^~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:69:40:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L69) *style:* **Put spaces around all infix operators.**\n```r\n​  fit_optima <- (opt_diff / sd_vals[4])^2;\n                                      ~^~\n```\n[R/ABC_SMC.R:77:21:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L77) *style:* **Variable and function names should be all lowercase.**\n```r\n​ABC_SMC <- function(numParticles, species_fallout, taxa, esppres, n_traits,\n                    ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:79:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L79) *style:* **lines should not be more than 80 characters.**\n```r\n​                    abundances, frequencies, stopRate, Ord, continue_from_file = TRUE,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:79:46:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L79) *style:* **Variable and function names should be all lowercase.**\n```r\n​                    abundances, frequencies, stopRate, Ord, continue_from_file = TRUE,\n                                             ^~~~~~~~\n```\n[R/ABC_SMC.R:82:6:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L82) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​  for(i in seq_along(sd_vals)) {\n     ^\n```\n[R/ABC_SMC.R:83:7:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L83) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​    if(sd_vals[[i]] == 0.000) {\n      ^\n```\n[R/ABC_SMC.R:85:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L85) *style:* **lines should not be more than 80 characters.**\n```r\n​           \"one of the community summary statistics shows no variation in your dataset\")\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:88:10:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L88) *style:* **Variable and function names should be all lowercase.**\n```r\n​  res <- detMnbsp(Ord, abundances)\n         ^~~~~~~~\n```\n[R/ABC_SMC.R:88:10:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L88) *warning:* **no visible global function definition for ‘detMnbsp’**\n```r\n​  res <- detMnbsp(Ord, abundances)\n         ^~~~~~~~\n```\n[R/ABC_SMC.R:91:18:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L91) *style:* **Variable and function names should be all lowercase.**\n```r\n​  disp_vals <- 1:numParticles\n                 ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:92:18:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L92) *style:* **Variable and function names should be all lowercase.**\n```r\n​  filt_vals <- 1:numParticles\n                 ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:93:18:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L93) *style:* **Variable and function names should be all lowercase.**\n```r\n​  comp_vals <- 1:numParticles\n                 ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:95:13:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L95) *style:* **Variable and function names should be all lowercase.**\n```r\n​  fits <- 1:numParticles\n            ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:96:17:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L96) *style:* **Variable and function names should be all lowercase.**\n```r\n​  rich_vec <- 1:numParticles\n                ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:97:16:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L97) *style:* **Variable and function names should be all lowercase.**\n```r\n​  eve_vec <- 1:numParticles\n               ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:98:16:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L98) *style:* **Variable and function names should be all lowercase.**\n```r\n​  div_vec <- 1:numParticles\n               ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:99:16:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L99) *style:* **Variable and function names should be all lowercase.**\n```r\n​  opt_vec <- 1:numParticles\n               ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:105:21:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L105) *style:* **Variable and function names should be all lowercase.**\n```r\n​  weights <- rep(1, numParticles)\n                    ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:106:26:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L106) *style:* **Variable and function names should be all lowercase.**\n```r\n​  next_weights <- rep(1, numParticles)\n                         ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:107:16:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L107) *style:* **Variable and function names should be all lowercase.**\n```r\n​  indices <- 1:numParticles\n               ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:114:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L114) *style:* **lines should not be more than 80 characters.**\n```r\n​    cat(\"Found previous output, continuing from that output\\n\"); flush.console();\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:118:7:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L118) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​    if(d[numParticles,1] == numParticles) {\n      ^\n```\n[R/ABC_SMC.R:118:10:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L118) *style:* **Variable and function names should be all lowercase.**\n```r\n​    if(d[numParticles,1] == numParticles) {\n         ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:118:23:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L118) *style:* **Commas should always have a space after.**\n```r\n​    if(d[numParticles,1] == numParticles) {\n                      ^\n```\n[R/ABC_SMC.R:118:29:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L118) *style:* **Variable and function names should be all lowercase.**\n```r\n​    if(d[numParticles,1] == numParticles) {\n                            ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:139:5:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L139) *style:* **Variable and function names should be all lowercase.**\n```r\n​    numberAccepted <- 0\n    ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:140:28:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L140) *style:* **Variable and function names should be all lowercase.**\n```r\n​    if (t != 1) weights <- normalizeWeights(weights)\n                           ^~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:140:28:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L140) *warning:* **no visible global function definition for ‘normalizeWeights’**\n```r\n​    if (t != 1) weights <- normalizeWeights(weights)\n                           ^~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:148:12:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L148) *style:* **Variable and function names should be all lowercase.**\n```r\n​    while (numberAccepted <= numParticles) {\n           ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:148:30:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L148) *style:* **Variable and function names should be all lowercase.**\n```r\n​    while (numberAccepted <= numParticles) {\n                             ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:152:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L152) *style:* **Variable and function names should be all lowercase.**\n```r\n​        params <- getRandomVals(species_fallout)\n                  ^~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:152:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L152) *warning:* **no visible global function definition for ‘getRandomVals’**\n```r\n​        params <- getRandomVals(species_fallout)\n                  ^~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:154:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L154) *style:* **Variable and function names should be all lowercase.**\n```r\n​        params <- getFromPrevious(indices, weights,\n                  ^~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:156:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L156) *warning:* **no visible global function definition for ‘perturb’**\n```r\n​        params <- perturb(params, sigma)\n                  ^~~~~~~\n```\n[R/ABC_SMC.R:166:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L166) *style:* **Trailing whitespace is superfluous.**\n```r\n​     \n^~~~~\n```\n[R/ABC_SMC.R:170:40:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L170) *style:* **Commas should always have a space after.**\n```r\n​      traits <- as.data.frame(species[,c(2:(n_traits+1))],row.names=c(1:taxa));\n                                       ^\n```\n[R/ABC_SMC.R:170:53:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L170) *style:* **Put spaces around all infix operators.**\n```r\n​      traits <- as.data.frame(species[,c(2:(n_traits+1))],row.names=c(1:taxa));\n                                                   ~^~\n```\n[R/ABC_SMC.R:170:59:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L170) *style:* **Commas should always have a space after.**\n```r\n​      traits <- as.data.frame(species[,c(2:(n_traits+1))],row.names=c(1:taxa));\n                                                          ^\n```\n[R/ABC_SMC.R:170:68:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L170) *style:* **Put spaces around all infix operators.**\n```r\n​      traits <- as.data.frame(species[,c(2:(n_traits+1))],row.names=c(1:taxa));\n                                                                  ~^~\n```\n[R/ABC_SMC.R:173:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L173) *style:* **Trailing whitespace is superfluous.**\n```r\n​      \n^~~~~~\n```\n[R/ABC_SMC.R:174:8:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L174) *style:* **Commented code should be removed.**\n```r\n​     # source(\"/Users/janzen/GitHub/STEPCAM/R/modified_dbFD.R\")\n       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:175:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L175) *style:* **lines should not be more than 80 characters.**\n```r\n​      FD_output <- strippedDbFd(Ord, communities, m = res[[1]], nb.sp = res[[2]]) \n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:175:20:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L175) *style:* **Variable and function names should be all lowercase.**\n```r\n​      FD_output <- strippedDbFd(Ord, communities, m = res[[1]], nb.sp = res[[2]]) \n                   ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:175:20:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L175) *warning:* **no visible global function definition for ‘strippedDbFd’**\n```r\n​      FD_output <- strippedDbFd(Ord, communities, m = res[[1]], nb.sp = res[[2]]) \n                   ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:175:82:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L175) *style:* **Trailing whitespace is superfluous.**\n```r\n​      FD_output <- strippedDbFd(Ord, communities, m = res[[1]], nb.sp = res[[2]]) \n                                                                                 ^\n```\n[R/ABC_SMC.R:176:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L176) *style:* **Trailing whitespace is superfluous.**\n```r\n​  \n^~\n```\n[R/ABC_SMC.R:177:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L177) *style:* **lines should not be more than 80 characters.**\n```r\n​      FRic <- FD_output$FRic # FRic = functional richness (Villeger et al, 2008, Ecology)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:178:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L178) *style:* **lines should not be more than 80 characters.**\n```r\n​      FEve <- FD_output$FEve # FEve = functional evenness (Villeger et al, 2008, Ecology)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:179:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L179) *style:* **lines should not be more than 80 characters.**\n```r\n​      FDiv <- FD_output$FDiv # FDiv = functional diversity (Villeger et al, 2008, Ecology)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:188:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L188) *style:* **lines should not be more than 80 characters.**\n```r\n​      # calculate distance of trait mean simulated community from that of observed\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:191:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L191) *style:* **lines should not be more than 80 characters.**\n```r\n​      # (inverse) fit of model: euclidian distance of FD and trait mean values of\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:193:14:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L193) *style:* **Variable and function names should be all lowercase.**\n```r\n​      fit <- calculateDistance(FRic[[1]], FEve[[1]], FDiv[[1]],\n             ^~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:195:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L195) *style:* **Trailing whitespace is superfluous.**\n```r\n​      \n^~~~~~\n```\n[R/ABC_SMC.R:198:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L198) *style:* **Variable and function names should be all lowercase.**\n```r\n​        next_disp[numberAccepted] <- params[1]\n                  ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:199:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L199) *style:* **Variable and function names should be all lowercase.**\n```r\n​        next_filt[numberAccepted] <- params[2]\n                  ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:200:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L200) *style:* **Variable and function names should be all lowercase.**\n```r\n​        next_comp[numberAccepted] <- params[3]\n                  ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:202:14:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L202) *style:* **Variable and function names should be all lowercase.**\n```r\n​        fits[numberAccepted] <- fit\n             ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:203:18:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L203) *style:* **Variable and function names should be all lowercase.**\n```r\n​        rich_vec[numberAccepted] <- FRic[[1]]\n                 ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:204:17:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L204) *style:* **Variable and function names should be all lowercase.**\n```r\n​        eve_vec[numberAccepted] <- FEve[[1]]\n                ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:205:17:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L205) *style:* **Variable and function names should be all lowercase.**\n```r\n​        div_vec[numberAccepted] <- FDiv[[1]]\n                ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:206:17:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L206) *style:* **Variable and function names should be all lowercase.**\n```r\n​        opt_vec[numberAccepted] <- mean_optimum;\n                ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:209:24:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L209) *style:* **Variable and function names should be all lowercase.**\n```r\n​          next_weights[numberAccepted] = 1\n                       ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:209:40:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L209) *style:* **Use <-, not =, for assignment.**\n```r\n​          next_weights[numberAccepted] = 1\n                                       ^\n```\n[R/ABC_SMC.R:211:24:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L211) *style:* **Variable and function names should be all lowercase.**\n```r\n​          next_weights[numberAccepted] =\n                       ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:211:40:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L211) *style:* **Use <-, not =, for assignment.**\n```r\n​          next_weights[numberAccepted] =\n                                       ^\n```\n[R/ABC_SMC.R:212:13:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L212) *style:* **Variable and function names should be all lowercase.**\n```r\n​            calculateWeight(params, changed, sigma, disp_vals, filt_vals,\n            ^~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:215:9:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L215) *style:* **Variable and function names should be all lowercase.**\n```r\n​        numberAccepted <- numberAccepted + 1\n        ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:215:27:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L215) *style:* **Variable and function names should be all lowercase.**\n```r\n​        numberAccepted <- numberAccepted + 1\n                          ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:216:13:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L216) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​        if ((numberAccepted) %% (numParticles / PRINT_FREQ) == 0) {\n            ^\n```\n[R/ABC_SMC.R:216:14:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L216) *style:* **Variable and function names should be all lowercase.**\n```r\n​        if ((numberAccepted) %% (numParticles / PRINT_FREQ) == 0) {\n             ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:216:34:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L216) *style:* **Variable and function names should be all lowercase.**\n```r\n​        if ((numberAccepted) %% (numParticles / PRINT_FREQ) == 0) {\n                                 ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:222:21:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L222) *style:* **Put spaces around all infix operators.**\n```r\n​      if (tried > (1/stopRate) && tried > 50)  {\n                   ~^~\n```\n[R/ABC_SMC.R:222:22:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L222) *style:* **Variable and function names should be all lowercase.**\n```r\n​      if (tried > (1/stopRate) && tried > 50)  {\n                     ^~~~~~~~\n```\n[R/ABC_SMC.R:224:13:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L224) *style:* **Variable and function names should be all lowercase.**\n```r\n​        if (numberAccepted / tried < stopRate) {\n            ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:224:38:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L224) *style:* **Variable and function names should be all lowercase.**\n```r\n​        if (numberAccepted / tried < stopRate) {\n                                     ^~~~~~~~\n```\n[R/ABC_SMC.R:242:54:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L242) *style:* **Put spaces around all infix operators.**\n```r\n​    file_name <- paste(\"particles_t=\", t, \".txt\", sep=\"\", collapse = NULL)\n                                                    ~^~\n```\n[R/ABC_SMC.R:245:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L245) *style:* **lines should not be more than 80 characters.**\n```r\n​    cat(\" \", mean(disp_vals), mean(filt_vals), mean(comp_vals), \"\\t\", \"accept rate = \",\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:246:9:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L246) *style:* **Variable and function names should be all lowercase.**\n```r\n​        numberAccepted / (tried-1), \"\\n\")\n        ^~~~~~~~~~~~~~\n```\n[R/ABC_SMC.R:246:32:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L246) *style:* **Put spaces around all infix operators.**\n```r\n​        numberAccepted / (tried-1), \"\\n\")\n                              ~^~\n```\n[R/ABC_SMC.R:249:27:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L249) *style:* **Commas should always have a space after.**\n```r\n​    next_weights <- rep(1,numParticles)\n                          ^\n```\n[R/ABC_SMC.R:249:27:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L249) *style:* **Variable and function names should be all lowercase.**\n```r\n​    next_weights <- rep(1,numParticles)\n                          ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:250:20:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L250) *style:* **Variable and function names should be all lowercase.**\n```r\n​    next_disp <- 1:numParticles\n                   ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:251:20:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L251) *style:* **Variable and function names should be all lowercase.**\n```r\n​    next_filt <- 1:numParticles\n                   ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:252:20:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L252) *style:* **Variable and function names should be all lowercase.**\n```r\n​    next_comp <- 1:numParticles\n                   ^~~~~~~~~~~~\n```\n[R/ABC_SMC.R:262:61:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L262) *style:* **Put spaces around all infix operators.**\n```r\n​    d <- read.table(paste(\"particles_t=\", t - 1, \".txt\", sep=\"\",\n                                                           ~^~\n```\n[R/ABC_SMC.R:266:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/ABC_SMC.R#L266) *style:* **lines should not be more than 80 characters.**\n```r\n​           \"Can't stop at iteration 1 - please set stop_at_iteration to 2 if you only want to generate from the prior\")\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/generateArtificialData.R:4:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L4) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**\n```r\n​generate.Artificial.Data <- function(n_species, n_traits, n_communities,\n^~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/generateArtificialData.R:6:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L6) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tpool_richness <- n_species\n^\n```\n[R/generateArtificialData.R:8:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L8) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\ttraits_pool <- matrix( round( rnorm(n = (pool_richness * n_traits),\n^\n```\n[R/generateArtificialData.R:9:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L9) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t                                    mean = 0, sd = 1), 3),\n^\n```\n[R/generateArtificialData.R:9:23:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L9) *style:* **Put spaces around all infix operators.**\n```r\n​\tpool_richness <- n_species\n                     ~^~~\n```\n[R/generateArtificialData.R:10:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L10) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t                       ncol = n_traits, nrow = pool_richness)\n^\n```\n[R/generateArtificialData.R:11:21:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L11) *style:* **Put spaces around all infix operators.**\n```r\n​\ttraits_pool <- matrix( round( rnorm(n = (pool_richness * n_traits),\n                   ~^~~\n```\n[R/generateArtificialData.R:11:47:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L11) *style:* **Put spaces around all infix operators.**\n```r\n​\ttraits_pool <- matrix( round( rnorm(n = (pool_richness * n_traits),\n                                             ~^~\n```\n[R/generateArtificialData.R:11:49:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L11) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\ttraits_pool <- matrix( round( rnorm(n = (pool_richness * n_traits),\n                                                ^\n```\n[R/generateArtificialData.R:11:64:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L11) *style:* **Put spaces around all infix operators.**\n```r\n​\ttraits_pool <- matrix( round( rnorm(n = (pool_richness * n_traits),\n                                                              ~^~\n```\n[R/generateArtificialData.R:12:50:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L12) *style:* **Put spaces around all infix operators.**\n```r\n​\t                                    mean = 0, sd = 1), 3),\n                                                ~^~\n```\n[R/generateArtificialData.R:12:58:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L12) *style:* **Put spaces around all infix operators.**\n```r\n​\t                                    mean = 0, sd = 1), 3),\n                                                        ~^~\n```\n[R/generateArtificialData.R:13:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L13) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tfor(i in 1:pool_richness) {\n^\n```\n[R/generateArtificialData.R:13:37:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L13) *style:* **Put spaces around all infix operators.**\n```r\n​\t                       ncol = n_traits, nrow = pool_richness)\n                                   ~^~\n```\n[R/generateArtificialData.R:13:54:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L13) *style:* **Put spaces around all infix operators.**\n```r\n​\t                       ncol = n_traits, nrow = pool_richness)\n                                                    ~^~\n```\n[R/generateArtificialData.R:14:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L14) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t  column1[i] <- paste(\"species\", i, sep = \"\")\n^\n```\n[R/generateArtificialData.R:15:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L15) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t}\n^\n```\n[R/generateArtificialData.R:16:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L16) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\trow1 <- rep(NA, (n_traits + 1))\n^\n```\n[R/generateArtificialData.R:16:12:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tfor(i in 1:pool_richness) {\n           ^\n```\n[R/generateArtificialData.R:17:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L17) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tfor(i in 1:n_traits + 1) {\n^\n```\n[R/generateArtificialData.R:17:22:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L17) *style:* **Put spaces around all infix operators.**\n```r\n​\t  column1[i] <- paste(\"species\", i, sep = \"\")\n                    ~^~~\n```\n[R/generateArtificialData.R:18:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L18) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t  row1[i] <- paste(\"trait\", (i - 1), sep=\"\")\n^\n```\n[R/generateArtificialData.R:19:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L19) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t}\n^\n```\n[R/generateArtificialData.R:19:14:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L19) *style:* **Put spaces around all infix operators.**\n```r\n​\trow1 <- rep(NA, (n_traits + 1))\n            ~^~~\n```\n[R/generateArtificialData.R:19:25:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L19) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\trow1 <- rep(NA, (n_traits + 1))\n                        ^\n```\n[R/generateArtificialData.R:20:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L20) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\trow1[1] <- \"species\"\n^\n```\n[R/generateArtificialData.R:20:12:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tfor(i in 1:n_traits + 1) {\n           ^\n```\n[R/generateArtificialData.R:21:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L21) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tcolumns <- matrix(cbind(column1, traits_pool), ncol = (n_traits + 1))\n^\n```\n[R/generateArtificialData.R:21:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L21) *style:* **Put spaces around all infix operators.**\n```r\n​\t  row1[i] <- paste(\"trait\", (i - 1), sep=\"\")\n                 ~^~~\n```\n[R/generateArtificialData.R:21:37:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t  row1[i] <- paste(\"trait\", (i - 1), sep=\"\")\n                                    ^\n```\n[R/generateArtificialData.R:21:40:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L21) *style:* **Put spaces around all infix operators.**\n```r\n​\t  row1[i] <- paste(\"trait\", (i - 1), sep=\"\")\n                                      ~^~\n```\n[R/generateArtificialData.R:22:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L22) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\ttraits_pool_df <- as.data.frame(columns)\n^\n```\n[R/generateArtificialData.R:23:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L23) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tnames(traits_pool_df) <- row1\n^\n```\n[R/generateArtificialData.R:23:17:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L23) *style:* **Put spaces around all infix operators.**\n```r\n​\trow1[1] <- \"species\"\n               ~^~~\n```\n[R/generateArtificialData.R:24:17:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L24) *style:* **Put spaces around all infix operators.**\n```r\n​\tcolumns <- matrix(cbind(column1, traits_pool), ncol = (n_traits + 1))\n               ~^~~\n```\n[R/generateArtificialData.R:24:61:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L24) *style:* **Put spaces around all infix operators.**\n```r\n​\tcolumns <- matrix(cbind(column1, traits_pool), ncol = (n_traits + 1))\n                                                           ~^~\n```\n[R/generateArtificialData.R:24:63:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tcolumns <- matrix(cbind(column1, traits_pool), ncol = (n_traits + 1))\n                                                              ^\n```\n[R/generateArtificialData.R:25:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L25) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tcomm_spec_matrix <- matrix(rep(0, (n_communities * pool_richness)),\n^\n```\n[R/generateArtificialData.R:25:24:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L25) *style:* **Put spaces around all infix operators.**\n```r\n​\ttraits_pool_df <- as.data.frame(columns)\n                      ~^~~\n```\n[R/generateArtificialData.R:26:31:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L26) *style:* **Put spaces around all infix operators.**\n```r\n​\tnames(traits_pool_df) <- row1\n                             ~^~~\n```\n[R/generateArtificialData.R:28:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L28) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\toccurence <- 10^rnorm(pool_richness, mean = 0, sd = occurence_distribution)\n^\n```\n[R/generateArtificialData.R:28:26:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L28) *style:* **Put spaces around all infix operators.**\n```r\n​\tcomm_spec_matrix <- matrix(rep(0, (n_communities * pool_richness)),\n                        ~^~~\n```\n[R/generateArtificialData.R:28:43:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tcomm_spec_matrix <- matrix(rep(0, (n_communities * pool_richness)),\n                                          ^\n```\n[R/generateArtificialData.R:28:58:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L28) *style:* **Put spaces around all infix operators.**\n```r\n​\tcomm_spec_matrix <- matrix(rep(0, (n_communities * pool_richness)),\n                                                        ~^~\n```\n[R/generateArtificialData.R:30:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L30) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n^\n```\n[R/generateArtificialData.R:31:19:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L31) *style:* **Put spaces around all infix operators.**\n```r\n​\toccurence <- 10^rnorm(pool_richness, mean = 0, sd = occurence_distribution)\n                 ~^~~\n```\n[R/generateArtificialData.R:31:24:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L31) *style:* **Put spaces around all infix operators.**\n```r\n​\toccurence <- 10^rnorm(pool_richness, mean = 0, sd = occurence_distribution)\n                      ~^~\n```\n[R/generateArtificialData.R:31:51:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L31) *style:* **Put spaces around all infix operators.**\n```r\n​\toccurence <- 10^rnorm(pool_richness, mean = 0, sd = occurence_distribution)\n                                                 ~^~\n```\n[R/generateArtificialData.R:31:59:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L31) *style:* **Put spaces around all infix operators.**\n```r\n​\toccurence <- 10^rnorm(pool_richness, mean = 0, sd = occurence_distribution)\n                                                         ~^~\n```\n[R/generateArtificialData.R:32:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L32) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\trichness_values[which(richness_values > pool_richness)] <- pool_richness\n^\n```\n[R/generateArtificialData.R:33:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\trichness_values[which(richness_values < 0)] <- 0\n^\n```\n[R/generateArtificialData.R:33:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **lines should not be more than 80 characters.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/generateArtificialData.R:33:25:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                       ~^~~\n```\n[R/generateArtificialData.R:33:34:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                                 ^\n```\n[R/generateArtificialData.R:33:61:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                                                           ~^~\n```\n[R/generateArtificialData.R:33:69:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                                                                    ^~\n```\n[R/generateArtificialData.R:33:74:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                                                                        ~^~\n```\n[R/generateArtificialData.R:33:76:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                                                                           ^\n```\n[R/generateArtificialData.R:33:89:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L33) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values <- round((rnorm(n_communities, mean = 0, sd = 1) * (sd_richness * pool_richness) +\n                                                                                       ~^~\n```\n[R/generateArtificialData.R:34:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L34) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tfor(i in 1:n_communities){\n^\n```\n[R/generateArtificialData.R:35:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L35) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t  if(mechanism_random == T){\n^\n```\n[R/generateArtificialData.R:35:47:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L35) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values[which(richness_values > pool_richness)] <- pool_richness\n                                             ~^~\n```\n[R/generateArtificialData.R:35:65:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L35) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values[which(richness_values > pool_richness)] <- pool_richness\n                                                               ~^~~\n```\n[R/generateArtificialData.R:36:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L36) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    present_species <- sample(c(1:pool_richness), richness_values[i],\n^\n```\n[R/generateArtificialData.R:36:47:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L36) *style:* **Put spaces around all infix operators.**\n```r\n​\trichness_values[which(richness_values < 0)] <- 0\n                                             ~^\n```\n[R/generateArtificialData.R:37:12:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tfor(i in 1:n_communities){\n           ^\n```\n[R/generateArtificialData.R:38:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L38) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t  }else{\n^\n```\n[R/generateArtificialData.R:38:13:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L38) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t  if(mechanism_random == T){\n            ^\n```\n[R/generateArtificialData.R:39:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L39) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    opt_traits <- rnorm(n_traits, mean = 0, sd = 1)\n^\n```\n[R/generateArtificialData.R:39:29:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L39) *style:* **Put spaces around all infix operators.**\n```r\n​\t    present_species <- sample(c(1:pool_richness), richness_values[i],\n                           ~^~~\n```\n[R/generateArtificialData.R:40:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L40) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    opt_traits_matrix <- c()\n^\n```\n[R/generateArtificialData.R:41:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L41) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    for(j in 1:n_traits){\n^\n```\n[R/generateArtificialData.R:42:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L42) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t      for(k in 1:pool_richness){\n^\n```\n[R/generateArtificialData.R:42:24:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L42) *style:* **Put spaces around all infix operators.**\n```r\n​\t    opt_traits <- rnorm(n_traits, mean = 0, sd = 1)\n                      ~^~~\n```\n[R/generateArtificialData.R:42:48:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L42) *style:* **Put spaces around all infix operators.**\n```r\n​\t    opt_traits <- rnorm(n_traits, mean = 0, sd = 1)\n                                              ~^~\n```\n[R/generateArtificialData.R:43:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L43) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t\t      l <- (j - 1) * pool_richness + k\n^~\n```\n[R/generateArtificialData.R:44:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L44) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t\t      opt_traits_matrix[l] <- opt_traits[j]\n^~\n```\n[R/generateArtificialData.R:44:16:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t    for(j in 1:n_traits){\n               ^\n```\n[R/generateArtificialData.R:45:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L45) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t      }\n^\n```\n[R/generateArtificialData.R:45:18:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t      for(k in 1:pool_richness){\n                 ^\n```\n[R/generateArtificialData.R:46:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L46) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    }\n^\n```\n[R/generateArtificialData.R:46:25:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L46) *style:* **Put spaces around all infix operators.**\n```r\n​\t\t      l <- (j - 1) * pool_richness + k\n                       ~^~~\n```\n[R/generateArtificialData.R:46:28:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t\t      l <- (j - 1) * pool_richness + k\n                           ^\n```\n[R/generateArtificialData.R:46:31:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L46) *style:* **Put spaces around all infix operators.**\n```r\n​\t\t      l <- (j - 1) * pool_richness + k\n                             ~^~\n```\n[R/generateArtificialData.R:46:36:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L46) *style:* **Put spaces around all infix operators.**\n```r\n​\t\t      l <- (j - 1) * pool_richness + k\n                                  ~^\n```\n[R/generateArtificialData.R:47:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L47) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    opt_traits_matrix <- matrix(opt_traits_matrix, ncol = n_traits)\n^\n```\n[R/generateArtificialData.R:47:44:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L47) *style:* **Put spaces around all infix operators.**\n```r\n​\t\t      opt_traits_matrix[l] <- opt_traits[j]\n                                          ~^~~\n```\n[R/generateArtificialData.R:48:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L48) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    traits_distances <- abs(traits_pool - opt_traits_matrix)\n^\n```\n[R/generateArtificialData.R:49:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L49) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    trait_distances_onedimen <- c()\n^\n```\n[R/generateArtificialData.R:50:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L50) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    for(m in 1:pool_richness){\n^\n```\n[R/generateArtificialData.R:50:31:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L50) *style:* **Put spaces around all infix operators.**\n```r\n​\t    opt_traits_matrix <- matrix(opt_traits_matrix, ncol = n_traits)\n                             ~^~~\n```\n[R/generateArtificialData.R:50:65:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L50) *style:* **Put spaces around all infix operators.**\n```r\n​\t    opt_traits_matrix <- matrix(opt_traits_matrix, ncol = n_traits)\n                                                               ~^~\n```\n[R/generateArtificialData.R:51:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L51) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t      trait_distances_onedimen[m] <- sqrt(sum(traits_distances[m, ] * traits_distances[m, ]))\n^\n```\n[R/generateArtificialData.R:51:30:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L51) *style:* **Put spaces around all infix operators.**\n```r\n​\t    traits_distances <- abs(traits_pool - opt_traits_matrix)\n                            ~^~~\n```\n[R/generateArtificialData.R:51:49:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L51) *style:* **Put spaces around all infix operators.**\n```r\n​\t    traits_distances <- abs(traits_pool - opt_traits_matrix)\n                                               ~^~\n```\n[R/generateArtificialData.R:52:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L52) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    }\n^\n```\n[R/generateArtificialData.R:53:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L53) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    inv_distances <- -(trait_distances_onedimen - max(trait_distances_onedimen)) + 10^-99\n^\n```\n[R/generateArtificialData.R:53:16:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L53) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t    for(m in 1:pool_richness){\n               ^\n```\n[R/generateArtificialData.R:54:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L54) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t    present_species <- sample(c(1:pool_richness), richness_values[i],\n^\n```\n[R/generateArtificialData.R:54:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L54) *style:* **lines should not be more than 80 characters.**\n```r\n​\t      trait_distances_onedimen[m] <- sqrt(sum(traits_distances[m, ] * traits_distances[m, ]))\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/generateArtificialData.R:54:43:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L54) *style:* **Put spaces around all infix operators.**\n```r\n​\t      trait_distances_onedimen[m] <- sqrt(sum(traits_distances[m, ] * traits_distances[m, ]))\n                                         ~^~~\n```\n[R/generateArtificialData.R:54:77:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L54) *style:* **Put spaces around all infix operators.**\n```r\n​\t      trait_distances_onedimen[m] <- sqrt(sum(traits_distances[m, ] * traits_distances[m, ]))\n                                                                           ~^~\n```\n[R/generateArtificialData.R:56:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L56) *style:* **lines should not be more than 80 characters.**\n```r\n​\t    inv_distances <- -(trait_distances_onedimen - max(trait_distances_onedimen)) + 10^-99\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/generateArtificialData.R:56:27:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L56) *style:* **Put spaces around all infix operators.**\n```r\n​\t    inv_distances <- -(trait_distances_onedimen - max(trait_distances_onedimen)) + 10^-99\n                         ~^~~\n```\n[R/generateArtificialData.R:56:31:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L56) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\t    inv_distances <- -(trait_distances_onedimen - max(trait_distances_onedimen)) + 10^-99\n                              ^\n```\n[R/generateArtificialData.R:56:57:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L56) *style:* **Put spaces around all infix operators.**\n```r\n​\t    inv_distances <- -(trait_distances_onedimen - max(trait_distances_onedimen)) + 10^-99\n                                                       ~^~\n```\n[R/generateArtificialData.R:56:90:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L56) *style:* **Put spaces around all infix operators.**\n```r\n​\t    inv_distances <- -(trait_distances_onedimen - max(trait_distances_onedimen)) + 10^-99\n                                                                                        ~^~\n```\n[R/generateArtificialData.R:57:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L57) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t  comm_spec_matrix[i, c(present_species)] <- 1\n^\n```\n[R/generateArtificialData.R:57:29:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L57) *style:* **Put spaces around all infix operators.**\n```r\n​\t    present_species <- sample(c(1:pool_richness), richness_values[i],\n                           ~^~~\n```\n[R/generateArtificialData.R:58:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L58) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\t}\n^\n```\n[R/generateArtificialData.R:59:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L59) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tcomm_spec_matrix\n^\n```\n[R/generateArtificialData.R:60:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L60) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tif(length(which(colSums(comm_spec_matrix) == 0)) != 0) traits_pool_df <-\n^\n```\n[R/generateArtificialData.R:62:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L62) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\trow1 <- c(column1[-c(which(colSums(comm_spec_matrix) == 0))])\n^\n```\n[R/generateArtificialData.R:63:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L63) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tif(length(which(colSums(comm_spec_matrix) == 0)) != 0) comm_spec_matrix <-\n^\n```\n[R/generateArtificialData.R:63:11:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L63) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tif(length(which(colSums(comm_spec_matrix) == 0)) != 0) traits_pool_df <-\n          ^\n```\n[R/generateArtificialData.R:63:58:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L63) *style:* **Put spaces around all infix operators.**\n```r\n​\tif(length(which(colSums(comm_spec_matrix) == 0)) != 0) traits_pool_df <-\n                                                        ~^~~\n```\n[R/generateArtificialData.R:65:14:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L65) *style:* **Put spaces around all infix operators.**\n```r\n​\trow1 <- c(column1[-c(which(colSums(comm_spec_matrix) == 0))])\n            ~^~~\n```\n[R/generateArtificialData.R:65:62:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L65) *style:* **Put spaces around all infix operators.**\n```r\n​\trow1 <- c(column1[-c(which(colSums(comm_spec_matrix) == 0))])\n                                                            ~^~~\n```\n[R/generateArtificialData.R:66:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L66) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tcomm_spec_matrix <- as.data.frame(cbind(comm_spec_matrix, rep(\"\", n_communities)))\n^\n```\n[R/generateArtificialData.R:66:11:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L66) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​\tif(length(which(colSums(comm_spec_matrix) == 0)) != 0) comm_spec_matrix <-\n          ^\n```\n[R/generateArtificialData.R:66:58:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L66) *style:* **Put spaces around all infix operators.**\n```r\n​\tif(length(which(colSums(comm_spec_matrix) == 0)) != 0) comm_spec_matrix <-\n                                                        ~^~~\n```\n[R/generateArtificialData.R:67:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L67) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tnames(comm_spec_matrix) <- row1\n^\n```\n[R/generateArtificialData.R:69:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L69) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tplots <- as.data.frame(matrix(as.numeric(as.matrix(comm_spec_matrix[, -ncol(comm_spec_matrix)])),\n^\n```\n[R/generateArtificialData.R:69:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L69) *style:* **lines should not be more than 80 characters.**\n```r\n​\tcomm_spec_matrix <- as.data.frame(cbind(comm_spec_matrix, rep(\"\", n_communities)))\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/generateArtificialData.R:69:26:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L69) *style:* **Put spaces around all infix operators.**\n```r\n​\tcomm_spec_matrix <- as.data.frame(cbind(comm_spec_matrix, rep(\"\", n_communities)))\n                        ~^~~\n```\n[R/generateArtificialData.R:70:33:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L70) *style:* **Put spaces around all infix operators.**\n```r\n​\tnames(comm_spec_matrix) <- row1\n                               ~^~~\n```\n[R/generateArtificialData.R:72:1:](https://github.com/thijsjanzen/STEPCAM/blob/3397674888e9ff85e578f207325d1a60f8a3ca4f/R/generateArtificialData.R#L72) *style:* **Use two spaces to indent, never tabs.**\n```r\n​\tnames(plots) <- traits_pool_df[, 1]\n^\n```\n"}}
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