{"comment":{"url":"https://api.github.com/repos/thijsjanzen/isoSIM/comments/27928426","html_url":"https://github.com/thijsjanzen/isoSIM/commit/13a65f28c6b162662f562d9ae8161f4c76b3a81a#commitcomment-27928426","id":27928426,"user":{"login":"lintr-bot","id":10925265,"avatar_url":"https://avatars3.githubusercontent.com/u/10925265?v=4","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":"13a65f28c6b162662f562d9ae8161f4c76b3a81a","created_at":"2018-03-05T12:54:28Z","updated_at":"2018-03-05T12:54:28Z","author_association":"NONE","body":"[R/create_populations.R:44:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/create_populations.R#L44) *style:* **Variable and function names should not be longer than 30 characters.**\n```r\n​create_two_populations_migration <- function(pop_size,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/create_populations.R:69:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/create_populations.R#L69) *style:* **Variable and function names should not be longer than 30 characters.**\n```r\n​create_population_from_individuals <- function(individuals,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/create_populations.R:77:6:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/create_populations.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​  for(j in seq_along(individuals)) {\n     ^\n```\n[R/create_populations.R:78:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/create_populations.R#L78) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​    if(class(individuals[[j]]) != \"individual\") {\n      ^\n```\n[R/isoFemale.R:29:5:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/isoFemale.R#L29) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​  if(length(inbred_population) < 1) {\n    ^\n```\n[R/isoFemale.R:33:5:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/isoFemale.R#L33) *style:* **Place a space before left parenthesis, except in a function call.**\n```r\n​  if(length(inbred_population) == 1) {\n    ^\n```\n[R/LD.R:1:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L1) *style:* **Variable or function name should be snake_case.**\n```r\n​calculate_average_LD <- function(alleles_pos_1, alleles_pos_2) {\n^~~~~~~~~~~~~~~~~~~~\n```\n[R/LD.R:3:20:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L3) *style:* **Do not place spaces around code in parentheses or square brackets.**\n```r\n​  all_alleles <- c( as.vector(alleles_pos_1), as.vector(alleles_pos_2))\n                   ^\n```\n[R/LD.R:6:3:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L6) *style:* **Variable or function name should be snake_case.**\n```r\n​  LD <- 0\n  ^~\n```\n[R/LD.R:10:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L10) *style:* **Variable or function name should be snake_case.**\n```r\n​      p_A_i <- length(which(alleles_pos_1 == i)) / length(alleles_pos_1)\n      ^~~~~\n```\n[R/LD.R:11:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L11) *style:* **Variable or function name should be snake_case.**\n```r\n​      p_B_j <- length(which(alleles_pos_2 == j)) / length(alleles_pos_2)\n      ^~~~~\n```\n[R/LD.R:13:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L13) *style:* **Variable or function name should be snake_case.**\n```r\n​      countAB <- 0\n      ^~~~~~~\n```\n[R/LD.R:15:13:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L15) *style:* **Do not place spaces around code in parentheses or square brackets.**\n```r\n​        if ( (alleles_pos_1[a, 1]) == i && (alleles_pos_2[a, 1] == j)) {\n            ^\n```\n[R/LD.R:16:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L16) *style:* **Variable or function name should be snake_case.**\n```r\n​          countAB <- countAB + 1\n          ^~~~~~~\n```\n[R/LD.R:19:13:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**\n```r\n​        if ( (alleles_pos_1[a, 2]) == i && (alleles_pos_2[a, 2] == j)) {\n            ^\n```\n[R/LD.R:20:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L20) *style:* **Variable or function name should be snake_case.**\n```r\n​          countAB <- countAB + 1\n          ^~~~~~~\n```\n[R/LD.R:24:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L24) *style:* **Variable or function name should be snake_case.**\n```r\n​      p_A_i_B_j <- countAB / (length(alleles_pos_1[, 1]) +\n      ^~~~~~~~~\n```\n[R/LD.R:27:30:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L27) *style:* **Variable or function name should be snake_case.**\n```r\n​      if (is.nan(p_A_i_B_j)) p_A_i_B_j <- 0\n                             ^~~~~~~~~\n```\n[R/LD.R:29:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L29) *style:* **Variable or function name should be snake_case.**\n```r\n​      D_i_j <- p_A_i_B_j - p_A_i * p_B_j\n      ^~~~~\n```\n[R/LD.R:31:7:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L31) *style:* **Variable or function name should be snake_case.**\n```r\n​      D_i_j_max <- 1\n      ^~~~~~~~~\n```\n[R/LD.R:34:9:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L34) *style:* **Variable or function name should be snake_case.**\n```r\n​        D_i_j_max <- min(p_A_i * p_B_j, (1 - p_A_i) * (1 - p_B_j))\n        ^~~~~~~~~\n```\n[R/LD.R:36:9:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L36) *style:* **Variable or function name should be snake_case.**\n```r\n​        D_i_j_max <- min(p_A_i * (1 - p_B_j), (1 - p_A_i) * p_B_j)\n        ^~~~~~~~~\n```\n[R/LD.R:40:9:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L40) *style:* **Variable or function name should be snake_case.**\n```r\n​        LD <- LD + p_A_i * p_B_j * abs(D_i_j / D_i_j_max)\n        ^~\n```\n[R/LD.R:52:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L52) *style:* **Variable or function name should be snake_case.**\n```r\n​calculate_LD <- function(pop,\n^~~~~~~~~~~~\n```\n[R/LD.R:91:3:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L91) *style:* **Variable or function name should be snake_case.**\n```r\n​  LD_matrix   <- matrix(nrow = length(markers), ncol = length(markers), NA)\n  ^~~~~~~~~\n```\n[R/LD.R:98:21:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L98) *style:* **Do not place spaces around code in parentheses or square brackets.**\n```r\n​        index1 <- c( (x - 1) * 2 + 1, (x - 1) * 2 + 2)\n                    ^\n```\n[R/LD.R:99:21:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L99) *style:* **Do not place spaces around code in parentheses or square brackets.**\n```r\n​        index2 <- c( (y - 1) * 2 + 1, (y - 1) * 2 + 2)\n                    ^\n```\n[R/LD.R:103:15:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/LD.R#L103) *warning:* **no visible global function definition for ‘calculate_average_LD’**\n```r\n​        ld <- calculate_average_LD(g1, g2)\n              ^~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:4:47:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​calculate_allele_spectrum_cpp <- function(v1, numFounders, step_size) {\n                                              ^~~~~~~~~~~\n```\n[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L5) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_calculate_allele_spectrum_cpp', PACKAGE = 'isoSIM', v1, numFounders, step_size)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:5:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L5) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_calculate_allele_spectrum_cpp', PACKAGE = 'isoSIM', v1, numFounders, step_size)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:5:62:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L5) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_calculate_allele_spectrum_cpp', PACKAGE = 'isoSIM', v1, numFounders, step_size)\n                                                             ^~~~~~~~\n```\n[R/RcppExports.R:8:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L8) *style:* **Lines should not be more than 80 characters.**\n```r\n​simulate_from_population <- function(file_name, total_runtime, morgan, number_of_markers, seed) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:9:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L9) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_simulate_from_population', PACKAGE = 'isoSIM', file_name, total_runtime, morgan, number_of_markers, seed)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:9:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L9) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_simulate_from_population', PACKAGE = 'isoSIM', file_name, total_runtime, morgan, number_of_markers, seed)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:9:57:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L9) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_simulate_from_population', PACKAGE = 'isoSIM', file_name, total_runtime, morgan, number_of_markers, seed)\n                                                        ^~~~~~~~\n```\n[R/RcppExports.R:12:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L12) *style:* **Lines should not be more than 80 characters.**\n```r\n​create_population_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, writeToFile) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:12:94:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L12) *style:* **Variable or function name should be snake_case.**\n```r\n​create_population_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, writeToFile) {\n                                                                                             ^~~~~~~~~~~\n```\n[R/RcppExports.R:13:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L13) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_create_population_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, writeToFile)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:13:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L13) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_population_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, writeToFile)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:13:54:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L13) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_population_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, writeToFile)\n                                                     ^~~~~~~~\n```\n[R/RcppExports.R:16:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L16) *style:* **Lines should not be more than 80 characters.**\n```r\n​create_isofemale_line_cpp <- function(v, pop_size, total_runtime, morgan, seed) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:17:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L17) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_create_isofemale_line_cpp', PACKAGE = 'isoSIM', v, pop_size, total_runtime, morgan, seed)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:17:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L17) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_isofemale_line_cpp', PACKAGE = 'isoSIM', v, pop_size, total_runtime, morgan, seed)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:17:58:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L17) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_isofemale_line_cpp', PACKAGE = 'isoSIM', v, pop_size, total_runtime, morgan, seed)\n                                                         ^~~~~~~~\n```\n[R/RcppExports.R:20:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L20) *style:* **Lines should not be more than 80 characters.**\n```r\n​create_two_populations_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, overlap, writeToFile) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:20:108:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L20) *style:* **Variable or function name should be snake_case.**\n```r\n​create_two_populations_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, overlap, writeToFile) {\n                                                                                                           ^~~~~~~~~~~\n```\n[R/RcppExports.R:21:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L21) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_create_two_populations_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, overlap, writeToFile)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:21:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L21) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_two_populations_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, overlap, writeToFile)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:21:59:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L21) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_two_populations_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, overlap, writeToFile)\n                                                          ^~~~~~~~\n```\n[R/RcppExports.R:24:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L24) *style:* **Lines should not be more than 80 characters.**\n```r\n​create_two_populations_migration_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, migration, writeToFile) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:24:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L24) *style:* **Variable and function names should not be longer than 30 characters.**\n```r\n​create_two_populations_migration_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, migration, writeToFile) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:24:120:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L24) *style:* **Variable or function name should be snake_case.**\n```r\n​create_two_populations_migration_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, seed, migration, writeToFile) {\n                                                                                                                       ^~~~~~~~~~~\n```\n[R/RcppExports.R:25:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L25) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_create_two_populations_migration_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, migration, writeToFile)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:25:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L25) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_two_populations_migration_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, migration, writeToFile)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:25:69:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L25) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_two_populations_migration_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, seed, migration, writeToFile)\n                                                                    ^~~~~~~~\n```\n[R/RcppExports.R:29:21:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L29) *style:* **Only use double-quotes.**\n```r\n​    invisible(.Call('_isoSIM_test_fish_functions', PACKAGE = 'isoSIM'))\n                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:29:62:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L29) *style:* **Only use double-quotes.**\n```r\n​    invisible(.Call('_isoSIM_test_fish_functions', PACKAGE = 'isoSIM'))\n                                                             ^~~~~~~~\n```\n[R/RcppExports.R:32:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L32) *style:* **Lines should not be more than 80 characters.**\n```r\n​select_population_cpp <- function(v1, selectM, s, population_size, run_time, morgan, seed, writeToFile) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:32:39:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L32) *style:* **Variable or function name should be snake_case.**\n```r\n​select_population_cpp <- function(v1, selectM, s, population_size, run_time, morgan, seed, writeToFile) {\n                                      ^~~~~~~\n```\n[R/RcppExports.R:32:92:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L32) *style:* **Variable or function name should be snake_case.**\n```r\n​select_population_cpp <- function(v1, selectM, s, population_size, run_time, morgan, seed, writeToFile) {\n                                                                                           ^~~~~~~~~~~\n```\n[R/RcppExports.R:33:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L33) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_select_population_cpp', PACKAGE = 'isoSIM', v1, selectM, s, population_size, run_time, morgan, seed, writeToFile)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:33:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L33) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_select_population_cpp', PACKAGE = 'isoSIM', v1, selectM, s, population_size, run_time, morgan, seed, writeToFile)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:33:54:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L33) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_select_population_cpp', PACKAGE = 'isoSIM', v1, selectM, s, population_size, run_time, morgan, seed, writeToFile)\n                                                     ^~~~~~~~\n```\n[R/RcppExports.R:36:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L36) *style:* **Lines should not be more than 80 characters.**\n```r\n​create_population_selection_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, select_matrix, selection, seed, write_to_file) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:36:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L36) *style:* **Variable and function names should not be longer than 30 characters.**\n```r\n​create_population_selection_cpp <- function(pop_size, number_of_founders, total_runtime, morgan, select_matrix, selection, seed, write_to_file) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:37:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L37) *style:* **Lines should not be more than 80 characters.**\n```r\n​    .Call('_isoSIM_create_population_selection_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, select_matrix, selection, seed, write_to_file)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:37:11:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L37) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_population_selection_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, select_matrix, selection, seed, write_to_file)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/RcppExports.R:37:64:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L37) *style:* **Only use double-quotes.**\n```r\n​    .Call('_isoSIM_create_population_selection_cpp', PACKAGE = 'isoSIM', pop_size, number_of_founders, total_runtime, morgan, select_matrix, selection, seed, write_to_file)\n                                                               ^~~~~~~~\n```\n[R/RcppExports.R:39:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/RcppExports.R#L39) *style:* **Trailing blank lines are superfluous.**\n```r\n​\n^\n```\n[R/select_population.R:74:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/select_population.R#L74) *style:* **Lines should not be more than 80 characters.**\n```r\n​  pop <- create_population_selection_cpp(pop_size, number_of_founders, total_runtime, morgan,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/select_population.R:75:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/select_population.R#L75) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                  select_matrix, selection, seed, write_to_file)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/select_population.R:76:16:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/R/select_population.R#L76) *warning:* **no visible global function definition for ‘create_pop_class’**\n```r\n​  popstruct <- create_pop_class(pop$population)\n               ^~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:44:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L44) *style:* **Lines should not be more than 80 characters.**\n```r\n​  expected <- junctions::number_of_junctions(N = pop_size, H_0 = 0.5, C = 1, t = run_time)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:216:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L216) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                         pop_size = 100, total_runtime = 100,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:217:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L217) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                         morgan = 1, seed = 42, write_to_file = FALSE)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:234:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L234) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                         pop_size = 100, total_runtime = 100,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:235:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L235) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                       morgan = 1, seed = 42, write_to_file = FALSE)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:238:23:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L238) *style:* **Commas should always have a space after.**\n```r\n​test_that(\"migration\",{\n                      ^\n```\n[tests/testthat/test-createPopulations.R:240:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L240) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                             number_of_founders = 10,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:241:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L241) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                             total_runtime = 1000,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:245:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L245) *style:* **Lines should not be more than 80 characters.**\n```r\n​                                                             write_to_file = FALSE)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-createPopulations.R:252:3:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-createPopulations.R#L252) *style:* **Variable or function name should be snake_case.**\n```r\n​  FST <- calculate_fst(pops_migration$Population_1,\n  ^~~\n```\n[tests/testthat/test-isoFemales.R:35:1:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-isoFemales.R#L35) *style:* **Lines should not be more than 80 characters.**\n```r\n​  vy <- isoSIM::create_population_from_individuals(list(female_1[[1]], female_2[[1]]),\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test-selection.R:4:17:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-selection.R#L4) *style:* **Use <-, not =, for assignment.**\n```r\n​  select_matrix = matrix(ncol = 3, nrow = 2)\n                ^\n```\n[tests/testthat/test-selection.R:30:17:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-selection.R#L30) *style:* **Use <-, not =, for assignment.**\n```r\n​  select_matrix = matrix(ncol = 3, nrow = 2)\n                ^\n```\n[tests/testthat/test-selection.R:102:46:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-selection.R#L102) *style:* **Put spaces around all infix operators.**\n```r\n​  testthat::expect_equal(mean(b$mean_freq), 1/number_founders, tolerance = 0.01)\n                                            ~^~\n```\n[tests/testthat/test-selection.R:119:46:](https://github.com/thijsjanzen/isoSIM/blob/13a65f28c6b162662f562d9ae8161f4c76b3a81a/tests/testthat/test-selection.R#L119) *style:* **Put spaces around all infix operators.**\n```r\n​  testthat::expect_equal(mean(b$mean_freq), 1/number_founders, tolerance = 0.01)\n                                            ~^~\n```"}}
{"actor":{"display_login":"lintr-bot"}}