[R/feature_growth.R:56:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_growth.R#L56) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.growth <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~
```
[R/feature_growth.R:77:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_growth.R#L77) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.growth <- conv_to_ms_arg.growth
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_growth.R:81:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_growth.R#L81) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.growth <- conv_to_ms_arg.growth
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_growth.R:85:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_growth.R#L85) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.growth <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_migration.R:88:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_migration.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.migration <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_migration.R:90:12:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_migration.R#L90) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( paste0("-eM', ", feature$get_time(), ", ",
           ^
```
[R/feature_migration.R:101:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_migration.R#L101) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.migration <- conv_to_ms_arg.migration
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_migration.R:105:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_migration.R#L105) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.migration <- conv_to_ms_arg.migration
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_migration.R:109:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_migration.R#L109) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.migration <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:71:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
#' for all loci, but it is possible to change this with \code{\link{par_variation}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:99:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L99) *style:* **Lines should not be more than 80 characters.**
```r
#' The infinite sites mutation (\strong{IFS}) model is a frequently used simplification
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:109:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L109) *style:* **Lines should not be more than 80 characters.**
```r
#' The Hasegawa, Kishino and Yano (\strong{HKY}) model (Hasegawa et al., 1985) allows
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:114:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
#' The general reversible process (\strong{GTR}) model (e.g. Yang, 1994) is more general
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:174:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L174) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.mutation <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:185:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L185) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.mutation <- conv_to_ms_arg.mutation
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:189:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L189) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.mutation <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_mutation.R:199:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_mutation.R#L199) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.mutation <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:16:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_outgroup.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
#' to determine the ancestral allele in finite sites simulations and are required
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:58:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_outgroup.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.outgroup <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:64:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_outgroup.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.outgroup <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:70:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_outgroup.R#L70) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.outgroup <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_outgroup.R:76:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_outgroup.R#L76) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.outgroup <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_pop_merge.R:54:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_pop_merge.R#L54) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.pop_merge <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_pop_merge.R:62:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_pop_merge.R#L62) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.pop_merge <- conv_to_ms_arg.pop_merge
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_pop_merge.R:66:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_pop_merge.R#L66) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.pop_merge <- conv_to_ms_arg.pop_merge
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_pop_merge.R:70:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_pop_merge.R#L70) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.pop_merge <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:11:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_recombination.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' This feature adds intra-locus recombination to a model.  The rate is per locus
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:13:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_recombination.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
#' \link[=locus_trio]{locus trios}. By default, the same recombination rate is used
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:14:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_recombination.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
#' for all loci, but it is possible to change this with \code{\link{par_variation}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:40:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_recombination.R#L40) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.recombination <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:46:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_recombination.R#L46) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.recombination <- conv_to_ms_arg.recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_recombination.R:50:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_recombination.R#L50) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.recombination <- conv_to_ms_arg.recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:92:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sample.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.sample <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:101:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sample.R#L101) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.sample <- conv_to_ms_arg.sample
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:105:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sample.R#L105) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.sample <- conv_to_ms_arg.sample
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sample.R:109:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sample.R#L109) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.sample <- function(feature, model) ""
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_selection.R:14:27:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
    initialize = function(strength_AA, strength_Aa, strength_aa,
                          ^~~~~~~~~~~
```
[R/feature_selection.R:14:40:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
    initialize = function(strength_AA, strength_Aa, strength_aa,
                                       ^~~~~~~~~~~
```
[R/feature_selection.R:16:51:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                          start, start_frequency, Ne, position, force_keep,
                                                  ^~
```
[R/feature_selection.R:29:15:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
      private$Ne <- Ne
              ^~
```
[R/feature_selection.R:37:15:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
      private$strength_Aa <- private$add_parameter(strength_Aa)
              ^~~~~~~~~~~
```
[R/feature_selection.R:39:17:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L39) *style:* **Variable and function name style should be snake_case.**
```r
        private$strength_AA <- private$add_parameter(strength_AA)
                ^~~~~~~~~~~
```
[R/feature_selection.R:84:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L84) *style:* **Lines should not be more than 80 characters.**
```r
#'   past-wards from either time 0 on if \code{start = TRUE}, or from \code{time}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_selection.R:112:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L112) *style:* **Lines should not be more than 80 characters.**
```r
#' @param force_keep Whether to restart simulations in which the selected goes to
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_selection.R:133:28:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L133) *style:* **Variable and function name style should be snake_case.**
```r
feat_selection <- function(strength_AA = 0,
                           ^~~~~~~~~~~
```
[R/feature_selection.R:134:28:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L134) *style:* **Variable and function name style should be snake_case.**
```r
                           strength_Aa = 0,
                           ^~~~~~~~~~~
```
[R/feature_selection.R:136:28:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L136) *style:* **Variable and function name style should be snake_case.**
```r
                           strength_A = NULL,
                           ^~~~~~~~~~
```
[R/feature_selection.R:141:28:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L141) *style:* **Variable and function name style should be snake_case.**
```r
                           Ne = 10000,
                           ^~
```
[R/feature_selection.R:167:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L167) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.selection <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_selection.R:173:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L173) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.selection <- conv_to_ms_arg.selection
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_selection.R:177:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L177) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.selection <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_selection.R:232:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_selection.R#L232) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.selection <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_size_change.R:54:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_size_change.R#L54) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.size_change <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_size_change.R:75:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_size_change.R#L75) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.size_change <- conv_to_ms_arg.size_change
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_size_change.R:79:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_size_change.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.size_change <- conv_to_ms_arg.size_change
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_size_change.R:83:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_size_change.R#L83) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.size_change <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:10:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.seg_sites_feat <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:40:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L40) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.trees_feat <- function(feature, model) "-T "
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:44:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L44) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.trees_feat <- conv_to_ms_arg.trees_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:48:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.trees_feat <- conv_to_ms_arg.trees_feat
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:52:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L52) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.trees_feat <- function(feature, model) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:67:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.files_feat <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:71:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.files_feat <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:75:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L75) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.files_feat <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_sumstats.R:79:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_sumstats.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.files_feat <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:79:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_unphased.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_ms_arg.unphased <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:83:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_unphased.R#L83) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_msms_arg.unphased <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:87:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_unphased.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_scrm_arg.unphased <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature_unphased.R:91:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature_unphased.R#L91) *style:* **Variable and function name style should be snake_case.**
```r
conv_to_seqgen_arg.unphased <- ignore_par
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/feature.R:3:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature.R#L3) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
feature_class <- R6Class("feature", inherit = model_part,
^
```
[R/feature.R:59:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/feature.R#L59) *style:* **Variable and function name style should be snake_case.**
```r
is.feature <- function(feature) inherits(feature, "feature")
^~~~~~~~~~
```
[R/locus.R:42:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/locus.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
is.locus <- function(locus) any("locus" == class(locus))
^~~~~~~~
```
[R/locus.R:48:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/locus.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
#' stretch of DNA of a given length. All loci are simulated independently of each
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/locus.R:99:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/locus.R#L99) *style:* **Lines should not be more than 80 characters.**
```r
#' linked to each other. They are still unlinked to all other loci or locus trios
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/locus.R:119:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/locus.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
#'   locus_trio(locus_length=c(1250, 1017, 980), distance=c(257, 814), number = 10)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_build.R:65:65:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/model_build.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if (any(!pop %in% get_populations(model)) && pop[1] != "all" ) {
                                                                ^
```
[R/model_check.R:9:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/model_check.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso Do view the priority of the simulators: \code{\link{list_simulators}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/model_simulate.R:36:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/model_simulate.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
simulate.coalmodel <- function(object, nsim = 1, seed, ...,
^~~~~~~~~~~~~~~~~~
```
[R/model.R:5:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/model.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' can be simulated using the \code{\link[=simulate.coalmodel]{simulate}} function.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/model.R:18:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/model.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso The 'coala-intro' vignette for a general description on how to extend
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/model.R:83:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/model.R#L83) *style:* **Variable and function name style should be snake_case.**
```r
is.model <- function(model) {
^~~~~~~~
```
[R/onLoad.R:1:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/onLoad.R#L1) *style:* **Variable and function name style should be snake_case.**
```r
.onLoad <- function(libname, pkgname) {
^~~~~~~
```
[R/parameter_prior.R:34:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter_prior.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
is.prior_par <- function(par) inherits(par, "prior_par")
^~~~~~~~~~~~
```
[R/parameter_variation.R:35:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter_variation.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
is.par_variation <- function(object) inherits(object, "variation_par")
^~~~~~~~~~~~~~~~
```
[R/parameter_variation.R:52:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter_variation.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso For parameters that are identical for all loci: \code{\link{parameter}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/parameter_zero_inflation.R:40:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter_zero_inflation.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso For parameters that are identical for all loci: \code{\link{parameter}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/parameter_zero_inflation.R:44:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter_zero_inflation.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
#'   feat_recombination(par_zero_inflation(par_named("rho"), .5, random = FALSE)) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/parameter.R:21:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter.R#L21) *style:* **Variable and function name style should be snake_case.**
```r
is.par <- function(par) {
^~~~~~
```
[R/parameter.R:58:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
is.named_par <- function(par) {
^~~~~~~~~~~~
```
[R/parameter.R:114:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
#' @describeIn parameter Creates a parameter with value determined by evaluating an expression.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/parameter.R:178:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/parameter.R#L178) *style:* **Variable and function name style should be snake_case.**
```r
is.ranged_par <- function(par) inherits(par, "range_par")
^~~~~~~~~~~~~
```
[R/segsites.R:29:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/segsites.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso For converting biological data to segsites: \code{\link{as.segsites}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/segsites.R:115:27:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/segsites.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      rep( 0, ncol(middle[[locus]])),
                          ^
```
[R/segsites.R:116:27:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/segsites.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      rep( 1, ncol(right[[locus]]))),
                          ^
```
[R/segsites.R:136:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/segsites.R#L136) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso Further instructions are provided in the `coala-data-import` vignette
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/segsites.R:139:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/segsites.R#L139) *style:* **Variable and function name style should be snake_case.**
```r
as.segsites <- function(data, ...) UseMethod("as.segsites")
^~~~~~~~~~~
```
[R/simulator_msms.R:13:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/simulator_msms.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
msms_class <- R6Class("Msms", inherit = ms_class,
^
```
[R/sumstat_ihh.R:5:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/sumstat_ihh.R#L5) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stat_ihh_class <- R6Class("stat_ihh", inherit = sumstat_class,
^
```
[R/sumstat_mcmf.R:73:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/sumstat_mcmf.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
#' @param type_expand Specifies the type of expanded MCMF to be used. See Details
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_omega.R:116:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/sumstat_omega.R#L116) *style:* **Lines should not be more than 80 characters.**
```r
#' \href{http://sco.h-its.org/exelixis/web/software/omegaplus/index.html}{OmegaPlus},
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat_seg_sites.R:23:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/sumstat_seg_sites.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso For a description of the segregating sites class: \code{\link{create_segsites}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sumstat.R:45:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/sumstat.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
is.sum_stat <- function(sumstat) inherits(sumstat, "sumstat")
^~~~~~~~~~~
```
[R/sumstat.R:53:1:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/R/sumstat.R#L53) *style:* **Variable and function name style should be snake_case.**
```r
add_to_model.sumstat <- function(sum_stat, model, feat_name) {
^~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-simulator-seqgen.R:150:3:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/tests/testthat/test-simulator-seqgen.R#L150) *style:* **Variable and function name style should be snake_case.**
```r
  model.hky <- model_hky()
  ^~~~~~~~~
```
[tests/testthat/test-sumstat-sfs.R:4:3:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/tests/testthat/test-sumstat-sfs.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  seg.sites <- list(create_segsites(matrix(c(1, 0, 0, 0,
  ^~~~~~~~~
```
[tests/testthat/test-sumstat-sfs.R:45:3:](https://github.com/statgenlmu/coala/blob/483cc39b0289cd029a090e17f989defca24f940f/tests/testthat/test-sumstat-sfs.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  seg.sites <- list(create_segsites(cbind(ss, ss, ss),
  ^~~~~~~~~
```


Additional blank line at EOF.


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{
	"version": 2,
<<<<<<>>>>>> 40bc047ffef309c58379ab43c70bfc610eb01192
		"env": {
			"GITHUB_TOKEN": "@github_token"
		}
	},
	"env": {
		"GITHUB_TOKEN": "@github_token"
	}
}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


Shouldn't be there also some generic footer too?


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Don't instanciate on every method call. Under server load this severely slows things down and may allow DoS.


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kui välismaalased liituvad?


Missing upstream license spec. Cannot be used unless license declared and compatible.


Belajar


SVG version of logo as base for favicon preferred if scaling or editing was required.


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This is still in consideration.
It seems that it should be
`pMax.x = min(pMax.x, sysLaunch_Dim.x); pMax.y = min(pMax.y, sysLaunch_Dim.y);`
to be compatible with the code below:
> for (int y = pMin.y; y < pMax.y; ++y)
        {
            for (int x = pMin.x; x < pMax.x; ++x)

x and y could have reached the critical value sysLaunch_Dim.x-1 and sysLaunch_Dim.y-1, respectively.


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you  have changed


sub_total and subtotal in file - make consistent


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Deployment failed with the following error:

~~~
The chosen alias "preloader.now.sh" is already in use by another account.
~~~


<img width="562" alt="Screenshot 2019-11-02 14 16 03" src="https://user-images.githubusercontent.com/15629602/68070132-5e83a000-fd7b-11e9-85c2-f6020dbfc340.png">

Well received.


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Although definitely cleaner code-wise, this method has the side effect of removing the title label 100% of the time. In software such as `gnome-mahjongg` this label is used to show which board layout is being used. This information is not shown in the window frame (it just says "Mahjongg") and as a result, it is no longer shown anywhere. In the previous commit, this label was still shown. This is not an issue with programs such as `gedit` in which the contents of the top label are also shown in the window frame.

Attached are screenshots of `gnome-mahjongg` running under `gtk3-nocsd` at this commit (`3ca2d27`) and the previous commit (`3f91a6b`) to illustrate the aforementioned side-effect.

![gnome-mahjongg running under gtk3-nocsd commit 3ca2d27 (HEAD as of this message) - the label at the top of the program window is missing](https://user-images.githubusercontent.com/48707689/68070068-0bc8d900-fdb9-11e9-8e3d-7026614f0bed.png)

![gnome-mahjongg running under gtk3-nocsd commit 3f91a6b (HEAD~1 as of this message) - the label showing the selected board layout is being shown](https://user-images.githubusercontent.com/48707689/68070084-5185a180-fdb9-11e9-9804-8caf5e06433c.png)


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~~~
Failed to validate now.json: Invalid request: meta['githubCommitAuthorName'] should NOT be shorter than 1 characters
~~~


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Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

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"магические цифры" лучше хранить в константах с понятными именами


Review:

- The instructions asked: **try not to use just strings**.
Could you attempt to use other data structures?

Just testing your understanding:
- What's the data structure/ data type in `line 9`?


Masuk ke situasi itu sulit


It seems there's extra `(pos` that should not be there. Without it, code is working


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{
	"version": 2,
<<<<<<>>>>>> 40bc047ffef309c58379ab43c70bfc610eb01192
		"env": {
			"GITHUB_TOKEN": "@github_token"
		}
	},
	"env": {
		"GITHUB_TOKEN": "@github_token"
	}
}

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[R/network-structure.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/network-structure.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
              i <- tmp[seq_len(length(tmp) - 1)] != tmp[seq_len(length(tmp))[-1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/network-summary.R:262:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/network-summary.R#L262) *style:* **functions should have cyclomatic complexity of less than 15, this has 38.**
```r
setMethod("NetworkSummary",
^
```
[R/out-degree.R:119:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/out-degree.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the OutDegree for a data.frame with movements, see details and examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:67:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/outgoing-contact-chain.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
##'     The \code{\link{OutgoingContactChain}} of the root within the time-interval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:77:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/outgoing-contact-chain.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
##'     Get the OutgoingContactChain for a data.frame with movements, see examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/outgoing-contact-chain.R:137:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/outgoing-contact-chain.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Unable to determine OutgoingContactChain for ingoing contacts")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:82:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/plot.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
              tree$ingoing$bg <- ifelse(tree$ingoing$level > 0, "white", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:95:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/plot.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
              tree$outgoing$bg <- ifelse(tree$outgoing$level > 0, "gray", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:74:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/report.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
    as.character(unlist(by(contacts, sprintf("%s - %s", contacts$lhs, contacts$rhs), function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:79:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/report.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                   sprintf('<h3><a name="%s-%s-%s">%s %s %s</a></h3>', direction,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:82:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/report.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
                   "<tr><th>Date</th><th>Id</th><th>N</th><th>Category</th><th>Source</th><th>Destination</th></tr>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:142:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/report.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
        lines <- c(lines, "<p>No ingoing contacts during the search period.</p>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:276:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/report.R#L276) *style:* **Lines should not be more than 80 characters.**
```r
##' @param template the Sweave template file to use. If none is provided, the default
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/report.R:369:38:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/report.R#L369) *style:* **Put spaces around all infix operators.**
```r
              Sweave(template, syntax="SweaveSyntaxNoweb")
                                    ~^~
```
[R/shortest-paths.R:168:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L168) *style:* **functions should have cyclomatic complexity of less than 15, this has 41.**
```r
setMethod("ShortestPaths",
^
```
[R/shortest-paths.R:239:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:240:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:254:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:274:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:279:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:282:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:365:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L365) *style:* **Lines should not be more than 80 characters.**
```r
              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shortest-paths.R:411:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/shortest-paths.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
                                         destination = x$destination[sp$outRowid],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:167:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L167) *style:* **functions should have cyclomatic complexity of less than 15, this has 56.**
```r
Trace <- function(movements,
^
```
[R/trace.R:207:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L207) *style:* **Lines should not be more than 80 characters.**
```r
    if (any(is.factor(movements$destination), is.integer(movements$destination))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:252:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L252) *style:* **Lines should not be more than 80 characters.**
```r
        if (any(is.factor(movements$category), is.integer(movements$category))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:306:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L306) *style:* **Lines should not be more than 80 characters.**
```r
        if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:307:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L307) *style:* **Lines should not be more than 80 characters.**
```r
            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:318:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L318) *style:* **Lines should not be more than 80 characters.**
```r
        ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:335:31:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                             ~^~
```
[R/trace.R:335:38:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                    ~^~
```
[R/trace.R:335:57:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L335) *style:* **Put spaces around all infix operators.**
```r
        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                                       ~^~
```
[R/trace.R:336:32:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L336) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                              ~^~
```
[R/trace.R:336:51:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L336) *style:* **Put spaces around all infix operators.**
```r
        inEnd <- rep(tEnd, each=n.days, length.out=n)
                                                 ~^~
```
[R/trace.R:337:42:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                        ~^~
```
[R/trace.R:337:56:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L337) *style:* **Put spaces around all infix operators.**
```r
        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                                      ~^~
```
[R/trace.R:340:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L340) *style:* **Lines should not be more than 80 characters.**
```r
    } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:345:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:348:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L348) *style:* **Lines should not be more than 80 characters.**
```r
        stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:458:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L458) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:459:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L459) *style:* **Lines should not be more than 80 characters.**
```r
                            as.integer(factor(movements$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:471:16:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L471) *style:* **Put spaces around all infix operators.**
```r
        j <- (i-1) * 4
              ~^~
```
[R/trace.R:481:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L481) *style:* **Lines should not be more than 80 characters.**
```r
        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:483:12:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L483) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:484:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L484) *style:* **Lines should not be more than 80 characters.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:484:76:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L484) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:485:72:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L485) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:509:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L509) *style:* **Lines should not be more than 80 characters.**
```r
        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:511:12:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L511) *style:* **Commented code should be removed.**
```r
        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:512:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L512) *style:* **Lines should not be more than 80 characters.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:512:76:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L512) *style:* **Put spaces around all infix operators.**
```r
        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~
```
[R/trace.R:513:72:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L513) *style:* **Put spaces around all infix operators.**
```r
                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~
```
[R/trace.R:535:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L535) *style:* **Lines should not be more than 80 characters.**
```r
    ## Name each list item with ContactTrace objects to the name of the ContactTrace root.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/trace.R:536:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/trace.R#L536) *style:* **Lines should not be more than 80 characters.**
```r
    names(result) <-  sapply(result, function(listItem) listItem@ingoingContacts@root)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree.R:64:38:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/tree.R#L64) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(dst)>0)
                                    ~^~
```
[R/tree.R:94:38:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/tree.R#L94) *style:* **Put spaces around all infix operators.**
```r
                stopifnot(length(src)>0)
                                    ~^~
```
[R/tree.R:135:1:](https://github.com/stewid/EpiContactTrace/blob/b3f92b2025741443ea7b48057453da5bf815fb64/R/tree.R#L135) *style:* **functions should have cyclomatic complexity of less than 15, this has 48.**
```r
position_tree <- function(tree,
^
```


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