[R/are_equal_mcmcs.R:17:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/are_equal_mcmcs.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 29.**
```r
are_equal_mcmcs <- function(
^
```
[R/check_mcmc.R:9:3:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/check_mcmc.R#L9) *warning:* **no visible global function definition for ‘check_store_every’**
```r
  check_store_every(mcmc$store_every)
  ^~~~~~~~~~~~~~~~~
```
[R/check_mrca_prior.R:27:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/check_mrca_prior.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
check_mrca_prior <- function(mrca_prior) {
^
```
[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/clock_model_to_xml_prior_distr.R#L14) *warning:* **no visible global function definition for ‘rln_clock_model_to_xml_mean_rate_prior’**
```r
      text <- c(text, rln_clock_model_to_xml_mean_rate_prior(clock_model)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:32:23:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/clock_models_to_xml_state.R#L32) *warning:* **no visible global function definition for ‘clock_model_to_xml_state’**
```r
    line_to_remove <- clock_model_to_xml_state(clock_models[[1]]) # nolint
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:9:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_distr.R#L9) *warning:* **no visible global function definition for ‘tree_priors_to_xml_prior_distr’**
```r
  text <- c(text, tree_priors_to_xml_prior_distr(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:10:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_distr.R#L10) *warning:* **no visible global function definition for ‘gamma_site_models_to_xml_prior_distr’**
```r
  text <- c(text, gamma_site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:11:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_distr.R#L11) *warning:* **no visible global function definition for ‘site_models_to_xml_prior_distr’**
```r
  text <- c(text, site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:27:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_operators.R#L27) *warning:* **no visible global function definition for ‘site_models_to_xml_operators’**
```r
  text <- c(text, site_models_to_xml_operators(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_run.R:23:11:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_run.R#L23) *warning:* **no visible global function definition for ‘mcmc_to_xml_run’**
```r
  text <- mcmc_to_xml_run(mcmc) # nolint beautier function
          ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:24:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_state.R#L24) *warning:* **no visible global function definition for ‘site_models_to_xml_state’**
```r
  text <- c(text, site_models_to_xml_state(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:33:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_beast2_input_state.R#L33) *warning:* **no visible global function definition for ‘tree_priors_to_xml_state’**
```r
  text <- c(text, tree_priors_to_xml_state(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_clock_models_from_names.R:5:26:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_clock_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_clock_model_from_name’**
```r
    clock_models[[i]] <- create_clock_model_from_name(clock_model_name) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:41:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_mcmc_nested_sampling.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @aliases create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:42:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_mcmc_nested_sampling.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
#' @export create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_site_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_site_model_from_name’**
```r
    site_models[[i]] <- create_site_model_from_name(site_model_name) # nolint beautier function
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:17:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_tracelog_xml.R#L17) *warning:* **no visible global function definition for ‘tree_models_to_xml_tracelog’**
```r
  text <- c(text, tree_models_to_xml_tracelog(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:32:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/create_tracelog_xml.R#L32) *warning:* **no visible global function definition for ‘tree_priors_to_xml_tracelog’**
```r
  text <- c(text, tree_priors_to_xml_tracelog(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_operators_from_lines.R:13:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/extract_xml_operators_from_lines.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
  last_line <- beautier::find_last_regex_line(lines, "(<operator id=\")|(</operator>)")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/extract_xml_section_from_lines.R#L7) *warning:* **no visible global function definition for ‘extract_xml_operators_from_lines’**
```r
    return(extract_xml_operators_from_lines(lines)) # nolint beautier function
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_last_xml_closing_tag_line.R:6:3:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/find_last_xml_closing_tag_line.R#L6) *warning:* **no visible global function definition for ‘find_last_regex_line’**
```r
  find_last_regex_line(lines, paste0("</", section, ">")) # nolint beautier function
  ^~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_id.R:5:9:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/get_alignment_id.R#L5) *warning:* **no visible global function definition for ‘get_file_base_sans_ext’**
```r
  id <- get_file_base_sans_ext(fasta_filename) # nolint beautier function
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/has_xml_opening_tag.R#L11) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
    tag <- get_xml_opening_tag(lines) # nolint
           ^~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:14:24:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/has_xml_opening_tag.R#L14) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !beautier::is_one_na(find_first_xml_opening_tag_line(lines, section))
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:10:10:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_clock_models.R#L10) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames) # nolint beautier function
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:13:26:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_clock_models.R#L13) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(ucldstdev_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:20:26:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_clock_models.R#L20) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(mean_rate_prior_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/init_inference_model.R:39:22:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_inference_model.R#L39) *warning:* **no visible global function definition for ‘init_mrca_prior’**
```r
  inference_model <- init_mrca_prior(input_filename, inference_model)
                     ^~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:8:50:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_mrca_prior.R#L8) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
      inference_model$mrca_prior$alignment_id <- get_alignment_id(input_filename) # nolint beautier function
                                                 ^~~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:11:48:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_mrca_prior.R#L11) *warning:* **no visible global function definition for ‘get_taxa_names’**
```r
      inference_model$mrca_prior$taxa_names <- get_taxa_names(input_filename) # nolint beautier function
                                               ^~~~~~~~~~~~~~
```
[R/init_site_models.R:44:28:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_site_models.R#L44) *warning:* **no visible global function definition for ‘get_site_model_n_params’**
```r
    param_id <- param_id + get_site_model_n_params(site_model) # nolint beautier function
                           ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:198:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_site_models.R#L198) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(gtr_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:220:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_site_models.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
  if (!beautier::is_one_na(hky_site_model$gamma_site_model$gamma_shape_prior_distr)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:299:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_site_models.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(jc69_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:327:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/init_site_models.R#L327) *style:* **Lines should not be more than 80 characters.**
```r
    !beautier::is_one_na(tn93_site_model$gamma_site_model$gamma_shape_prior_distr)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/interspace.R:6:11:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/interspace.R#L6) *warning:* **no visible global function definition for ‘count_trailing_spaces’**
```r
  nsni <- count_trailing_spaces(lines[1]) # nolint beautier function
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_clock_model_name.R:2:13:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_clock_model_name.R#L2) *warning:* **no visible global function definition for ‘get_clock_model_names’**
```r
  name %in% get_clock_model_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_default_mcmc.R:2:8:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_default_mcmc.R#L2) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(mcmc)) return(FALSE) # nolint beautier function
       ^~~~~~~
```
[R/is_default_mcmc.R:3:39:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_default_mcmc.R#L3) *warning:* **no visible global function definition for ‘create_mcmc’**
```r
  length(names(mcmc)) == length(names(create_mcmc()))
                                      ^~~~~~~~~~~
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_freq_equilibrium_name.R:4:13:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_freq_equilibrium_name.R#L4) *warning:* **no visible global function definition for ‘get_freq_equilibrium_names’**
```r
  name %in% get_freq_equilibrium_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_id.R:4:32:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_id.R#L4) *warning:* **no visible global function definition for ‘is_one_int’**
```r
  assertive::is_a_string(x) || is_one_int(x) # nolint beautier function
                               ^~~~~~~~~~
```
[R/is_init_distr.R:26:20:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_init_distr.R#L26) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(x))
                   ^~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_init_site_model.R#L36) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
is_init_gtr_site_model <- function(
^
```
[R/is_mrca_align_id_in_fasta.R:6:9:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_mrca_align_id_in_fasta.R#L6) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
  id <- get_alignment_id(fasta_filename)
        ^~~~~~~~~~~~~~~~
```
[R/is_mrca_align_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_mrca_align_ids_in_fastas.R#L6) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:8:8:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L8) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE) # nolint beautier function
       ^~~~~~~~
```
[R/is_site_model.R:10:8:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L10) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:18:10:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L18) *warning:* **no visible global function definition for ‘is_distr’**
```r
    if (!is_distr(expected_distr)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:24:10:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L24) *warning:* **no visible global function definition for ‘is_param’**
```r
    if (!is_param(expected_param)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:27:8:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L27) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/is_tree_prior_name.R:2:13:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_tree_prior_name.R#L2) *warning:* **no visible global function definition for ‘get_tree_prior_names’**
```r
  name %in% get_tree_prior_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/mcmc_to_xml_run.R:47:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/mcmc_to_xml_run.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    xml <- paste0(xml, " numInitializationAttempts=\"", mcmc$n_init_attempts, "\"")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mrca_prior_to_xml_lh_distr.R:6:34:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/mrca_prior_to_xml_lh_distr.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_prior) == 1 && is_one_na(mrca_prior)) return(NULL) # nolint beautier function
                                 ^~~~~~~~~
```
[R/mrca_priors_to_xml_state.R:6:35:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/mrca_priors_to_xml_state.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_priors) == 1 && is_one_na(mrca_priors)) return(NULL) # nolint beautier function
                                  ^~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_model_to_xml_state.R#L25) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_model_to_xml_state.R#L51) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_2_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_subst_model.R:6:18:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_model_to_xml_subst_model.R#L6) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/site_model_to_xml_subst_model.R:7:18:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_model_to_xml_subst_model.R#L7) *warning:* **no visible global function definition for ‘is_jc69_site_model’**
```r
  testit::assert(is_jc69_site_model(site_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_models_to_xml_operators.R#L4) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_tracelog.R:6:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/site_models_to_xml_tracelog.R#L6) *warning:* **no visible global function definition for ‘site_model_to_xml_tracelog’**
```r
    text <- c(text, site_model_to_xml_tracelog(site_model)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:10:22:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_prior_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior) # nolint beautier function
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:7:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_prior_to_xml_prior_distr.R#L7) *warning:* **no visible global function definition for ‘bd_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, bd_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:9:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_prior_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘cbs_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cbs_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:11:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_prior_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘ccp_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, ccp_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:13:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_prior_to_xml_prior_distr.R#L13) *warning:* **no visible global function definition for ‘cep_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cep_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:16:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_prior_to_xml_prior_distr.R#L16) *warning:* **no visible global function definition for ‘yule_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, yule_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_distr.R:8:21:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_priors_to_xml_distr.R#L8) *warning:* **no visible global function definition for ‘tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_operators.R:6:18:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/R/tree_priors_to_xml_operators.R#L6) *warning:* **no visible global function definition for ‘are_tree_priors’**
```r
  testit::assert(are_tree_priors(tree_priors)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[tests/testthat/test-are_equal_mcmcs.R:57:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/tests/testthat/test-are_equal_mcmcs.R#L57) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-check_file_and_model_agree.R:16:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/tests/testthat/test-check_file_and_model_agree.R#L16) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-check_file_and_model_agree.R:35:19:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/tests/testthat/test-check_file_and_model_agree.R#L35) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-create_treelog_xml.R:15:1:](https://github.com/ropensci/beautier/blob/7779f08f4a8ca368e8f5599334951929e938b15a/tests/testthat/test-create_treelog_xml.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
    "    <log id=\"TreeWithMetaDataLogger.t:test_output_0\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:test_output_0\"/>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://gaboom-nh0bte8z2.now.sh
* https://gaboom.now.sh
* https://gaboom.dolf99.now.sh
* https://gaboom-git-master.dolf99.now.sh


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

SyntaxError at template.tasks.metadata.owner: unexpected EOF for '{$eval: "len(event.repository.forks)"} > 2 && "@" in event.repository.forks' at '$eval: "len(event.repository.forks)"} > 2 && "@" in event.repository.forks'

</details>


Successfully deployed to following URLs:

* https://bequia-forum-85o1c7sny.now.sh
* https://bequiaforum.com
* https://bequia-forum.ryancarville.now.sh
* https://bequia-forum-git-master.ryancarville.now.sh


I would use toETH(1), toETH(0.999) etc. here. You might need to modify toETH to allow for more decimal places.


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

can not read a block mapping entry; a multiline key may not be an implicit key at line 26, column 15:
              then: ${event.pusher.email}
                  ^

</details>


wwwwwwwwwwwwwwwww


[Document (3).docx](https://github.com/abhi913/beee-cu19/files/3836154/Document.3.docx)


Henri, thanks very much.
Was there a commit to make a corresponding update in the sentence in the manual in the sentence that says
"Only the two color models gray and rgb are supported."
?


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

BuiltinError at template.tasks.metadata.lengthMail: invalid arguments to builtin: len

</details>


[R/create_temp_output_state_filename.R:2:20:](https://github.com/ropensci/beastier/blob/647bd3dbcd2f823a90a66f82b6f337a07cb14805/R/create_temp_output_state_filename.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#' stores its state
                   ^
```
[R/create_temp_output_state_filename.R:4:1:](https://github.com/ropensci/beastier/blob/647bd3dbcd2f823a90a66f82b6f337a07cb14805/R/create_temp_output_state_filename.R#L4) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_temp_output_state_filename <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Maybe there is a misunderstanding, but I was worried that, say,
```
let g:UltiSnipsSnippetDirectories = [$HOME . '/.vim/UltiSnips', $HOME . '/.vim/plugged/vim-snippets/UltiSnips']
```
would not find snippets in one of the two directories listed above because the documentation insists that there must be a single global path. However, all snippets defined in both directories expand.


**vbucket** and **bucket id** are used before being defined. Maybe it's better to link here to the definition below?


ребята, я создала новую страницу. посмотрите. вчерашний урок не писала, поэтому просто страница.


Successfully deployed to following URLs:

* https://new-york-times-cvvz4z8yi.now.sh
* https://new-york-times-eta-one.now.sh
* https://new-york-times.char502.now.sh
* https://new-york-times-git-master.char502.now.sh


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

InterpreterError at template.tasks.metadata.owner: unknown context value lengthMail

</details>


But then, we need to keep on updating the source independently, right? That is work I would like to avoid.


This is a fix for issue #1129 .


just


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
check_pir_out <- function(
^
```
[R/check_sim_true_alignment_function.R:9:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/check_sim_true_alignment_function.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_true_alignment_function <- function(sim_true_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/check_sim_twin_alignment_function.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_twin_alignment_function <- function(sim_twin_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:10:3:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_alignment_obsolete.R#L10) *warning:* **local variable ‘n_taxa’ assigned but may not be used**
```r
  n_taxa <- ape::Ntip(phylogeny)
  ^~~~~~
```
[R/create_alignment_obsolete.R:11:3:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_alignment_obsolete.R#L11) *warning:* **local variable ‘n_nucleotides’ assigned but may not be used**
```r
  n_nucleotides <- nchar(alignment_params$root_sequence)
  ^~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:67:9:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_alignment_obsolete.R#L67) *style:* **Commented code should be removed.**
```r
    #   alignment_params = alignment_params
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:98:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_alignment_obsolete.R#L98) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_alignment_obsolete.R#L115) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:144:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_alignment_obsolete.R#L144) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_all_experiments.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
create_all_experiments <- function(
^
```
[R/create_copy_twin_tree_from_true_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_copy_twin_tree_from_true_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_bd_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_sim_bd_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_bd_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_yule_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:273:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/default_params_doc.R#L273) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_linked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:277:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/default_params_doc.R#L277) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_unlinked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_alignment_n_taxa.R:14:5:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_alignment_n_taxa.R#L14) *style:* **Commented code should be removed.**
```r
  # length(labels(alignment))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_sequences.R:5:3:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_copy_true_alignment_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_copy_true_alignment_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_copy_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/get_sim_twin_alignment_with_standard_site_model_function.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run.R:24:17:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/pir_run.R#L24) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/pir_to_pics.R:10:17:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/pir_to_pics.R#L10) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/pir_to_tables.R:7:17:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/pir_to_tables.R#L7) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_true_alignment_with_linked_node_sub_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_true_alignment_with_standard_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_standard_site_model.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_twin_alignment_with_standard_site_model.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_unlinked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/R/sim_twin_alignment_with_unlinked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_experiments.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
  cand_experiment_1$inference_model$mcmc <- cand_experiment_2$inference_model$mcmc
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:32:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
      pirouette::get_sim_true_alignment_with_linked_node_sub_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:38:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
      pirouette::get_sim_true_alignment_with_unlinked_node_sub_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:56:9:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:56:11:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { }
          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:58:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:63:75:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L63) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:63:77:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L63) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:71:9:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) {}
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:71:10:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) {}
         ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:81:9:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L81) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:81:25:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L81) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_true_alignment_function.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:62:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:64:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:42:62:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:42:64:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:51:9:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "irrelevant" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:51:24:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "irrelevant" }
                       ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:62:9:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:62:25:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:64:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_alignment_function.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:66:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                 ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:68:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                   ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:74:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                         ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:90:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                                ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_tree_function' must be a function with one argument called 'true_phylogeny'"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:72:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                       ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:88:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                                ^
```
[tests/testthat/test-check_twinning_params.R:209:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-check_twinning_params.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
        sim_twin_alignment_function = get_sim_twin_alignment_with_standard_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-create_error_measure_params.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
      list.files(dirname(experiment$errors_filename), pattern = basename(experiment$errors_filename))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_twin_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-create_twin_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:111:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_alignment_n_taxa.R#L111) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:112:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_alignment_n_taxa.R#L112) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_experiments_filenames.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_experiments_filenames.R:32:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_experiments_filenames.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:14:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_pir_params_filenames.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:41:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_pir_params_filenames.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:65:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_pir_params_filenames.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:107:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_pir_params_filenames.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_temp_errors_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_temp_errors_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-get_temp_fasta_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-get_temp_fasta_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-pir_run.R:127:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-pir_run.R#L127) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment <- readLines(pir_params$twinning_params$twin_alignment_filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_alignment_with_n_mutations.R:88:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-sim_alignment_with_n_mutations.R#L88) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/06ca84356641bf92c97a1fba6e435c7514aec8f9/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


gradient descent step functions code


This setting includes the `@Component` annotation to the generated implementation:

```java
@Generated(
    value = "org.mapstruct.ap.MappingProcessor",
    date = "2019-11-12T13:40:20+0100",
    comments = "version: 1.3.0.Final, compiler: javac, environment: Java 1.8.0_212 (Azul Systems, Inc.)"
)
@Component
public class CategoryMapperImpl implements CategoryMapper {

}
```


Hi,
Latest commit shoud have fixed this. If not, please open an issue.
Cheers,


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

SyntaxError at template.tasks.metadata.lengthMail: unexpected EOF for 'len(${event.repository.forks})' at '${event.repository.forks})'

</details>


[tests/testthat/test-generics.R:34:7:](https://github.com/IndrajeetPatil/broomExtra/blob/7696b181a16f4e327fe0add077f58386f10d14dc/tests/testthat/test-generics.R#L34) *style:* **Commented code should be removed.**
```r
    # testthat::expect_equal(dim(broomExtra::tidy(mtcars)), c(32L, 12L))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-generics.R:35:7:](https://github.com/IndrajeetPatil/broomExtra/blob/7696b181a16f4e327fe0add077f58386f10d14dc/tests/testthat/test-generics.R#L35) *style:* **Commented code should be removed.**
```r
    # testthat::expect_identical(names(broomExtra::tidy(mtcars))[1], "rownames")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


yes


@Bnaya Any reason why allowStateReadsEnd(prevAllowStateReads) is not called to restore allowStateReads when the catch clause in line 106-110 (above this comment) is executed? Did you miss it?


for  666


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
check_pir_out <- function(
^
```
[R/check_sim_true_alignment_function.R:9:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/check_sim_true_alignment_function.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_true_alignment_function <- function(sim_true_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/check_sim_twin_alignment_function.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_twin_alignment_function <- function(sim_twin_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:10:3:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_alignment_obsolete.R#L10) *warning:* **local variable ‘n_taxa’ assigned but may not be used**
```r
  n_taxa <- ape::Ntip(phylogeny)
  ^~~~~~
```
[R/create_alignment_obsolete.R:11:3:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_alignment_obsolete.R#L11) *warning:* **local variable ‘n_nucleotides’ assigned but may not be used**
```r
  n_nucleotides <- nchar(alignment_params$root_sequence)
  ^~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:67:9:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_alignment_obsolete.R#L67) *style:* **Commented code should be removed.**
```r
    #   alignment_params = alignment_params
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:98:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_alignment_obsolete.R#L98) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_alignment_obsolete.R#L115) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_obsolete.R:144:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_alignment_obsolete.R#L144) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_all_experiments.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
create_all_experiments <- function(
^
```
[R/create_copy_twin_tree_from_true_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_copy_twin_tree_from_true_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_bd_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_sim_bd_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_bd_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_yule_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:273:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/default_params_doc.R#L273) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_linked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:277:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/default_params_doc.R#L277) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_unlinked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_alignment_n_taxa.R:14:5:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_alignment_n_taxa.R#L14) *style:* **Commented code should be removed.**
```r
  # length(labels(alignment))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_sequences.R:5:3:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_copy_true_alignment_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_copy_true_alignment_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_copy_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/get_sim_twin_alignment_with_standard_site_model_function.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run.R:24:17:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/pir_run.R#L24) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/pir_to_pics.R:10:17:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/pir_to_pics.R#L10) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/pir_to_tables.R:7:17:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/pir_to_tables.R#L7) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_true_alignment_with_linked_node_sub_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_true_alignment_with_standard_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_standard_site_model.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_twin_alignment_with_standard_site_model.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_unlinked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/R/sim_twin_alignment_with_unlinked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_experiments.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
  cand_experiment_1$inference_model$mcmc <- cand_experiment_2$inference_model$mcmc
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:32:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
      pirouette::get_sim_true_alignment_with_linked_node_sub_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:38:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
      pirouette::get_sim_true_alignment_with_unlinked_node_sub_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:56:9:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:56:11:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { }
          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:58:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:63:75:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L63) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:63:77:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L63) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:71:9:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) {}
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:71:10:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) {}
         ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:81:9:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L81) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:81:25:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L81) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_true_alignment_function.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:62:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:64:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:42:62:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:42:64:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:51:9:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "irrelevant" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:51:24:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "irrelevant" }
                       ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:62:9:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:62:25:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:64:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_alignment_function.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:66:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                 ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:68:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                   ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:74:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                         ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:90:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                                ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_tree_function' must be a function with one argument called 'true_phylogeny'"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:72:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                       ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:88:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                                ^
```
[tests/testthat/test-check_twinning_params.R:209:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-check_twinning_params.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
        sim_twin_alignment_function = get_sim_twin_alignment_with_standard_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-create_error_measure_params.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
      list.files(dirname(experiment$errors_filename), pattern = basename(experiment$errors_filename))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_twin_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-create_twin_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:111:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_alignment_n_taxa.R#L111) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:112:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_alignment_n_taxa.R#L112) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_experiments_filenames.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_experiments_filenames.R:32:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_experiments_filenames.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:14:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_pir_params_filenames.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:41:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_pir_params_filenames.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:65:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_pir_params_filenames.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:107:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_pir_params_filenames.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_temp_errors_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_temp_errors_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-get_temp_fasta_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-get_temp_fasta_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-pir_run.R:127:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-pir_run.R#L127) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment <- readLines(pir_params$twinning_params$twin_alignment_filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_alignment_with_n_mutations.R:88:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-sim_alignment_with_n_mutations.R#L88) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/4b274dd2e79b15047d904caaee5a04b5d9401fa8/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Tried to release, but tests are failing. Will try again