[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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.R:10:3:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/create_alignment.R#L10) *warning:* **local variable ‘n_taxa’ assigned but may not be used**
```r
  n_taxa <- ape::Ntip(phylogeny)
  ^~~~~~
```
[R/create_alignment.R:11:3:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/create_alignment.R#L11) *warning:* **local variable ‘n_nucleotides’ assigned but may not be used**
```r
  n_nucleotides <- nchar(alignment_params$root_sequence)
  ^~~~~~~~~~~~~
```
[R/create_alignment.R:67:9:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/create_alignment.R#L67) *style:* **Commented code should be removed.**
```r
    #   alignment_params = alignment_params
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:98:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/create_alignment.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.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/create_alignment.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.R:144:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/create_alignment.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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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:272:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/default_params_doc.R#L272) *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:276:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/R/default_params_doc.R#L276) *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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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:125:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/tests/testthat/test-pir_run.R#L125) *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:86:1:](https://github.com/richelbilderbeek/pirouette/blob/3049a3486798b0773f5e45cc70a1e86b4ae899d2/tests/testthat/test-sim_alignment_with_n_mutations.R#L86) *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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/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/3049a3486798b0773f5e45cc70a1e86b4ae899d2/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


[R/get_paths.R:4:21:](https://github.com/ropensci/mauricer/blob/2fa7a6afa96a183ca8f8ebba3e215e2e7d71e956/R/get_paths.R#L4) *warning:* **no visible global function definition for ‘get_mrc_path’**
```r
    filenames[i] <- get_mrc_path(filenames[i]) # nolint internal function
                    ^~~~~~~~~~~~
```
[R/mauricer.R:35:1:](https://github.com/ropensci/mauricer/blob/2fa7a6afa96a183ca8f8ebba3e215e2e7d71e956/R/mauricer.R#L35) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mauricer.R:36:1:](https://github.com/ropensci/mauricer/blob/2fa7a6afa96a183ca8f8ebba3e215e2e7d71e956/R/mauricer.R#L36) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Successfully deployed to following URLs:

* https://jonnodev-rcmxdz93i.now.sh
* https://jonno.dev
* https://jonnodev.barrythepenguin.now.sh
* https://jonnodev-git-master.barrythepenguin.now.sh


Successfully deployed to following URLs:

* https://flamme-rouge-tour-rdus3qds3.now.sh
* https://tour.jonathanbyrne.net
* https://flamme-rouge-tour.jpbyrne.now.sh
* https://flamme-rouge-tour-git-master.jpbyrne.now.sh


Successfully deployed to following URLs:

* https://next-sga-2amoblqca.now.sh
* https://sgagymfem.com
* https://www.sgagymfem.com
* https://sgagymfem.fr
* https://next-sga.aureltrouble.now.sh
* https://next-sga-git-master.aureltrouble.now.sh


Successfully deployed to following URLs:

* https://jonnodev-15bs6utp0.now.sh
* https://jonno.dev
* https://jonnodev.barrythepenguin.now.sh
* https://jonnodev-git-master.barrythepenguin.now.sh


Note that this script doesn't update the French (fr_FR, 100% complete on POeditor) and Norwegian (no_NO, 12% complete) languages.


ns


> `script` and `language` are swapped here.

Thanks, it's fixed now.

> This code feels a bit over-engineered to me, why not just `return "x-hbot" .. language .. "-hbsc" .. script` without the rest of the code?

Well, the `script_to_ot` stuff isn't used right now, but it will be needed soon so I pushed them together.
The problem with just returning the "language" part without the script is that we have to determine the script anyway, so we can also do this together. Passing the script only through `-hbscXXXX` together with some generic script would select the wrong shaper.


Successfully deployed to following URLs:

* https://tietokoneen-toiminnan-jatkokurssi-material-8t7glvg0z.now.sh
* https://tietokoneen-toiminnan-jatkokurssi.mooc.fi
* https://tietokoneen-toiminnan-jatkokurssi-material.mooc.now.sh
* https://tietokoneen-toiminnan-jatkokurssi-material-git-master.mooc.now.sh


The above code snippet is repeated a lot throughout the tendermint_rs codebase. If we agree on this approach we can replace many occurrences where we do actually operate on the encoded bytes directly, e.g., when hashing, generating sign-bytes etc (instead of just writing them into a `BufMut`).

See `hash_bytes` and the changes in the tests as an example.


Successfully deployed to following URLs:

* https://eurobrake-10-1rx60r6r5.now.sh
* https://eurobrake-10.waveflow18.now.sh
* https://eurobrake-10-git-master.waveflow18.now.sh


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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.R:10:3:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/create_alignment.R#L10) *warning:* **local variable ‘n_taxa’ assigned but may not be used**
```r
  n_taxa <- ape::Ntip(phylogeny)
  ^~~~~~
```
[R/create_alignment.R:11:3:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/create_alignment.R#L11) *warning:* **local variable ‘n_nucleotides’ assigned but may not be used**
```r
  n_nucleotides <- nchar(alignment_params$root_sequence)
  ^~~~~~~~~~~~~
```
[R/create_alignment.R:67:9:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/create_alignment.R#L67) *style:* **Commented code should be removed.**
```r
    #   alignment_params = alignment_params
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:98:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/create_alignment.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.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/create_alignment.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.R:144:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/create_alignment.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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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:272:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/default_params_doc.R#L272) *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:276:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/R/default_params_doc.R#L276) *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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/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:125:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/tests/testthat/test-pir_run.R#L125) *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:86:1:](https://github.com/richelbilderbeek/pirouette/blob/e09576b18c115eea2750d59c48104622ec1ef036/tests/testthat/test-sim_alignment_with_n_mutations.R#L86) *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/e09576b18c115eea2750d59c48104622ec1ef036/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/e09576b18c115eea2750d59c48104622ec1ef036/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Great, merged into `Distance` in 35f54b7.


Successfully deployed to following URLs:

* https://gluons-1opth2gvi.now.sh
* https://gluons-ecru-ten.now.sh
* https://gluons.euonymus.now.sh
* https://gluons-git-master.euonymus.now.sh


@iamjustarandomguy this is now fixed and fully working:
https://github.com/TheHolyRogerCoin/RogerXplorer/commit/cf0ad6d38dbee39f31e1d30ba2570680dab6d158

https://explorer.theholyroger.com/markets/altmarkets


Good catch, I wasn't sure about it.


Trash


can be added with the


Did you mean `-` ?


My Data has value '$$$$$$$', so how to solve ?


Did you mean `*` ?


I have no idea how to fix this TBH.


There is `this.apiRequest`, which works. So, all good!


Successfully deployed to following URLs:

* https://ui-6gy38imlm.now.sh
* https://ui.roleypoly.com
* https://ui.roleypoly.now.sh
* https://ui-git-master.roleypoly.now.sh


Sorry about breaking the build with unintended side-effects.

Let's discuss what to put in the author and maintainer fields in the upcoming call on boost-histogram.


Did you mean `/` ?


Successfully deployed to following URLs:

* https://today-i-learned-content-gt4r4jseb.now.sh
* https://today-i-learned-content.cybertec.now.sh
* https://today-i-learned-content-git-master.cybertec.now.sh


![Blackjackgreen](https://user-images.githubusercontent.com/57557443/68586028-07b94d00-0484-11ea-91f6-44762162dfa0.png)
![Imagepage1](https://user-images.githubusercontent.com/57557443/68586029-0851e380-0484-11ea-9de7-b619207181a8.jpg)

![machinesous - Gray](https://user-images.githubusercontent.com/57557443/68586032-0851e380-0484-11ea-9715-9da70edb4f6b.png)
![machinesous](https://user-images.githubusercontent.com/57557443/68586033-08ea7a00-0484-11ea-928f-b88da1b12ed9.png)

![Roulette - Gray](https://user-images.githubusercontent.com/57557443/68586034-09831080-0484-11ea-907e-a64241bbdf3c.png)
![Roulette](https://user-images.githubusercontent.com/57557443/68586035-09831080-0484-11ea-8d92-ff239e22cd2b.png)

![Blackjack - Gray](https://user-images.githubusercontent.com/57557443/68586038-0a1ba700-0484-11ea-8def-32f6d13f5737.png)
![Blackjack](https://user-images.githubusercontent.com/57557443/68586039-0ab43d80-0484-11ea-9fdb-0e22996b6744.png)


new


Good catch @emmanuel099, please open a new issue regarding this topic, because I'll try to rebase this branch to `master` first and then we can fix open problems like this later.


Did you mean `%` ?


<img width="1279" alt="cover" src="https://user-images.githubusercontent.com/55451953/68586081-24558500-0484-11ea-9df2-d2c9c2432e0a.png">


There is only one operand...


Did you mean `==` ?


Did you mean `!=` ?


Have you ever considered using [classnames](https://github.com/JedWatson/classnames) for building strings of classes? It's extremely lightweight (50 lines of code) but seems quite useful.


Did you mean `<` ?


He arreglado la issue que he informado. Ahora mi nombre sale en la página web.


Did you mean `<=` ?