[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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_distr.R:9:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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:55:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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.R:5:8:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


<!-- PMABOT:SPACE -->
This commit contains trailing whitespace, what is prohibited in phpMyAdmin. Please check our [Developer guidelines](https://github.com/phpmyadmin/phpmyadmin/wiki/Developer_guidelines#Indentation) for more information.

Offending files: libraries/classes/UserPassword.php


Это мне надо сесть за комп и поизучать.... Попробую не забыть


This was actually a bug introduced by me recently. I just submitted a PR for that: https://github.com/apache/airflow/pull/6718


Successfully deployed to following URLs:

* https://ripe-components-vue-3omt735mq.now.sh
* https://ripe-components-vue.platforme.now.sh
* https://ripe-components-vue-git-master.platforme.now.sh


Successfully deployed to following URLs:

* https://gatsby-functions-6j3ha1v2g.now.sh
* https://gatsby-functions-three-khaki.now.sh
* https://gatsby-functions.dam6pl.now.sh
* https://gatsby-functions-git-master.dam6pl.now.sh


Successfully deployed to following URLs:

* https://kauri-serverless-migration-102s5oaii.now.sh
* https://kauri-serverless-migration-omega-ten.now.sh
* https://dev.kauri.io
* https://kauri-serverless-migration.kauri.now.sh
* https://kauri-serverless-migration-git-master.kauri.now.sh


[R/calc_required_node_time.R:15:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_required_node_time.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
calc_required_node_time <- function(phy,
^
```
[R/calc_required_node_time.R:50:18:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_required_node_time.R#L50) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:51:16:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_required_node_time.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_required_node_time.R:66:18:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_required_node_time.R#L66) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:67:16:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_required_node_time.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_summary_statistics.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  output <- c( calc_beta(focal_tree),
              ^
```
[R/calc_time_spent_at_node.R:15:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_time_spent_at_node.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
calc_time_spent_at_node <- function(phy,
^
```
[R/calc_time_spent_at_node.R:53:36:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                   ^
```
[R/calc_time_spent_at_node.R:53:57:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                                        ^
```
[R/calc_time_spent_at_node.R:69:37:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                    ^
```
[R/calc_time_spent_at_node.R:69:58:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/count_hidden.R:10:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/count_hidden.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
  extinct_species <- tree$tip.label[(num_extant_species+1):length(tree$tip.label)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:10:56:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/count_hidden.R#L10) *style:* **Put spaces around all infix operators.**
```r
  extinct_species <- tree$tip.label[(num_extant_species+1):length(tree$tip.label)]
                                                      ~^~
```
[R/count_hidden.R:20:15:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/count_hidden.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    b <- desc[ desc %in% extinct_species]
              ^
```
[R/count_hidden.R:27:9:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/count_hidden.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(n == root_node && length(b) == 1)  {
        ^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_independent.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:187:7:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L187) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:207:42:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_linked.R#L207) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:43:15:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/util.R#L43) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (compress){
              ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-calc-dist.R:19:26:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:22:26:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-create_equal_alignment.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/d8c5cf2837ec0fb34f425e89dba89e3bc1233a7f/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


Merge master


This version of MUD.MIC has extra blank lines and the HIGH locations will crash the game on a simh PDP10 system. There is a revised mud.mic (lowercase) which corrects these issues. Having both an upper case and lowercase MUD.MIC is confusing because TOPS-10 is case insensitive as are some unix derived oses (eg OSX).


`Array<{src: string}>` ? Or I guess jsdoc also supports `{src: string}[]`


Please remove


Successfully deployed to following URLs:

* https://afrotech-events-api-4reyvgklz.now.sh
* https://afrotech-events-api.now.sh
* https://api.afrotech.events
* https://afrotech-events-api.ezeikel.now.sh
* https://afrotech-events-api-git-master.ezeikel.now.sh


The name of the method must begin start with a small letter.


I guess there is another way around I use sometimes:
```ruby
    def self.flat_find object, &block
      object if yield object unless object.respond_to? :each
      object.find do |x|
        result = flat_find x, &block
        return result unless result.nil?
      end
    end
```
It is abusing `find` -- if it does not find it returns `nil`, if it does the `return` throws it out. In previous variant it was `each` that on running out of the loop would return the object that it was iterating, not `nil` so you had to return `nil` explicitly but here you can avoid it. It saves lines of code but is again ugly. It also allows to use `break` instead of `return` if that ever matters.
You also can use `throw`/`catch` so instead of moving the result up from recursion level by level it would throw it through all levels but it would need one more method or lambda to throw out of them but not out of `flat_find`.


Successfully deployed to following URLs:

* https://nordnet-ui-newxamhwp.now.sh
* https://nordnet-ui.nordnet1.now.sh
* https://nordnet-ui-git-master.nordnet1.now.sh


The POWER program if not required for the 1986 MUD1, for which this is the source. It only works with the 84 MUD1 that is on the tape.


scale ratio has nf(number of flavors) dependence and the power is actually affected.


@ale0xb congrats for finding an easter-egg! 😂


keep the final result as EQ 4.11


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
check_pir_out <- function(
^
```
[R/create_alignment_with_std_site_model.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/create_alignment_with_std_site_model.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/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_fun.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/create_copy_twin_tree_from_true_fun.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_fun <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_sim_true_alignment_with_lns_site_model_fun.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_true_alignment_with_lns_site_model_fun.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_lns_site_model_fun <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_std_site_model_fun.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_true_alignment_with_std_site_model_fun.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_std_site_model_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_uns_site_model_fun.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_true_alignment_with_uns_site_model_fun.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_uns_site_model_fun <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_fun.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_twin_alignment_with_same_n_mutation_fun.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_std_site_model_fun.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_twin_alignment_with_std_site_model_fun.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_std_site_model_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/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_alignment_with_std_site_model.R:15:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_alignment_with_std_site_model.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_lns_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_true_alignment_with_lns_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_lns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_std_site_model.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_true_alignment_with_std_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_uns_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_true_alignment_with_uns_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_uns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_lns_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_lns_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_lns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/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_std_site_model_raw.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_std_site_model_raw.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_std_site_model.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_uns_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_uns_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_uns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


@tristantarrant how about these strings for the splash page?


at mt scale 6 quarks all active and at hadron scale(1 GeV) only three could be active


similar here


the name of the function must be clear