[R/are_mrca_taxa_names_in_fastas.R:11:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/are_mrca_taxa_names_in_fastas.R#L11) *warning:* **no visible global function definition for ‘are_mrca_priors’**
```r
  testit::assert(are_mrca_priors(mrca_priors))
                 ^~~~~~~~~~~~~~~
```
[R/are_mrca_taxa_non_intersecting.R:12:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/are_mrca_taxa_non_intersecting.R#L12) *warning:* **no visible global function definition for ‘are_mrca_priors’**
```r
  testit::assert(are_mrca_priors(mrca_priors))
                 ^~~~~~~~~~~~~~~
```
[R/clock_model_to_xml_operators.R:12:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_operators.R#L12) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
  testit::assert(is_clock_model(clock_model))
                 ^~~~~~~~~~~~~~
```
[R/clock_model_to_xml_operators.R:19:22:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_operators.R#L19) *warning:* **no visible global function definition for ‘is_id’**
```r
      testit::assert(is_id(id))
                     ^~~~~
```
[R/clock_model_to_xml_operators.R:34:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_operators.R#L34) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
    testit::assert(is_rln_clock_model(clock_model))
                   ^~~~~~~~~~~~~~~~~~
```
[R/clock_model_to_xml_operators.R:37:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_operators.R#L37) *warning:* **no visible global function definition for ‘is_id’**
```r
    testit::assert(is_id(id))
                   ^~~~~
```
[R/clock_model_to_xml_prior_distr.R:20:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_prior_distr.R#L20) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
  testit::assert(is_clock_model(clock_model))
                 ^~~~~~~~~~~~~~
```
[R/clock_model_to_xml_prior_distr.R:30:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_prior_distr.R#L30) *warning:* **no visible global function definition for ‘is_id’**
```r
    testit::assert(is_id(id))
                   ^~~~~
```
[R/clock_model_to_xml_prior_distr.R:45:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_prior_distr.R#L45) *warning:* **no visible global function definition for ‘is_strict_clock_model’**
```r
    testit::assert(is_strict_clock_model(clock_model))
                   ^~~~~~~~~~~~~~~~~~~~~
```
[R/clock_model_to_xml_prior_distr.R:49:22:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_prior_distr.R#L49) *warning:* **no visible global function definition for ‘is_id’**
```r
      testit::assert(is_id(id))
                     ^~~~~
```
[R/clock_model_to_xml_state.R:11:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_state.R#L11) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
  testit::assert(is_clock_model(clock_model))
                 ^~~~~~~~~~~~~~
```
[R/clock_model_to_xml_state.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_state.R#L13) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(clock_model$id))
                 ^~~~~
```
[R/clock_model_to_xml_state.R:26:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_state.R#L26) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
    testit::assert(is_rln_clock_model(clock_model))
                   ^~~~~~~~~~~~~~~~~~
```
[R/clock_model_to_xml_tracelog.R:17:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_tracelog.R#L17) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
  testit::assert(is_clock_model(clock_model))
                 ^~~~~~~~~~~~~~
```
[R/clock_model_to_xml_tracelog.R:19:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_tracelog.R#L19) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/clock_model_to_xml_tracelog.R:34:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_tracelog.R#L34) *warning:* **no visible global function definition for ‘is_strict_clock_model’**
```r
    testit::assert(is_strict_clock_model(clock_model))
                   ^~~~~~~~~~~~~~~~~~~~~
```
[R/clock_model_to_xml_treelogger.R:9:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_treelogger.R#L9) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
  testit::assert(is_clock_model(clock_model))
                 ^~~~~~~~~~~~~~
```
[R/clock_model_to_xml_treelogger.R:24:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_model_to_xml_treelogger.R#L24) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
    testit::assert(is_rln_clock_model(clock_model))
                   ^~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_operators.R:10:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_models_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_models_to_xml_state.R#L13) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:17:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_models_to_xml_state.R#L17) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_tracelog.R:16:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_models_to_xml_tracelog.R#L16) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_tracelog.R:23:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/clock_models_to_xml_tracelog.R#L23) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
    testit::assert(is_clock_model(clock_model))
                   ^~~~~~~~~~~~~~
```
[R/create_beast2_input_1_12.R:39:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_1_12.R#L39) *warning:* **no visible global function definition for ‘are_initial_phylogenies’**
```r
    testit::assert(are_initial_phylogenies(initial_phylogenies))
                   ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_beast.R:41:11:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_beast.R#L41) *warning:* **no visible global function definition for ‘create_beast2_beast_xml’**
```r
  text <- create_beast2_beast_xml(beast2_version = misc_options$beast2_version)
          ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:182:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L182) *warning:* **no visible global function definition for ‘are_mrca_priors’**
```r
    testit::assert(are_mrca_priors(mrca_priors))
                   ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:186:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L186) *warning:* **no visible global function definition for ‘is_mrca_prior’**
```r
    testit::assert(is_mrca_prior(mrca_prior))
                   ^~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:235:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L235) *warning:* **no visible global function definition for ‘is_bd_tree_prior’**
```r
  testit::assert(is_bd_tree_prior(bd_tree_prior))
                 ^~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:237:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L237) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/create_beast2_input_distr.R:296:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L296) *warning:* **no visible global function definition for ‘is_cbs_tree_prior’**
```r
  testit::assert(is_cbs_tree_prior(cbs_tree_prior))
                 ^~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:298:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L298) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/create_beast2_input_distr.R:332:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L332) *warning:* **no visible global function definition for ‘is_ccp_tree_prior’**
```r
  testit::assert(is_ccp_tree_prior(ccp_tree_prior))
                 ^~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:334:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L334) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/create_beast2_input_distr.R:383:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L383) *warning:* **no visible global function definition for ‘is_cep_tree_prior’**
```r
  testit::assert(is_cep_tree_prior(cep_tree_prior))
                 ^~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:385:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L385) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/create_beast2_input_distr.R:446:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L446) *warning:* **no visible global function definition for ‘is_yule_tree_prior’**
```r
  testit::assert(is_yule_tree_prior(yule_tree_prior))
                 ^~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:448:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_distr.R#L448) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/create_beast2_input_init.R:9:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_init.R#L9) *warning:* **no visible global function definition for ‘are_initial_phylogenies’**
```r
  testit::assert(are_initial_phylogenies(initial_phylogenies))
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_loggers.R:97:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_loggers.R#L97) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/create_beast2_input_loggers.R:175:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input_loggers.R#L175) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/create_beast2_input.R:45:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input.R#L45) *warning:* **no visible global function definition for ‘is_mrca_prior’**
```r
    testit::assert(is_mrca_prior(mrca_priors[[1]]))
                   ^~~~~~~~~~~~~
```
[R/create_beast2_input.R:126:17:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input.R#L126) *warning:* **no visible global function definition for ‘get_n_taxa’**
```r
      n_taxa <- get_n_taxa(fasta_filename)
                ^~~~~~~~~~
```
[R/create_beast2_input.R:140:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_beast2_input.R#L140) *warning:* **no visible global function definition for ‘are_mrca_priors’**
```r
    testit::assert(are_mrca_priors(mrca_priors))
                   ^~~~~~~~~~~~~~~
```
[R/create_gamma_site_model.R:77:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_gamma_site_model.R#L77) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  testit::assert(is_gamma_site_model(gamma_site_model))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc.R:41:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_mcmc.R#L41) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/create_mrca_prior.R:63:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_mrca_prior.R#L63) *warning:* **no visible global function definition for ‘is_mrca_prior’**
```r
  testit::assert(is_mrca_prior(mrca_prior))
                 ^~~~~~~~~~~~~
```
[R/create_random.R:60:3:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L60) *warning:* **no visible global function definition for ‘create_cbs_tree_prior’**
```r
  create_cbs_tree_prior()
  ^~~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:333:21:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L333) *warning:* **no visible global function definition for ‘get_taxa_names’**
```r
  all_taxa_names <- get_taxa_names(fasta_filename)
                    ^~~~~~~~~~~~~~
```
[R/create_random.R:356:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L356) *warning:* **no visible global function definition for ‘create_rnd_mrca_prior’**
```r
    create_rnd_mrca_prior(fasta_filename)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:398:3:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L398) *warning:* **no visible global function definition for ‘create_one_div_x_distr’**
```r
  create_one_div_x_distr()
  ^~~~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:407:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L407) *warning:* **no visible global function definition for ‘create_alpha_param’**
```r
    create_alpha_param()
    ^~~~~~~~~~~~~~~~~~
```
[R/create_random.R:409:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L409) *warning:* **no visible global function definition for ‘create_beta_param’**
```r
    create_beta_param()
    ^~~~~~~~~~~~~~~~~
```
[R/create_random.R:411:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L411) *warning:* **no visible global function definition for ‘create_clock_rate_param’**
```r
    create_clock_rate_param()
    ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:413:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L413) *warning:* **no visible global function definition for ‘create_kappa_1_param’**
```r
    create_kappa_1_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:415:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L415) *warning:* **no visible global function definition for ‘create_kappa_2_param’**
```r
    create_kappa_2_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:417:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L417) *warning:* **no visible global function definition for ‘create_lambda_param’**
```r
    create_lambda_param()
    ^~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:419:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L419) *warning:* **no visible global function definition for ‘create_m_param’**
```r
    create_m_param()
    ^~~~~~~~~~~~~~
```
[R/create_random.R:421:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L421) *warning:* **no visible global function definition for ‘create_mean_param’**
```r
    create_mean_param()
    ^~~~~~~~~~~~~~~~~
```
[R/create_random.R:423:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L423) *warning:* **no visible global function definition for ‘create_mu_param’**
```r
    create_mu_param()
    ^~~~~~~~~~~~~~~
```
[R/create_random.R:425:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L425) *warning:* **no visible global function definition for ‘create_rate_ac_param’**
```r
    create_rate_ac_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:427:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L427) *warning:* **no visible global function definition for ‘create_rate_ag_param’**
```r
    create_rate_ag_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:429:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L429) *warning:* **no visible global function definition for ‘create_rate_at_param’**
```r
    create_rate_at_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:431:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L431) *warning:* **no visible global function definition for ‘create_rate_cg_param’**
```r
    create_rate_cg_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:433:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L433) *warning:* **no visible global function definition for ‘create_rate_ct_param’**
```r
    create_rate_ct_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:435:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L435) *warning:* **no visible global function definition for ‘create_rate_gt_param’**
```r
    create_rate_gt_param()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_random.R:437:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L437) *warning:* **no visible global function definition for ‘create_s_param’**
```r
    create_s_param()
    ^~~~~~~~~~~~~~
```
[R/create_random.R:439:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L439) *warning:* **no visible global function definition for ‘create_scale_param’**
```r
    create_scale_param()
    ^~~~~~~~~~~~~~~~~~
```
[R/create_random.R:442:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_random.R#L442) *warning:* **no visible global function definition for ‘create_sigma_param’**
```r
    create_sigma_param()
    ^~~~~~~~~~~~~~~~~~
```
[R/create_site_model.R:76:3:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/create_site_model.R#L76) *warning:* **no visible global function definition for ‘check_gamma_site_model’**
```r
  check_gamma_site_model(gamma_site_model)
  ^~~~~~~~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:39:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L39) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(distr))
                   ^~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:54:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L54) *warning:* **no visible global function definition for ‘is_beta_distr’**
```r
  testit::assert(is_beta_distr(distr))
                 ^~~~~~~~~~~~~
```
[R/distr_to_xml.R:56:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L56) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:84:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L84) *warning:* **no visible global function definition for ‘is_exp_distr’**
```r
  testit::assert(is_exp_distr(distr))
                 ^~~~~~~~~~~~
```
[R/distr_to_xml.R:86:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L86) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:109:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L109) *warning:* **no visible global function definition for ‘is_gamma_distr’**
```r
  testit::assert(is_gamma_distr(distr))
                 ^~~~~~~~~~~~~~
```
[R/distr_to_xml.R:111:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L111) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:140:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L140) *warning:* **no visible global function definition for ‘is_inv_gamma_distr’**
```r
  testit::assert(is_inv_gamma_distr(distr))
                 ^~~~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:142:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L142) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:171:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L171) *warning:* **no visible global function definition for ‘is_laplace_distr’**
```r
  testit::assert(is_laplace_distr(distr))
                 ^~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:173:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L173) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:201:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L201) *warning:* **no visible global function definition for ‘is_log_normal_distr’**
```r
  testit::assert(is_log_normal_distr(distr))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:203:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L203) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:233:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L233) *warning:* **no visible global function definition for ‘is_normal_distr’**
```r
  testit::assert(is_normal_distr(distr))
                 ^~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:235:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L235) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:264:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L264) *warning:* **no visible global function definition for ‘is_one_div_x_distr’**
```r
  testit::assert(is_one_div_x_distr(distr))
                 ^~~~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:266:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L266) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:282:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L282) *warning:* **no visible global function definition for ‘is_poisson_distr’**
```r
  testit::assert(is_poisson_distr(distr))
                 ^~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:284:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L284) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/distr_to_xml.R:308:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L308) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
  testit::assert(is_uniform_distr(distr))
                 ^~~~~~~~~~~~~~~~
```
[R/distr_to_xml.R:310:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/distr_to_xml.R#L310) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/fastas_to_phylos.R:42:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/fastas_to_phylos.R#L42) *warning:* **no visible global function definition for ‘fasta_to_phylo’**
```r
    phylos[[i]] <- fasta_to_phylo(fasta_filename, crown_age)
                   ^~~~~~~~~~~~~~
```
[R/gamma_site_model_to_xml_prior_distr.R:9:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/gamma_site_model_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  testit::assert(is_site_model(site_model))
                 ^~~~~~~~~~~~~
```
[R/gamma_site_model_to_xml_prior_distr.R:11:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/gamma_site_model_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/gamma_site_model_to_xml_state.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/gamma_site_model_to_xml_state.R#L13) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  testit::assert(is_gamma_site_model(gamma_site_model))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/gamma_site_model_to_xml_state.R:14:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/gamma_site_model_to_xml_state.R#L14) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/get_alignment_ids.R:16:22:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_alignment_ids.R#L16) *warning:* **no visible binding for global variable ‘get_alignment_id’**
```r
  unlist(lapply(ids, get_alignment_id))
                     ^~~~~~~~~~~~~~~~
```
[R/get_clock_model_name.R:17:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_clock_model_name.R#L17) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
    testit::assert(is_rln_clock_model(clock_model))
                   ^~~~~~~~~~~~~~~~~~
```
[R/get_clock_models_ids.R:8:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_clock_models_ids.R#L8) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/get_distr_n_params.R:65:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_distr_n_params.R#L65) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(distr))
                   ^~~~~~~~~~~~~~~~
```
[R/get_gamma_site_model_n_distrs.R:20:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_gamma_site_model_n_distrs.R#L20) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  testit::assert(is_gamma_site_model(gamma_site_model))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/get_gamma_site_model_n_params.R:28:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_gamma_site_model_n_params.R#L28) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  testit::assert(is_gamma_site_model(gamma_site_model))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/get_gamma_site_model_n_params.R:32:5:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_gamma_site_model_n_params.R#L32) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
    get_distr_n_params(gamma_site_model$gamma_shape_prior_distr)
    ^~~~~~~~~~~~~~~~~~
```
[R/get_has_non_strict_clock_model.R:7:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_has_non_strict_clock_model.R#L7) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/get_site_model_n_distrs.R:33:32:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_site_model_n_distrs.R#L33) *warning:* **no visible global function definition for ‘get_gamma_site_model_n_distrs’**
```r
  gamma_site_model_n_distrs <- get_gamma_site_model_n_distrs(gamma_site_model)
                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_site_model_n_distrs.R:41:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_site_model_n_distrs.R#L41) *warning:* **no visible global function definition for ‘is_tn93_site_model’**
```r
    testit::assert(is_tn93_site_model(site_model))
                   ^~~~~~~~~~~~~~~~~~
```
[R/get_site_model_n_params.R:50:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_site_model_n_params.R#L50) *warning:* **no visible global function definition for ‘is_tn93_site_model’**
```r
    testit::assert(is_tn93_site_model(site_model))
                   ^~~~~~~~~~~~~~~~~~
```
[R/get_site_models_n_distrs.R:27:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_site_models_n_distrs.R#L27) *warning:* **no visible global function definition for ‘is_site_model’**
```r
    testit::assert(is_site_model(site_model))
                   ^~~~~~~~~~~~~
```
[R/get_site_models_n_params.R:27:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_site_models_n_params.R#L27) *warning:* **no visible global function definition for ‘is_site_model’**
```r
    testit::assert(is_site_model(site_model))
                   ^~~~~~~~~~~~~
```
[R/get_tree_prior_n_distrs.R:46:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_tree_prior_n_distrs.R#L46) *warning:* **no visible global function definition for ‘is_yule_tree_prior’**
```r
    testit::assert(is_yule_tree_prior(tree_prior))
                   ^~~~~~~~~~~~~~~~~~
```
[R/get_tree_prior_n_params.R:48:12:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_tree_prior_n_params.R#L48) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
    return(get_distr_n_params(tree_prior$pop_size_distr))
           ^~~~~~~~~~~~~~~~~~
```
[R/get_tree_prior_n_params.R:55:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_tree_prior_n_params.R#L55) *warning:* **no visible global function definition for ‘is_yule_tree_prior’**
```r
    testit::assert(is_yule_tree_prior(tree_prior))
                   ^~~~~~~~~~~~~~~~~~
```
[R/get_tree_priors_n_distrs.R:22:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_tree_priors_n_distrs.R#L22) *warning:* **no visible global function definition for ‘is_tree_prior’**
```r
    testit::assert(is_tree_prior(tree_prior))
                   ^~~~~~~~~~~~~
```
[R/get_tree_priors_n_distrs.R:23:14:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_tree_priors_n_distrs.R#L23) *warning:* **no visible global function definition for ‘get_tree_prior_n_distrs’**
```r
    n <- n + get_tree_prior_n_distrs(tree_prior)
             ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_unlinked_clock_models.R:6:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_unlinked_clock_models.R#L6) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/get_unlinked_clock_models.R:17:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_unlinked_clock_models.R#L17) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(results))
                 ^~~~~~~~~~~~~~~~
```
[R/get_unlinked_site_models.R:6:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_unlinked_site_models.R#L6) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/get_unlinked_site_models.R:17:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/get_unlinked_site_models.R#L17) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(results))
                 ^~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:19:10:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/has_xml_opening_tag.R#L19) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !is.na(find_first_xml_opening_tag_line(lines, section))
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:15:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L15) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:22:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L22) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
    testit::assert(is_clock_model(clock_model))
                   ^~~~~~~~~~~~~~
```
[R/init_clock_models.R:45:22:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L45) *warning:* **no visible global function definition for ‘is_strict_clock_model’**
```r
      testit::assert(is_strict_clock_model(clock_model))
                     ^~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:78:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L78) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
  testit::assert(is_rln_clock_model(rln_clock_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:85:26:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L85) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(ucldstdev_distr)
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:92:26:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L92) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(mean_rate_prior_distr)
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:125:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_clock_models.R#L125) *warning:* **no visible global function definition for ‘is_strict_clock_model’**
```r
  testit::assert(is_strict_clock_model(strict_clock_model))
                 ^~~~~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:14:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_distr.R#L14) *warning:* **no visible global function definition for ‘is_distr’**
```r
  testit::assert(is_distr(distr))
                 ^~~~~~~~
```
[R/init_distr.R:100:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_distr.R#L100) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(distr))
                   ^~~~~~~~~~~~~~~~
```
[R/init_gamma_site_model.R:20:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_gamma_site_model.R#L20) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  testit::assert(is_gamma_site_model(gamma_site_model))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/init_gamma_site_model.R:33:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_gamma_site_model.R#L33) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  testit::assert(is_gamma_site_model(gamma_site_model))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/init_mrca_priors.R:14:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_mrca_priors.R#L14) *warning:* **no visible global function definition for ‘are_mrca_priors’**
```r
  testit::assert(are_mrca_priors(mrca_priors))
                 ^~~~~~~~~~~~~~~
```
[R/init_mrca_priors.R:19:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_mrca_priors.R#L19) *warning:* **no visible global function definition for ‘is_mrca_prior’**
```r
    testit::assert(is_mrca_prior(mrca_prior))
                   ^~~~~~~~~~~~~
```
[R/init_mrca_priors.R:37:30:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_mrca_priors.R#L37) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
      param_id <- param_id + get_distr_n_params(mrca_prior$mrca_distr)
                             ^~~~~~~~~~~~~~~~~~
```
[R/init_mrca_priors.R:40:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_mrca_priors.R#L40) *warning:* **no visible global function definition for ‘is_mrca_prior’**
```r
    testit::assert(is_mrca_prior(mrca_prior))
                   ^~~~~~~~~~~~~
```
[R/init_param.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_param.R#L13) *warning:* **no visible global function definition for ‘is_param’**
```r
  testit::assert(is_param(param))
                 ^~~~~~~~
```
[R/init_site_models.R:14:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L14) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/init_site_models.R:19:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L19) *warning:* **no visible global function definition for ‘is_site_model’**
```r
    testit::assert(is_site_model(site_model))
                   ^~~~~~~~~~~~~
```
[R/init_site_models.R:42:22:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L42) *warning:* **no visible global function definition for ‘is_tn93_site_model’**
```r
      testit::assert(is_tn93_site_model(site_model))
                     ^~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:54:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L54) *warning:* **no visible global function definition for ‘is_init_site_model’**
```r
    testit::assert(is_init_site_model(site_model)) # Not yet
                   ^~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:74:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L74) *warning:* **no visible global function definition for ‘is_gtr_site_model’**
```r
  testit::assert(is_gtr_site_model(gtr_site_model))
                 ^~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:207:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L207) *warning:* **no visible global function definition for ‘is_hky_site_model’**
```r
  testit::assert(is_hky_site_model(hky_site_model))
                 ^~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:259:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L259) *warning:* **no visible global function definition for ‘is_jc69_site_model’**
```r
  testit::assert(is_jc69_site_model(jc69_site_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:299:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_site_models.R#L299) *warning:* **no visible global function definition for ‘is_tn93_site_model’**
```r
  testit::assert(is_tn93_site_model(tn93_site_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/init_tree_priors.R:66:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_tree_priors.R#L66) *warning:* **no visible global function definition for ‘is_bd_tree_prior’**
```r
  testit::assert(is_bd_tree_prior(bd_tree_prior))
                 ^~~~~~~~~~~~~~~~
```
[R/init_tree_priors.R:94:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_tree_priors.R#L94) *warning:* **no visible global function definition for ‘is_ccp_tree_prior’**
```r
  testit::assert(is_ccp_tree_prior(ccp_tree_prior))
                 ^~~~~~~~~~~~~~~~~
```
[R/init_tree_priors.R:115:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_tree_priors.R#L115) *warning:* **no visible global function definition for ‘is_cep_tree_prior’**
```r
  testit::assert(is_cep_tree_prior(cep_tree_prior))
                 ^~~~~~~~~~~~~~~~~
```
[R/init_tree_priors.R:146:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/init_tree_priors.R#L146) *warning:* **no visible global function definition for ‘is_yule_tree_prior’**
```r
  testit::assert(is_yule_tree_prior(yule_tree_prior))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_clock_model_name.R:10:13:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_clock_model_name.R#L10) *warning:* **no visible global function definition for ‘get_clock_model_names’**
```r
  name %in% get_clock_model_names()
            ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_clock_model.R:11:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_clock_model.R#L11) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
  if (is_rln_clock_model(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~~~
```
[R/is_clock_model.R:12:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_clock_model.R#L12) *warning:* **no visible global function definition for ‘is_strict_clock_model’**
```r
  if (is_strict_clock_model(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_clock_model.R:68:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_clock_model.R#L68) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$clock_rate_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_clock_model.R:70:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_clock_model.R#L70) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$clock_rate_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_default_mcmc.R:15:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_default_mcmc.R#L15) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(mcmc)) return(FALSE)
       ^~~~~~~
```
[R/is_distr.R:23:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L23) *warning:* **no visible global function definition for ‘is_beta_distr’**
```r
  if (is_beta_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~
```
[R/is_distr.R:24:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L24) *warning:* **no visible global function definition for ‘is_exp_distr’**
```r
  if (is_exp_distr(x)) return(TRUE)
      ^~~~~~~~~~~~
```
[R/is_distr.R:25:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L25) *warning:* **no visible global function definition for ‘is_gamma_distr’**
```r
  if (is_gamma_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~
```
[R/is_distr.R:26:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L26) *warning:* **no visible global function definition for ‘is_inv_gamma_distr’**
```r
  if (is_inv_gamma_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~~~
```
[R/is_distr.R:27:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L27) *warning:* **no visible global function definition for ‘is_laplace_distr’**
```r
  if (is_laplace_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~
```
[R/is_distr.R:28:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L28) *warning:* **no visible global function definition for ‘is_log_normal_distr’**
```r
  if (is_log_normal_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~~~~
```
[R/is_distr.R:29:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L29) *warning:* **no visible global function definition for ‘is_normal_distr’**
```r
  if (is_normal_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~
```
[R/is_distr.R:30:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L30) *warning:* **no visible global function definition for ‘is_one_div_x_distr’**
```r
  if (is_one_div_x_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~~~
```
[R/is_distr.R:31:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L31) *warning:* **no visible global function definition for ‘is_poisson_distr’**
```r
  if (is_poisson_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~
```
[R/is_distr.R:32:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L32) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
  if (is_uniform_distr(x)) return(TRUE)
      ^~~~~~~~~~~~~~~~
```
[R/is_distr.R:53:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L53) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:55:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L55) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:76:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L76) *warning:* **no visible global function definition for ‘is_mean_param’**
```r
  if (!is_mean_param(x$mean)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:97:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L97) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:99:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L99) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:120:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L120) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:122:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L122) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:146:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L146) *warning:* **no visible global function definition for ‘is_mu_param’**
```r
  if (!is_mu_param(x$mu)) return(FALSE)
       ^~~~~~~~~~~
```
[R/is_distr.R:148:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L148) *warning:* **no visible global function definition for ‘is_scale_param’**
```r
  if (!is_scale_param(x$scale)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:181:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L181) *warning:* **no visible global function definition for ‘is_m_param’**
```r
  if (!is_m_param(x$m)) return(FALSE)
       ^~~~~~~~~~
```
[R/is_distr.R:183:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L183) *warning:* **no visible global function definition for ‘is_s_param’**
```r
  if (!is_s_param(x$s)) return(FALSE)
       ^~~~~~~~~~
```
[R/is_distr.R:204:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L204) *warning:* **no visible global function definition for ‘is_mean_param’**
```r
  if (!is_mean_param(x$mean)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:206:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L206) *warning:* **no visible global function definition for ‘is_sigma_param’**
```r
  if (!is_sigma_param(x$sigma)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:244:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_distr.R#L244) *warning:* **no visible global function definition for ‘is_lambda_param’**
```r
  if (!is_lambda_param(x$lambda)) return(FALSE)
       ^~~~~~~~~~~~~~~
```
[R/is_freq_equilibrium_name.R:17:13:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_freq_equilibrium_name.R#L17) *warning:* **no visible global function definition for ‘get_freq_equilibrium_names’**
```r
  name %in% get_freq_equilibrium_names()
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_index_of_first_shared_clock_model.R:12:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_index_of_first_shared_clock_model.R#L12) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/is_index_of_non_first_shared_clock_model.R:12:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_index_of_non_first_shared_clock_model.R#L12) *warning:* **no visible global function definition for ‘are_clock_models’**
```r
  testit::assert(are_clock_models(clock_models))
                 ^~~~~~~~~~~~~~~~
```
[R/is_init_clock_model.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_clock_model.R#L11) *warning:* **no visible global function definition for ‘is_clock_model’**
```r
  if (!is_clock_model(x)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_init_clock_model.R:15:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_clock_model.R#L15) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
    testit::assert(is_rln_clock_model(x))
                   ^~~~~~~~~~~~~~~~~~
```
[R/is_init_clock_model.R:29:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_clock_model.R#L29) *warning:* **no visible global function definition for ‘is_rln_clock_model’**
```r
  testit::assert(is_rln_clock_model(rln_clock_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_init_clock_model.R:43:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_clock_model.R#L43) *warning:* **no visible global function definition for ‘is_strict_clock_model’**
```r
  testit::assert(is_strict_clock_model(strict_clock_model))
                 ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L11) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_init_distr.R:33:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L33) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(x))
                   ^~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:47:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L47) *warning:* **no visible global function definition for ‘is_beta_distr’**
```r
  testit::assert(is_beta_distr(x))
                 ^~~~~~~~~~~~~
```
[R/is_init_distr.R:60:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L60) *warning:* **no visible global function definition for ‘is_exp_distr’**
```r
  testit::assert(is_exp_distr(x))
                 ^~~~~~~~~~~~
```
[R/is_init_distr.R:73:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L73) *warning:* **no visible global function definition for ‘is_gamma_distr’**
```r
  testit::assert(is_gamma_distr(x))
                 ^~~~~~~~~~~~~~
```
[R/is_init_distr.R:86:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L86) *warning:* **no visible global function definition for ‘is_inv_gamma_distr’**
```r
  testit::assert(is_inv_gamma_distr(x))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:99:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L99) *warning:* **no visible global function definition for ‘is_laplace_distr’**
```r
  testit::assert(is_laplace_distr(x))
                 ^~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:112:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L112) *warning:* **no visible global function definition for ‘is_log_normal_distr’**
```r
  testit::assert(is_log_normal_distr(x))
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:125:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L125) *warning:* **no visible global function definition for ‘is_normal_distr’**
```r
  testit::assert(is_normal_distr(x))
                 ^~~~~~~~~~~~~~~
```
[R/is_init_distr.R:138:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L138) *warning:* **no visible global function definition for ‘is_one_div_x_distr’**
```r
  testit::assert(is_one_div_x_distr(x))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:151:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L151) *warning:* **no visible global function definition for ‘is_poisson_distr’**
```r
  testit::assert(is_poisson_distr(x))
                 ^~~~~~~~~~~~~~~~
```
[R/is_init_distr.R:164:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_distr.R#L164) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
  testit::assert(is_uniform_distr(x))
                 ^~~~~~~~~~~~~~~~
```
[R/is_init_gamma_site_model.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_gamma_site_model.R#L11) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  if (!is_gamma_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_init_mrca_prior.R:10:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_mrca_prior.R#L10) *warning:* **no visible global function definition for ‘is_mrca_prior’**
```r
  if (!is_mrca_prior(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_init_mrca_prior.R:15:7:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_mrca_prior.R#L15) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (is_distr(x$mrca_distr) && !is_init_distr(x$mrca_distr)) return(FALSE)
      ^~~~~~~~
```
[R/is_init_mrca_prior.R:15:34:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_mrca_prior.R#L15) *warning:* **no visible global function definition for ‘is_init_distr’**
```r
  if (is_distr(x$mrca_distr) && !is_init_distr(x$mrca_distr)) return(FALSE)
                                 ^~~~~~~~~~~~~
```
[R/is_init_site_model.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_site_model.R#L11) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_init_site_model.R:19:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_site_model.R#L19) *warning:* **no visible global function definition for ‘is_tn93_site_model’**
```r
    testit::assert(is_tn93_site_model(x))
                   ^~~~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:71:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_site_model.R#L71) *warning:* **no visible global function definition for ‘is_hky_site_model’**
```r
  testit::assert(is_hky_site_model(x))
                 ^~~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:91:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_site_model.R#L91) *warning:* **no visible global function definition for ‘is_jc69_site_model’**
```r
  testit::assert(is_jc69_site_model(x))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:111:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_site_model.R#L111) *warning:* **no visible global function definition for ‘is_tn93_site_model’**
```r
  testit::assert(is_tn93_site_model(x))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_init_tree_prior.R:10:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_tree_prior.R#L10) *warning:* **no visible global function definition for ‘is_tree_prior’**
```r
  if (!is_tree_prior(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_init_tree_prior.R:20:20:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_tree_prior.R#L20) *warning:* **no visible global function definition for ‘is_yule_tree_prior’**
```r
    testit::assert(is_yule_tree_prior(x))
                   ^~~~~~~~~~~~~~~~~~
```
[R/is_init_tree_prior.R:34:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_tree_prior.R#L34) *warning:* **no visible global function definition for ‘is_bd_tree_prior’**
```r
  testit::assert(is_bd_tree_prior(x))
                 ^~~~~~~~~~~~~~~~
```
[R/is_init_tree_prior.R:50:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_tree_prior.R#L50) *warning:* **no visible global function definition for ‘is_cbs_tree_prior’**
```r
  testit::assert(is_cbs_tree_prior(x))
                 ^~~~~~~~~~~~~~~~~
```
[R/is_init_tree_prior.R:80:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_tree_prior.R#L80) *warning:* **no visible global function definition for ‘is_cep_tree_prior’**
```r
  testit::assert(is_cep_tree_prior(x))
                 ^~~~~~~~~~~~~~~~~
```
[R/is_init_tree_prior.R:95:18:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_init_tree_prior.R#L95) *warning:* **no visible global function definition for ‘is_yule_tree_prior’**
```r
  testit::assert(is_yule_tree_prior(x))
                 ^~~~~~~~~~~~~~~~~~
```
[R/is_mcmc.R:34:8:](https://github.com/richelbilderbeek/beautier/blob/c1b1a890a071b6540490d778ad6e4b9f81788277/R/is_mcmc.R#L34) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(x)) return(FALSE)
       ^~~~~~~
```


It would at least appear to me that there is some overlap between the security concept of integrity and consistency. Distributed systems papers don't often mention security and in some cases break down completely once a malicious entity is introduced (my favorite is introducing a malicious node into something like Chord). The potential of killing two birds with one stone is tempting. Though I would guess that confidentiality would be harder to work into the mix.


@cafferata `explode` do the same job (here) as `preg_split`, so it's clean code, thanks :-)


package com.muzahid.funtube.player.resolver;

import android.content.Context;
import android.net.Uri;
import android.support.annotation.NonNull;
import android.support.annotation.Nullable;

import com.google.android.exoplayer2.Format;
import com.google.android.exoplayer2.source.MediaSource;
import com.google.android.exoplayer2.source.MergingMediaSource;

import com.muzahid.funtube.extractor.MediaFormat;
import com.muzahid.funtube.extractor.stream.SubtitlesStream;
import com.muzahid.funtube.extractor.stream.AudioStream;
import com.muzahid.funtube.extractor.stream.StreamInfo;
import com.muzahid.funtube.extractor.stream.VideoStream;
import com.muzahid.funtube.player.helper.PlayerDataSource;
import com.muzahid.funtube.player.helper.PlayerHelper;
import com.muzahid.funtube.util.ListHelper;

import java.util.ArrayList;
import java.util.List;

import static com.google.android.exoplayer2.C.SELECTION_FLAG_AUTOSELECT;
import static com.google.android.exoplayer2.C.TIME_UNSET;

public class VideoPlaybackResolver implements PlaybackResolver {

    public interface QualityResolver {
        int getDefaultResolutionIndex(final List<VideoStream> sortedVideos);
        int getOverrideResolutionIndex(final List<VideoStream> sortedVideos,
                                       final String playbackQuality);
    }

    @NonNull private final Context context;
    @NonNull private final PlayerDataSource dataSource;
    @NonNull private final QualityResolver qualityResolver;

    @Nullable private String playbackQuality;

    public VideoPlaybackResolver(@NonNull final Context context,
                                 @NonNull final PlayerDataSource dataSource,
                                 @NonNull final QualityResolver qualityResolver) {
        this.context = context;
        this.dataSource = dataSource;
        this.qualityResolver = qualityResolver;
    }

    @Override
    @Nullable
    public MediaSource resolve(@NonNull StreamInfo info) {
        final MediaSource liveSource = maybeBuildLiveMediaSource(dataSource, info);
        if (liveSource != null) return liveSource;

        List<MediaSource> mediaSources = new ArrayList<>();

        // Create video stream source
        final List<VideoStream> videos = ListHelper.getSortedStreamVideosList(context,
                info.getVideoStreams(), info.getVideoOnlyStreams(), false);
        final int index;
        if (videos.isEmpty()) {
            index = -1;
        } else if (playbackQuality == null) {
            index = qualityResolver.getDefaultResolutionIndex(videos);
        } else {
            index = qualityResolver.getOverrideResolutionIndex(videos, getPlaybackQuality());
        }
        final MediaSourceTag tag = new MediaSourceTag(info, videos, index);
        @Nullable final VideoStream video = tag.getSelectedVideoStream();

        if (video != null) {
            final MediaSource streamSource = buildMediaSource(dataSource, video.getUrl(),
                    PlayerHelper.cacheKeyOf(info, video),
                    MediaFormat.getSuffixById(video.getFormatId()), tag);
            mediaSources.add(streamSource);
        }

        // Create optional audio stream source
        final List<AudioStream> audioStreams = info.getAudioStreams();
        final AudioStream audio = audioStreams.isEmpty() ? null : audioStreams.get(
                ListHelper.getDefaultAudioFormat(context, audioStreams));
        // Use the audio stream if there is no video stream, or
        // Merge with audio stream in case if video does not contain audio
        if (audio != null && ((video != null && video.isVideoOnly) || video == null)) {
            final MediaSource audioSource = buildMediaSource(dataSource, audio.getUrl(),
                    PlayerHelper.cacheKeyOf(info, audio),
                    MediaFormat.getSuffixById(audio.getFormatId()), tag);
            mediaSources.add(audioSource);
        }

        // If there is no audio or video sources, then this media source cannot be played back
        if (mediaSources.isEmpty()) return null;
        // Below are auxiliary media sources

        // Create subtitle sources
        for (final SubtitlesStream MediaFormat : info.getSubtitles()) {
            final String mimeType = PlayerHelper.mimeTypesOf(MediaFormat.getFileType());
            if (mimeType == null) continue;

            final Format textFormat = Format.createTextSampleFormat(null, mimeType,
                    SELECTION_FLAG_AUTOSELECT, PlayerHelper.captionLanguageOf(context, MediaFormat));
            final MediaSource textSource = dataSource.getSampleMediaSourceFactory()
                    .createMediaSource(Uri.parse(MediaFormat.getURL()), textFormat, TIME_UNSET);
            mediaSources.add(textSource);
        }

        if (mediaSources.size() == 1) {
            return mediaSources.get(0);
        } else {
            return new MergingMediaSource(mediaSources.toArray(
                    new MediaSource[mediaSources.size()]));
        }
    }

    @Nullable
    public String getPlaybackQuality() {
        return playbackQuality;
    }

    public void setPlaybackQuality(@Nullable String playbackQuality) {
        this.playbackQuality = playbackQuality;
    }
}

-------------------------------------------------------------------

what i am missing here?


Странные тут условия xD А 4 очка набрать нельзя :)


As I said in class this is just my gripe with most CS papers. Even the more benchmark and results rich papers don't provide enough context for whether or not their performance results are "good".


Ошибка: `printf("%s\n", "Vvedite koordinati x i y");`


Но тогда можно было и просто `printf("Vvedite koordinati x i y\n");`


`&*p1` - это тоже самое, что и `p1` )


Всё круто! :) Решено как и задумывалось.


Нет необходимости подключать `iostream`, если не используете её функционал(cin, cout и тд)


Игорь, вы сами это прорабатывали или где-то подсмотрели?


Oh f*ck, really? :-/


Много лишних переносов строк.


mrkněte se na https://github.com/spseol/PRG-kameny v README je to tam vysvětlené...


Yes, they will be run on the IO dispatcher. But the more important change here is the lock through the mutex.
Before when multiple db operations were performed synchronously this has lead to an invalid data structure, where the `Book` class had inconsistent data and therefore crashed, looking like this:

```
Caused by java.util.NoSuchElementException: Collection contains no element matching the predicate.
       at de.ph1b.audiobook.data.BookContent.(BookContent.kt:47)
       at de.ph1b.audiobook.data.repo.internals.BookStorage.books(BookStorage.kt:29)
       at de.ph1b.audiobook.data.repo.BookRepository$allBooks$2.invoke(BookRepository.kt:24)
       at de.ph1b.audiobook.data.repo.BookRepository$allBooks$2.invoke(BookRepository.kt:21)
       at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
       at de.ph1b.audiobook.data.repo.BookRepository.getAllBooks(Unknown Source:7)
       at de.ph1b.audiobook.data.repo.BookRepository.access$getAllBooks$p(BookRepository.kt:21)
       at de.ph1b.audiobook.data.repo.BookRepository$active$2.invoke(BookRepository.kt:26)
       at de.ph1b.audiobook.data.repo.BookRepository$active$2.invoke(BookRepository.kt:21)
       at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
       at de.ph1b.audiobook.data.repo.BookRepository.getActive(Unknown Source:7)
       at de.ph1b.audiobook.data.repo.BookRepository.access$getActive$p(BookRepository.kt:21)
       at de.ph1b.audiobook.data.repo.BookRepository$activeBooksSubject$2.invoke(BookRepository.kt:35)
       at de.ph1b.audiobook.data.repo.BookRepository$activeBooksSubject$2.invoke(BookRepository.kt:21)
       at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
       at de.ph1b.audiobook.data.repo.BookRepository.getActiveBooksSubject(Unknown Source:7)
       at de.ph1b.audiobook.data.repo.BookRepository.byId(BookRepository.kt:41)
       at de.ph1b.audiobook.features.widget.TriggerWidgetOnChange$currentBookChanged$1.apply(TriggerWidgetOnChange.kt:42)
       at de.ph1b.audiobook.features.widget.TriggerWidgetOnChange$currentBookChanged$1.apply(TriggerWidgetOnChange.kt:16)
       at io.reactivex.internal.operators.observable.ObservableSwitchMap$SwitchMapObserver.onNext(ObservableSwitchMap.java:111)
       at io.reactivex.internal.operators.observable.ObservableMap$MapObserver.onNext(ObservableMap.java:62)
       at io.reactivex.internal.operators.observable.ObservableConcatMap$ConcatMapDelayErrorObserver.drain(ObservableConcatMap.java:470)
       at io.reactivex.internal.operators.observable.ObservableConcatMap$ConcatMapDelayErrorObserver.onSubscribe(ObservableConcatMap.java:330)
       at io.reactivex.internal.operators.observable.ObservableFromArray.subscribeActual(ObservableFromArray.java:31)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.internal.operators.observable.ObservableConcatMap.subscribeActual(ObservableConcatMap.java:55)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.internal.operators.observable.ObservableMap.subscribeActual(ObservableMap.java:32)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.internal.operators.observable.ObservableSwitchMap.subscribeActual(ObservableSwitchMap.java:51)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.internal.operators.observable.ObservableDistinctUntilChanged.subscribeActual(ObservableDistinctUntilChanged.java:35)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.internal.operators.observable.ObservableFlatMap$MergeObserver.subscribeInner(ObservableFlatMap.java:165)
       at io.reactivex.internal.operators.observable.ObservableFlatMap$MergeObserver.onNext(ObservableFlatMap.java:139)
       at io.reactivex.internal.operators.observable.ObservableFromArray$FromArrayDisposable.run(ObservableFromArray.java:108)
       at io.reactivex.internal.operators.observable.ObservableFromArray.subscribeActual(ObservableFromArray.java:37)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.internal.operators.observable.ObservableFlatMap.subscribeActual(ObservableFlatMap.java:55)
       at io.reactivex.Observable.subscribe(Observable.java:12090)
       at io.reactivex.Observable.subscribe(Observable.java:12076)
       at io.reactivex.Observable.subscribe(Observable.java:11979)
       at de.ph1b.audiobook.features.widget.TriggerWidgetOnChange.init(TriggerWidgetOnChange.kt:26)
       at de.ph1b.audiobook.injection.App.onCreate(App.kt:81)
       at android.app.Instrumentation.callApplicationOnCreate(Instrumentation.java:1120)
       at android.app.ActivityThread.handleBindApplication(ActivityThread.java:5769)
       at android.app.ActivityThread.-wrap1(Unknown Source)
       at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1669)
       at android.os.Handler.dispatchMessage(Handler.java:106)
       at android.os.Looper.loop(Looper.java:164)
       at android.app.ActivityThread.main(ActivityThread.java:6543)
       at java.lang.reflect.Method.invoke(Method.java)
       at com.android.internal.os.RuntimeInit$MethodAndArgsCaller.run(RuntimeInit.java:438)
       at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:807)
```
We need to handle these cases and provide a migration fixing the structure.


В библиотеке math.h, есть эта константа. Рекомендую использовать её.


Проще сделать так:
```
leap_year = year % 4 == 0 && year % 100 != 0 || year % 400 == 0
days[1] += 1 if leap_year
```


Thanks to @flowck for suggestion.


`sin` может быть зарезервированным ключевым словом или функцией. Переименуйте :)


Can you tell me how to install your Project to my PC, thanks


I am starting to come around to the example as I get more used to it. It still strikes me as odd each time I see it.


你是不是不知道什么叫继承？？


Нет чёткого стиля форматирования кода. В if выше фигурная скобочка находится после закрывающей круглой и на той же строке, что и if. В блоке else фигурная скобка следует с новой строки. Аналогичное замечания про внутренность блоков. В первом случае `xdist= 500-a;` на новой строке с отступом, а во втором `xdist =a-500;` на той же строке что и фигурная скобка. Использование различных стилей в одной программе - плохой тон, т.к. сложней читать код.


Should get better next HB release, or whenever it hits chromium and its seventy billion buildbots ;p


@jandryuk I confirm.
if running commands from recovery, that line nées to be removed and gpg relaunched. If not present, /dev/tty is used, even though GPG_TTY is set to /dev/console in init.

I'm short of solutions. With the present, at least flash-gui and gui-init is working...

Any hints?


Как писал выше, `sin` - это функция вычисляющая синус угла. В вашем случае просто переменная. Может возникнуть путаница.


Посмотрел, вы используете `cmath`, там тоже есть эта константа.


Deployment failed with the following error:

~~~
One or more build specification(s) were not referenced
~~~