[R/create_beast2_input_distr.R:332:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_init.R:9:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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.R:126:17:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_gamma_site_model.R:77:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/create_mcmc.R#L41) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/create_random.R:60:3:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/distr_to_xml.R#L39) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(distr))
                   ^~~~~~~~~~~~~~~~
```
[R/fastas_to_phylos.R:42:20:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/get_alignment_ids.R:16:22:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_distr_n_params.R:65:20:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_site_model_n_distrs.R:33:32:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_priors_n_distrs.R:22:20:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_site_models.R:6:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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:125:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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:37:30:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_param.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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:115:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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:68:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_clock_model.R#L68) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$clock_rate_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_clock_model.R:70:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_clock_model.R#L70) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$clock_rate_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_default_mcmc.R:15:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L53) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:55:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L55) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:76:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L76) *warning:* **no visible global function definition for ‘is_mean_param’**
```r
  if (!is_mean_param(x$mean)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:97:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L97) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:99:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L99) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:120:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L120) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:122:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L122) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:146:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L146) *warning:* **no visible global function definition for ‘is_mu_param’**
```r
  if (!is_mu_param(x$mu)) return(FALSE)
       ^~~~~~~~~~~
```
[R/is_distr.R:148:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L148) *warning:* **no visible global function definition for ‘is_scale_param’**
```r
  if (!is_scale_param(x$scale)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:181:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L181) *warning:* **no visible global function definition for ‘is_m_param’**
```r
  if (!is_m_param(x$m)) return(FALSE)
       ^~~~~~~~~~
```
[R/is_distr.R:183:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L183) *warning:* **no visible global function definition for ‘is_s_param’**
```r
  if (!is_s_param(x$s)) return(FALSE)
       ^~~~~~~~~~
```
[R/is_distr.R:204:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L204) *warning:* **no visible global function definition for ‘is_mean_param’**
```r
  if (!is_mean_param(x$mean)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:206:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L206) *warning:* **no visible global function definition for ‘is_sigma_param’**
```r
  if (!is_sigma_param(x$sigma)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:244:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_distr.R#L244) *warning:* **no visible global function definition for ‘is_lambda_param’**
```r
  if (!is_lambda_param(x$lambda)) return(FALSE)
       ^~~~~~~~~~~~~~~
```
[R/is_freq_equilibrium_name.R:17:13:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_init_clock_model.R:43:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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_site_model.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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:80:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/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/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_mcmc.R#L34) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(x)) return(FALSE)
       ^~~~~~~
```
[R/is_mrca_prior_with_distr.R:13:3:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_mrca_prior_with_distr.R#L13) *warning:* **no visible global function definition for ‘is_distr’**
```r
  is_distr(x$mrca_distr)
  ^~~~~~~~
```
[R/is_mrca_prior.R:18:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_mrca_prior.R#L18) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$mrca_distr) && !is.na(x$mrca_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:30:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L30) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:45:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L45) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:60:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L60) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:79:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L79) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:102:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L102) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:124:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L124) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:139:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L139) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:153:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L153) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:172:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L172) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:191:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L191) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:209:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L209) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:228:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L228) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:247:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L247) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:266:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L266) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:285:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L285) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:300:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L300) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:315:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L315) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:330:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_param.R#L330) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:21:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L21) *warning:* **no visible global function definition for ‘is_site_model_name’**
```r
  if (!is_site_model_name(x$name)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:24:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L24) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  if (!is_gamma_site_model(x$gamma_site_model)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:40:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L40) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:54:10:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L54) *warning:* **no visible global function definition for ‘is_distr’**
```r
    if (!is_distr(expected_distr)) return(FALSE)
         ^~~~~~~~
```
[R/is_site_model.R:60:10:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L60) *warning:* **no visible global function definition for ‘is_param’**
```r
    if (!is_param(expected_param)) return(FALSE)
         ^~~~~~~~
```
[R/is_site_model.R:63:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L63) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:79:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L79) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:83:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L83) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:85:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L85) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:100:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L100) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:120:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L120) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:122:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L122) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_1_prior_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:124:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L124) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_2_prior_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:126:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L126) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$kappa_1_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:128:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L128) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$kappa_2_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:130:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_site_model.R#L130) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/is_tree_prior.R#L11) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~
```
[R/mcmc_to_xml_run.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/mcmc_to_xml_run.R#L13) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/mcmc_to_xml_run.R:33:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/mcmc_to_xml_run.R#L33) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/mcmc_to_xml_run.R:62:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/mcmc_to_xml_run.R#L62) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/mrca_prior_to_xml_prior_distr.R:73:21:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/mrca_prior_to_xml_prior_distr.R#L73) *warning:* **no visible global function definition for ‘indent’, Did you mean 'infert'?**
```r
    text <- c(text, indent(distr_to_xml(mrca_prior$mrca_distr), n_spaces = 4))
                    ^~~~~~
```
[R/mrca_prior_to_xml_prior_distr.R:73:28:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/mrca_prior_to_xml_prior_distr.R#L73) *warning:* **no visible global function definition for ‘distr_to_xml’**
```r
    text <- c(text, indent(distr_to_xml(mrca_prior$mrca_distr), n_spaces = 4))
                           ^~~~~~~~~~~~
```
[R/mrca_prior_to_xml_taxonset.R:29:11:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/mrca_prior_to_xml_taxonset.R#L29) *warning:* **no visible global function definition for ‘indent’, Did you mean 'infert'?**
```r
  text <- indent(text, n_spaces = 4)
          ^~~~~~
```
[R/parameter_to_xml.R:59:20:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/parameter_to_xml.R#L59) *warning:* **no visible global function definition for ‘is_sigma_param’**
```r
    testit::assert(is_sigma_param(parameter))
                   ^~~~~~~~~~~~~~
```
[R/phylo_to_xml_state.R:16:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/phylo_to_xml_state.R#L16) *warning:* **no visible global function definition for ‘is_phylo’**
```r
  testit::assert(is_phylo(phylo))
                 ^~~~~~~~
```
[R/site_model_to_xml_tracelog.R:14:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/site_model_to_xml_tracelog.R#L14) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  testit::assert(is_site_model(site_model))
                 ^~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:7:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/site_models_to_xml_operators.R#L7) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_state.R:11:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/site_models_to_xml_state.R#L11) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_state.R:15:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/site_models_to_xml_state.R#L15) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:16:22:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/tree_prior_to_xml_operators.R#L16) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior)
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:18:18:](https://github.com/richelbilderbeek/beautier/blob/f925670d6ea4ef1668f0a820369082a9bd9624bb/R/tree_prior_to_xml_prior_distr.R#L18) *warning:* **no visible global function definition for ‘is_tree_prior’**
```r
  testit::assert(is_tree_prior(tree_prior))
                 ^~~~~~~~~~~~~
```


getter setter missing


Test comment


+ Hello!
  2   + World!


Это случайно)


@muhammadhusnainmaqsood cpp and header file not separate


@muhammadhusnainmaqsood not checked for duplicates


Even with this change I still have the same error :(

Server version: 5.7.18-0ubuntu0.16.10.1


Please do not comment on releases or individual commits.
Create an issue if you ran into problems.
Thanks! 👍


@muhammadhusnainmaqsood will cause out of memory exception


I'm not saying you need to check in the loop (which you already did). I'm asking why you need to check again outside the loop.


@muhammadhusnainmaqsood not checked for errors.


I don't understand your question. return false will always return "false" to the calling function (in this case, main).


[R/create_beast2_input_loggers.R:97:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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.R:126:17:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_gamma_site_model.R:77:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/create_mcmc.R#L41) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/create_random.R:60:3:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/distr_to_xml.R#L39) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(distr))
                   ^~~~~~~~~~~~~~~~
```
[R/fastas_to_phylos.R:42:20:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/get_alignment_ids.R:16:22:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_distr_n_params.R:65:20:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_site_model_n_distrs.R:33:32:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_priors_n_distrs.R:22:20:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_site_models.R:6:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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:125:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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:37:30:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_param.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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:149:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/init_tree_priors.R#L149) *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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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:68:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_clock_model.R#L68) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$clock_rate_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_clock_model.R:70:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_clock_model.R#L70) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$clock_rate_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_default_mcmc.R:15:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L53) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:55:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L55) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:76:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L76) *warning:* **no visible global function definition for ‘is_mean_param’**
```r
  if (!is_mean_param(x$mean)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:97:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L97) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:99:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L99) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:120:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L120) *warning:* **no visible global function definition for ‘is_alpha_param’**
```r
  if (!is_alpha_param(x$alpha)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:122:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L122) *warning:* **no visible global function definition for ‘is_beta_param’**
```r
  if (!is_beta_param(x$beta)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:146:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L146) *warning:* **no visible global function definition for ‘is_mu_param’**
```r
  if (!is_mu_param(x$mu)) return(FALSE)
       ^~~~~~~~~~~
```
[R/is_distr.R:148:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L148) *warning:* **no visible global function definition for ‘is_scale_param’**
```r
  if (!is_scale_param(x$scale)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:181:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L181) *warning:* **no visible global function definition for ‘is_m_param’**
```r
  if (!is_m_param(x$m)) return(FALSE)
       ^~~~~~~~~~
```
[R/is_distr.R:183:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L183) *warning:* **no visible global function definition for ‘is_s_param’**
```r
  if (!is_s_param(x$s)) return(FALSE)
       ^~~~~~~~~~
```
[R/is_distr.R:204:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L204) *warning:* **no visible global function definition for ‘is_mean_param’**
```r
  if (!is_mean_param(x$mean)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_distr.R:206:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L206) *warning:* **no visible global function definition for ‘is_sigma_param’**
```r
  if (!is_sigma_param(x$sigma)) return(FALSE)
       ^~~~~~~~~~~~~~
```
[R/is_distr.R:244:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_distr.R#L244) *warning:* **no visible global function definition for ‘is_lambda_param’**
```r
  if (!is_lambda_param(x$lambda)) return(FALSE)
       ^~~~~~~~~~~~~~~
```
[R/is_freq_equilibrium_name.R:17:13:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_init_clock_model.R:43:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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_site_model.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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/b989b675b18c8c00b7d38c0f3648baa2b516482f/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:94:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_init_tree_prior.R#L94) *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/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_mcmc.R#L34) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(x)) return(FALSE)
       ^~~~~~~
```
[R/is_mrca_prior_with_distr.R:13:3:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_mrca_prior_with_distr.R#L13) *warning:* **no visible global function definition for ‘is_distr’**
```r
  is_distr(x$mrca_distr)
  ^~~~~~~~
```
[R/is_mrca_prior.R:18:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_mrca_prior.R#L18) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$mrca_distr) && !is.na(x$mrca_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:30:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L30) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:45:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L45) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:60:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L60) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:79:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L79) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:102:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L102) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:124:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L124) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:139:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L139) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:153:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L153) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:172:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L172) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:191:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L191) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:209:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L209) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:228:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L228) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:247:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L247) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:266:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L266) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:285:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L285) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:300:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L300) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:315:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L315) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_param.R:330:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_param.R#L330) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:21:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L21) *warning:* **no visible global function definition for ‘is_site_model_name’**
```r
  if (!is_site_model_name(x$name)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:24:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L24) *warning:* **no visible global function definition for ‘is_gamma_site_model’**
```r
  if (!is_gamma_site_model(x$gamma_site_model)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:40:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L40) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:54:10:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L54) *warning:* **no visible global function definition for ‘is_distr’**
```r
    if (!is_distr(expected_distr)) return(FALSE)
         ^~~~~~~~
```
[R/is_site_model.R:60:10:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L60) *warning:* **no visible global function definition for ‘is_param’**
```r
    if (!is_param(expected_param)) return(FALSE)
         ^~~~~~~~
```
[R/is_site_model.R:63:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L63) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:79:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L79) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:83:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L83) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:85:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L85) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:100:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L100) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:120:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L120) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  if (!is_site_model(x)) return(FALSE)
       ^~~~~~~~~~~~~
```
[R/is_site_model.R:122:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L122) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_1_prior_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:124:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L124) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_2_prior_distr)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:126:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L126) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$kappa_1_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:128:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L128) *warning:* **no visible global function definition for ‘is_param’**
```r
  if (!is_param(x$kappa_2_param)) return(FALSE)
       ^~~~~~~~
```
[R/is_site_model.R:130:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_site_model.R#L130) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:11:8:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/is_tree_prior.R#L11) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE)
       ^~~~~~~~~~~~~~~~~~
```
[R/mcmc_to_xml_run.R:13:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/mcmc_to_xml_run.R#L13) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/mcmc_to_xml_run.R:33:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/mcmc_to_xml_run.R#L33) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/mcmc_to_xml_run.R:62:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/mcmc_to_xml_run.R#L62) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  testit::assert(is_mcmc(mcmc))
                 ^~~~~~~
```
[R/mrca_prior_to_xml_prior_distr.R:73:21:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/mrca_prior_to_xml_prior_distr.R#L73) *warning:* **no visible global function definition for ‘indent’, Did you mean 'infert'?**
```r
    text <- c(text, indent(distr_to_xml(mrca_prior$mrca_distr), n_spaces = 4))
                    ^~~~~~
```
[R/mrca_prior_to_xml_prior_distr.R:73:28:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/mrca_prior_to_xml_prior_distr.R#L73) *warning:* **no visible global function definition for ‘distr_to_xml’**
```r
    text <- c(text, indent(distr_to_xml(mrca_prior$mrca_distr), n_spaces = 4))
                           ^~~~~~~~~~~~
```
[R/mrca_prior_to_xml_taxonset.R:29:11:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/mrca_prior_to_xml_taxonset.R#L29) *warning:* **no visible global function definition for ‘indent’, Did you mean 'infert'?**
```r
  text <- indent(text, n_spaces = 4)
          ^~~~~~
```
[R/parameter_to_xml.R:59:20:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/parameter_to_xml.R#L59) *warning:* **no visible global function definition for ‘is_sigma_param’**
```r
    testit::assert(is_sigma_param(parameter))
                   ^~~~~~~~~~~~~~
```
[R/phylo_to_xml_state.R:16:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/phylo_to_xml_state.R#L16) *warning:* **no visible global function definition for ‘is_phylo’**
```r
  testit::assert(is_phylo(phylo))
                 ^~~~~~~~
```
[R/site_model_to_xml_tracelog.R:14:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/site_model_to_xml_tracelog.R#L14) *warning:* **no visible global function definition for ‘is_site_model’**
```r
  testit::assert(is_site_model(site_model))
                 ^~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:7:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/site_models_to_xml_operators.R#L7) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_state.R:11:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/site_models_to_xml_state.R#L11) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_state.R:15:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/site_models_to_xml_state.R#L15) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models))
                 ^~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:16:22:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/tree_prior_to_xml_operators.R#L16) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior)
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:18:18:](https://github.com/richelbilderbeek/beautier/blob/b989b675b18c8c00b7d38c0f3648baa2b516482f/R/tree_prior_to_xml_prior_distr.R#L18) *warning:* **no visible global function definition for ‘is_tree_prior’**
```r
  testit::assert(is_tree_prior(tree_prior))
                 ^~~~~~~~~~~~~
```


You know how the program should work, not me. I'm just pointing out this function currently always return true, which is no different than defining it as void RegisterPage().


Think again.


Have you tried declaring them in main()?


If you return here, UserLogin will not be closed which will lead to memory leak.


@l164278talhaZaheer copy constructor not correct.
In order insertion does not check for errors.
No separate file for cpp and header


@l164278talhaZaheer local variable returned


![pic 1](https://user-images.githubusercontent.com/28492382/48310601-abdd8f00-e5b7-11e8-8c14-ca27f4099326.png)
![pic 2](https://user-images.githubusercontent.com/28492382/48310610-bac44180-e5b7-11e8-9722-da7c638ac97f.png)
---------------------
ISSUE FIXED


@l164278talhaZaheer not checked for errors