ropensci / beautier

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Coverage Reach
parameter_to_xml.R init_site_models.R create_distr.R create_beast2_input_distr.R distr_to_xml.R init_distr.R create_subst_model_xml.R create_param.R are_equivalent_xmls.R init_clock_models.R create_site_model.R init_tree_priors.R check_clock_model.R tree_prior_to_xml_operators.R is_distr.R site_model_to_xml_prior.R create_tracelog_xml.R site_model_to_xml_operators.R create_branch_rate_model_rln_xml.R clock_model_to_xml_operators.R site_model_to_xml_state.R taxa_to_xml_tree.R is_param.R create_beast2_input_beast.R mrca_prior_to_xml_prior_distr.R check_inference_model.R is_init_distr.R create_clock_model.R create_site_model_parameters_xml.R tree_prior_to_xml_state.R check_gtr_site_model.R create_tree_prior.R mcmc_to_xml_run.R check_mcmc.R create_beast2_input_run.R create_branch_rate_model_stuff_xml.R is_init_site_model.R check_gamma_site_model.R create_branch_rate_model_xml.R create_screenlog_xml.R create_beast2_input_data_sequences.R create_beast2_input_state.R is_site_model.R init_inference_model.R is_tree_prior.R clock_model_to_xml_state.R site_model_to_xml_tracelog.R get_site_model_n_params.R check_file_and_model_agree.R check_beauti_options.R create_treelog_xml.R tipdate_taxa_to_xml_trait.R create_beast2_input_data.R tree_prior_to_xml_tracelog.R check_tn93_site_model.R create_site_model_xml.R ccp_tree_prior_to_xml_state.R extract_xml_section_from_lines.R mrca_prior_to_xml_tracelog.R get_distr_n_params.R is_init_tree_prior.R init_mrca_priors.R clock_model_to_xml_prior_distr.R create_beast2_input_from_model.R create_beast2_input_map.R rnd_phylo_xml_init.R yule_tree_prior_to_xml_operators.R are_equal_xml_lines.R clock_rate_param_to_xml.R beta_parameter_to_xml.R alpha_parameter_to_xml.R create_beast2_input_file_from_model.R clock_model_to_xml_tracelog.R gamma_distr_to_xml.R check_mrca_prior.R m_param_to_xml.R get_param_names.R rln_clock_model_to_xml_prior_distr.R create_ucld_mean_state_node_param_xml.R create_clock_rate_state_node_parameter_xml.R create_tree_likelihood_distr_xml.R check_screenlog.R check_treelog.R check_tracelog.R check_site_model.R get_tree_prior_n_params.R check_empty_beautier_folder.R gamma_site_model_to_xml_prior_distr.R create_gamma_site_model.R mrca_prior_to_xml_state.R clock_model_to_xml_treelogger.R check_clock_models.R create_ucld_stdev_state_node_param_xml.R compare_lines.R check_mcmc_nested_sampling.R is_init_clock_model.R create_mcmc_nested_sampling.R check_alignment_id.R tree_prior_to_xml_prior_distr.R create_rate_categories_state_node_xml.R create_beast2_input_file.R check_param.R get_site_model_n_distrs.R is_mcmc.R get_tree_prior_n_distrs.R are_equal_xml_files.R create_strict_clock_rate_scaler_operator_xml.R rln_clock_model_to_xml_mean_rate_prior.R get_operator_id_pre.R freq_equilibrium_to_xml.R check_file_exists.R create_loggers_xml.R create_beast2_input.R get_replace_dir_fun.R mrca_prior_to_xml_taxonset.R interspace.R create_mcmc.R gamma_site_model_to_xml_state.R is_clock_model.R remove_multiline.R fasta_to_sequences.R init_gamma_site_model.R create_beast2_input_init.R rename_mcmc_filenames.R create_inference_model.R are_equal_mcmcs.R create_beast2_input_operators.R are_mrca_taxon_names_in_fasta.R are_clock_models.R create_test_mcmc.R are_equal_tracelogs.R create_ns_inference_model.R are_equal_treelogs.R check_mrca_prior_name.R create_beast2_beast_xml.R is_xml.R are_equal_screenlogs.R create_mrca_prior.R create_data_xml.R create_test_ns_inference_model.R create_beauti_options.R has_xml_opening_tag.R is_init_mrca_prior.R tree_model_to_tracelog_xml.R rename_inference_model_filenames.R are_mrca_priors.R check_store_every.R create_treelog.R create_tracelog.R create_test_inference_model.R create_trait_set_string.R indent.R create_site_model_from_name.R find_clock_model.R init_mrca_prior.R create_test_ns_mcmc.R create_screenlog.R has_xml_short_closing_tag.R is_mrca_align_id_in_fasta.R get_site_models_n_distrs.R check_rename_fun.R is_mrca_align_ids_in_fastas.R extract_xml_operators_from_lines.R get_tree_priors_n_distrs.R check_mrca_prior_taxa_names.R get_n_taxa.R check_tree_prior.R get_remove_hex_fun.R get_crown_age.R get_site_models_n_params.R create_tree_priors.R are_tree_priors.R are_ids.R get_alignment_ids.R get_clock_models_ids.R check_log_mode.R get_tree_prior_names.R create_beauti_options_v2_4.R are_fasta_filenames.R create_test_treelog.R check_log_sort.R create_test_tracelog.R create_test_screenlog.R is_inference_model.R is_mrca_prior.R get_mcmc_filenames.R site_models_to_xml_prior_distr.R get_tree_priors_n_params.R create_clock_models_from_names.R check_site_models.R is_one_int.R check_tree_priors.R gamma_site_models_to_xml_prior_distr.R has_xml_closing_tag.R is_in_patterns.R find_first_regex_line.R create_temp_screenlog_filename.R get_xml_closing_tag.R find_last_regex_line.R tree_priors_to_xml_distr.R is_one_double.R check_phylogeny.R create_temp_treelog_filename.R create_site_models_from_names.R create_temp_tracelog_filename.R get_xml_opening_tag.R site_models_to_xml_operators.R are_site_models.R create_site_models.R get_alignment_id.R tree_priors_to_xml_tracelog.R get_has_non_strict_clock_model.R mrca_priors_to_xml_distr.R is_gamma_site_model.R get_inference_model_filenames.R get_log_modes.R remove_empty_lines.R check_inference_models.R get_beautier_path.R unindent.R are_init_tree_priors.R get_gamma_site_model_n_distrs.R are_init_mrca_priors.R is_init_gamma_site_model.R get_clock_model_name.R are_init_clock_models.R get_remove_dir_fun.R is_beauti_options.R site_models_to_xml_tracelog.R get_log_sorts.R extract_xml_loggers_from_lines.R count_trailing_spaces.R create_clock_model_from_name.R are_init_site_models.R get_beautier_tempfilename.R are_mrca_align_ids_in_fasta.R init_param.R get_gamma_site_model_n_params.R mrca_priors_to_xml_tracelog.R get_distr_names.R is_mrca_prior_with_distr.R clock_models_to_xml_tracelog.R get_beautier_paths.R is_init_param.R create_beauti_options_v2_6.R tree_models_to_xml_tracelog.R has_mrca_prior_with_distr.R clock_models_to_xml_operators.R create_clock_models.R find_first_xml_opening_tag_line.R has_rln_clock_model.R is_param_name.R has_tip_dating.R has_strict_clock_model.R check_is_monophyletic.R has_mrca_prior.R get_taxa_names.R is_m_param.R find_last_xml_closing_tag_line.R is_one_na.R is_default_mcmc.R create_beast2_input_xml.R is_site_model_name.R clock_models_to_xml_state.R clock_models_to_xml_prior_distr.R get_clock_model_names.R get_beautier_folder.R is_distr_name.R is_phylo.R is_freq_equilibrium_name.R is_tree_prior_name.R get_site_model_names.R get_freq_equilibrium_names.R is_one_bool.R get_test_filenames.R is_id.R get_file_base_sans_ext.R tree_priors_to_xml_operators.R is_clock_model_name.R

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Files Coverage
R 99.94%
Project Totals (279 files) 99.94%
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