ropensci / beautier
Files Coverage
R/alpha_parameter_to_xml.R 100.00%
R/are_clock_models.R 100.00%
R/are_equal_mcmcs.R 100.00%
R/are_equal_screenlogs.R 100.00%
R/are_equal_tracelogs.R 100.00%
R/are_equal_treelogs.R 100.00%
R/are_equal_xml_files.R 100.00%
R/are_equal_xml_lines.R 100.00%
R/are_equivalent_xmls.R 100.00%
R/are_fasta_filenames.R 100.00%
R/are_ids.R 100.00%
R/are_init_clock_models.R 100.00%
R/are_init_mrca_priors.R 100.00%
R/are_init_site_models.R 100.00%
R/are_init_tree_priors.R 100.00%
R/are_mrca_align_ids_in_fasta.R 100.00%
R/are_mrca_priors.R 100.00%
R/are_mrca_taxon_names_in_fasta.R 100.00%
R/are_site_models.R 100.00%
R/are_tree_priors.R 100.00%
R/beta_parameter_to_xml.R 100.00%
R/ccp_tree_prior_to_xml_state.R 100.00%
R/check_alignment_id.R 100.00%
R/check_beauti_options.R 100.00%
R/check_clock_model.R 100.00%
R/check_clock_models.R 100.00%
R/check_empty_beautier_folder.R 100.00%
R/check_file_and_model_agree.R 100.00%
R/check_file_exists.R 100.00%
R/check_gamma_site_model.R 100.00%
R/check_gtr_site_model.R 100.00%
R/check_inference_model.R 100.00%
R/check_inference_models.R 100.00%
R/check_is_monophyletic.R 100.00%
R/check_log_mode.R 100.00%
R/check_log_sort.R 100.00%
R/check_mcmc.R 100.00%
R/check_mcmc_nested_sampling.R 100.00%
R/check_mrca_prior.R 100.00%
R/check_mrca_prior_name.R 100.00%
R/check_mrca_prior_taxa_names.R 100.00%
R/check_param.R 100.00%
R/check_phylogeny.R 100.00%
R/check_rename_fun.R 100.00%
R/check_screenlog.R 100.00%
R/check_site_model.R 100.00%
R/check_site_models.R 100.00%
R/check_store_every.R 100.00%
R/check_tn93_site_model.R 100.00%
R/check_tracelog.R 100.00%
R/check_tree_prior.R 100.00%
R/check_tree_priors.R 100.00%
R/check_treelog.R 100.00%
R/clock_model_to_xml_operators.R 100.00%
R/clock_model_to_xml_prior_distr.R 100.00%
R/clock_model_to_xml_state.R 100.00%
R/clock_model_to_xml_tracelog.R 100.00%
R/clock_model_to_xml_treelogger.R 100.00%
R/clock_models_to_xml_operators.R 100.00%
R/clock_models_to_xml_prior_distr.R 100.00%
R/clock_models_to_xml_state.R 100.00%
R/clock_models_to_xml_tracelog.R 100.00%
R/clock_rate_param_to_xml.R 100.00%
R/compare_lines.R 100.00%
R/count_trailing_spaces.R 100.00%
R/create_beast2_beast_xml.R 100.00%
R/create_beast2_input.R 100.00%
R/create_beast2_input_beast.R 100.00%
R/create_beast2_input_data.R 100.00%
R/create_beast2_input_data_sequences.R 100.00%
R/create_beast2_input_distr.R 100.00%
R/create_beast2_input_file.R 100.00%
R/create_beast2_input_file_from_model.R 100.00%
R/create_beast2_input_from_model.R 100.00%
R/create_beast2_input_init.R 100.00%
R/create_beast2_input_map.R 100.00%
R/create_beast2_input_operators.R 100.00%
R/create_beast2_input_run.R 100.00%
R/create_beast2_input_state.R 100.00%
R/create_beast2_input_xml.R 100.00%
R/create_beauti_options.R 100.00%
R/create_beauti_options_v2_4.R 100.00%
R/create_beauti_options_v2_6.R 100.00%
R/create_branch_rate_model_rln_xml.R 100.00%
R/create_branch_rate_model_stuff_xml.R 100.00%
R/create_branch_rate_model_xml.R 100.00%
R/create_clock_model.R 100.00%
R/create_clock_model_from_name.R 100.00%
R/create_clock_models.R 100.00%
R/create_clock_models_from_names.R 100.00%
R/create_clock_rate_state_node_parameter_xml.R 100.00%
R/create_data_xml.R 100.00%
R/create_distr.R 100.00%
R/create_gamma_site_model.R 100.00%
R/create_inference_model.R 100.00%
R/create_loggers_xml.R 100.00%
R/create_mcmc.R 100.00%
R/create_mcmc_nested_sampling.R 100.00%
R/create_mrca_prior.R 100.00%
R/create_ns_inference_model.R 100.00%
R/create_param.R 100.00%
R/create_rate_categories_state_node_xml.R 100.00%
R/create_screenlog.R 100.00%
R/create_screenlog_xml.R 100.00%
R/create_site_model.R 100.00%
R/create_site_model_from_name.R 100.00%
R/create_site_model_parameters_xml.R 100.00%
R/create_site_model_xml.R 100.00%
R/create_site_models.R 100.00%
R/create_site_models_from_names.R 100.00%
R/create_strict_clock_rate_scaler_operator_xml.R 100.00%
R/create_subst_model_xml.R 100.00%
R/create_temp_screenlog_filename.R 100.00%
R/create_temp_tracelog_filename.R 100.00%
R/create_temp_treelog_filename.R 100.00%
R/create_test_inference_model.R 100.00%
R/create_test_mcmc.R 100.00%
R/create_test_ns_inference_model.R 100.00%
R/create_test_ns_mcmc.R 100.00%
R/create_test_screenlog.R 100.00%
R/create_test_tracelog.R 100.00%
R/create_test_treelog.R 100.00%
R/create_tracelog.R 100.00%
R/create_tracelog_xml.R 100.00%
R/create_trait_set_string.R 100.00%
R/create_tree_likelihood_distr_xml.R 100.00%
R/create_tree_prior.R 100.00%
R/create_tree_priors.R 100.00%
R/create_treelog.R 100.00%
R/create_treelog_xml.R 100.00%
R/create_ucld_mean_state_node_param_xml.R 100.00%
R/create_ucld_stdev_state_node_param_xml.R 100.00%
R/distr_to_xml.R 100.00%
R/extract_xml_loggers_from_lines.R 100.00%
R/extract_xml_operators_from_lines.R 100.00%
R/extract_xml_section_from_lines.R 100.00%
R/fasta_to_sequences.R 100.00%
R/find_clock_model.R 100.00%
R/find_first_regex_line.R 100.00%
R/find_first_xml_opening_tag_line.R 100.00%
R/find_last_regex_line.R 100.00%
R/find_last_xml_closing_tag_line.R 100.00%
R/freq_equilibrium_to_xml.R 100.00%
R/gamma_distr_to_xml.R 100.00%
R/gamma_site_model_to_xml_prior_distr.R 100.00%
R/gamma_site_model_to_xml_state.R 100.00%
R/gamma_site_models_to_xml_prior_distr.R 100.00%
R/get_alignment_id.R 100.00%
R/get_alignment_ids.R 100.00%
R/get_beautier_folder.R 100.00%
R/get_beautier_path.R 100.00%
R/get_beautier_paths.R 100.00%
R/get_beautier_tempfilename.R 100.00%
R/get_clock_model_name.R 100.00%
R/get_clock_model_names.R 100.00%
R/get_clock_models_ids.R 100.00%
R/get_crown_age.R 100.00%
R/get_distr_n_params.R 100.00%
R/get_distr_names.R 100.00%
R/get_file_base_sans_ext.R 100.00%
R/get_freq_equilibrium_names.R 100.00%
R/get_gamma_site_model_n_distrs.R 100.00%
R/get_gamma_site_model_n_params.R 100.00%
R/get_has_non_strict_clock_model.R 100.00%
R/get_inference_model_filenames.R 100.00%
R/get_log_modes.R 100.00%
R/get_log_sorts.R 100.00%
R/get_mcmc_filenames.R 100.00%
R/get_n_taxa.R 100.00%
R/get_operator_id_pre.R 100.00%
R/get_param_names.R 100.00%
R/get_remove_dir_fun.R 100.00%
R/get_remove_hex_fun.R 100.00%
R/get_replace_dir_fun.R 100.00%
R/get_site_model_n_distrs.R 100.00%
R/get_site_model_n_params.R 100.00%
R/get_site_model_names.R 100.00%
R/get_site_models_n_distrs.R 100.00%
R/get_site_models_n_params.R 100.00%
R/get_taxa_names.R 100.00%
R/get_test_filenames.R 100.00%
R/get_tree_prior_n_distrs.R 100.00%
R/get_tree_prior_n_params.R 100.00%
R/get_tree_prior_names.R 100.00%
R/get_tree_priors_n_distrs.R 100.00%
R/get_tree_priors_n_params.R 100.00%
R/get_xml_closing_tag.R 100.00%
R/get_xml_opening_tag.R 100.00%
R/has_mrca_prior.R 100.00%
R/has_mrca_prior_with_distr.R 100.00%
R/has_rln_clock_model.R 100.00%
R/has_strict_clock_model.R 100.00%
R/has_tip_dating.R 100.00%
R/has_xml_closing_tag.R 100.00%
R/has_xml_opening_tag.R 100.00%
R/has_xml_short_closing_tag.R 100.00%
R/indent.R 100.00%
R/init_clock_models.R 100.00%
R/init_distr.R 100.00%
R/init_gamma_site_model.R 100.00%
R/init_inference_model.R 100.00%
R/init_mrca_prior.R 100.00%
R/init_mrca_priors.R 100.00%
R/init_param.R 100.00%
R/init_site_models.R 100.00%
R/init_tree_priors.R 100.00%
R/interspace.R 100.00%
R/is_beauti_options.R 100.00%
R/is_clock_model.R 100.00%
R/is_clock_model_name.R 100.00%
R/is_default_mcmc.R 100.00%
R/is_distr.R 100.00%
R/is_distr_name.R 100.00%
R/is_freq_equilibrium_name.R 100.00%
R/is_gamma_site_model.R 100.00%
R/is_id.R 100.00%
R/is_in_patterns.R 100.00%
R/is_inference_model.R 100.00%
R/is_init_clock_model.R 100.00%
R/is_init_distr.R 100.00%
R/is_init_gamma_site_model.R 100.00%
R/is_init_mrca_prior.R 100.00%
R/is_init_param.R 100.00%
R/is_init_site_model.R 100.00%
R/is_init_tree_prior.R 100.00%
R/is_m_param.R 100.00%
R/is_mcmc.R 100.00%
R/is_mrca_align_id_in_fasta.R 100.00%
R/is_mrca_align_ids_in_fastas.R 100.00%
R/is_mrca_prior.R 100.00%
R/is_mrca_prior_with_distr.R 100.00%
R/is_one_bool.R 100.00%
R/is_one_double.R 100.00%
R/is_one_int.R 100.00%
R/is_one_na.R 100.00%
R/is_param.R 100.00%
R/is_param_name.R 100.00%
R/is_phylo.R 100.00%
R/is_site_model.R 100.00%
R/is_site_model_name.R 100.00%
R/is_tree_prior.R 100.00%
R/is_tree_prior_name.R 100.00%
R/is_xml.R 100.00%
R/m_param_to_xml.R 100.00%
R/mcmc_to_xml_run.R 100.00%
R/mrca_prior_to_xml_prior_distr.R 100.00%
R/mrca_prior_to_xml_state.R 100.00%
R/mrca_prior_to_xml_taxonset.R 100.00%
R/mrca_prior_to_xml_tracelog.R 100.00%
R/mrca_priors_to_xml_distr.R 100.00%
R/mrca_priors_to_xml_tracelog.R 0.00%
R/parameter_to_xml.R 100.00%
R/remove_empty_lines.R 100.00%
R/remove_multiline.R 100.00%
R/rename_inference_model_filenames.R 100.00%
R/rename_mcmc_filenames.R 100.00%
R/rln_clock_model_to_xml_mean_rate_prior.R 100.00%
R/rln_clock_model_to_xml_prior_distr.R 100.00%
R/rnd_phylo_xml_init.R 100.00%
R/site_model_to_xml_operators.R 100.00%
R/site_model_to_xml_prior.R 100.00%
R/site_model_to_xml_state.R 100.00%
R/site_model_to_xml_tracelog.R 100.00%
R/site_models_to_xml_operators.R 100.00%
R/site_models_to_xml_prior_distr.R 100.00%
R/site_models_to_xml_tracelog.R 100.00%
R/taxa_to_xml_tree.R 100.00%
R/tipdate_taxa_to_xml_trait.R 100.00%
R/tree_model_to_tracelog_xml.R 100.00%
R/tree_models_to_xml_tracelog.R 100.00%
R/tree_prior_to_xml_operators.R 100.00%
R/tree_prior_to_xml_prior_distr.R 100.00%
R/tree_prior_to_xml_state.R 100.00%
R/tree_prior_to_xml_tracelog.R 100.00%
R/tree_priors_to_xml_distr.R 100.00%
R/tree_priors_to_xml_operators.R 100.00%
R/tree_priors_to_xml_tracelog.R 100.00%
R/unindent.R 100.00%
R/yule_tree_prior_to_xml_operators.R 100.00%
Project Totals (279 files) 99.94%
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