ropensci / beautier

Compare 96d327c ... +0 ... 5f3fe02

99.94% ø ø

Overview Diff Coverage Changes Files Commits
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

No flags found

Use flags to group coverage reports by test type, project and/or folders.
Then setup custom commit statuses and notifications for each flag.

e.g., #unittest #integration

#production #enterprise

#frontend #backend

Learn more about Codecov Flags here.

2 untracked files changed.
Other files ignored by Codecov
Singularity has changed.
scripts/build_singularity_container.sh is new.

No tracked files changed.

Everything is accounted for!

No changes detected that need to be reviewed.
What changes does Codecov check for?
Lines, not adjusted in diff, that have changed coverage data.
Files that introduced coverage data that had none before.
Files that have missing coverage data that once were tracked.

2 Commits

Richel Bilderbeek
99.94% ø ø
EOD
richelbilderbeek
5f3fe02
CI Passed
Richel Bilderbeek
99.94% ø ø
Fix Singularity script
richelbilderbeek
96d327c
CI Passed
Files Coverage
R 99.94%
Project Totals (279 files) 99.94%
Loading