ropensci / beautier

Compare 5ed40f2 ... +1 ... 2713f22

100.00% ø ø

Overview Diff Coverage Changes Files Commits
Coverage Reach
parameter_to_xml.R init_site_models.R create_beast2_input_distr.R distr_to_xml.R create_distr.R site_model_to_xml_subst_model.R create_param.R init_clock_models.R init_tree_priors.R create_site_model.R tree_prior_to_xml_operators.R check_clock_model.R are_equivalent_xmls.R is_distr.R create_tracelog_xml.R site_model_to_xml_prior.R site_model_to_xml_operators.R site_model_to_xml_state.R init_distr.R create_beast2_input_run.R clock_model_to_xml_operators.R clock_model_to_xml_lh_distr.R is_param.R create_beast2_input_file.R is_site_model.R create_beast2_input.R is_init_distr.R create_clock_model.R mrca_prior_to_xml_prior_distr.R check_inference_model.R create_tree_prior.R mcmc_to_xml_run.R check_mcmc.R is_init_site_model.R check_gamma_site_model.R site_model_to_xml_lh_distr.R tree_prior_to_xml_state.R create_beast2_input_beast.R create_screenlog_xml.R create_beast2_input_state.R taxa_to_xml_tree.R mrca_prior_to_xml_lh_distr.R is_tree_prior.R init_inference_model.R clock_model_to_xml_prior_distr.R site_model_to_xml_tracelog.R get_site_model_n_params.R check_beauti_options.R check_file_and_model_agree.R tree_prior_to_xml_tracelog.R extract_xml_section_from_lines.R get_distr_n_params.R is_init_tree_prior.R init_mrca_priors.R create_beast2_input_from_model.R create_beast2_input_data.R create_beast2_input_operators.R are_equal_xml_lines.R create_treelog_xml.R clock_model_to_xml_state.R check_mrca_prior.R create_beast2_input_file_from_model.R create_beast2_input_data_sequences.R clock_models_to_xml_state.R get_param_names.R create_beast2_beast_xml.R create_beast2_input_map.R check_screenlog.R check_tracelog.R check_treelog.R get_tree_prior_n_params.R gamma_site_model_to_xml_prior_distr.R create_gamma_site_model.R clock_model_to_xml_treelogger.R mrca_prior_to_xml_tracelog.R check_clock_models.R clock_model_to_xml_tracelog.R check_mcmc_nested_sampling.R is_init_clock_model.R mrca_priors_to_xml_distr.R create_mcmc_nested_sampling.R check_alignment_id.R tree_prior_to_xml_prior_distr.R rnd_phylo_xml_init.R get_site_model_n_distrs.R tree_priors_to_xml_operators.R is_mcmc.R get_tree_prior_n_distrs.R are_equal_xml_files.R rln_clock_model_to_xml_mean_rate_prior.R get_operator_id_pre.R freq_equilibrium_to_xml.R check_file_exists.R clock_models_to_xml_tracelog.R create_loggers_xml.R mrca_prior_to_xml_taxonset.R interspace.R create_mcmc.R gamma_site_model_to_xml_state.R mrca_prior_to_xml_state.R is_clock_model.R remove_multiline.R clock_models_to_xml_operators.R fasta_to_sequences.R init_gamma_site_model.R create_beast2_input_init.R clock_models_to_xml_prior_distr.R create_inference_model.R fastas_to_phylos.R mrca_priors_to_xml_state.R are_equal_mcmcs.R are_mrca_taxon_names_in_fasta.R mrca_priors_to_xml_tracelog.R are_clock_models.R create_test_mcmc.R are_equal_tracelogs.R are_equal_treelogs.R check_mrca_prior_name.R is_xml.R are_equal_screenlogs.R create_mrca_prior.R create_test_ns_inference_model.R create_beauti_options.R fasta_to_phylo.R is_init_mrca_prior.R are_mrca_priors.R check_store_every.R create_site_model_from_name.R create_test_inference_model.R create_treelog.R create_tracelog.R create_trait_set_string.R tree_models_to_xml_tracelog.R indent.R find_clock_model.R init_mrca_prior.R create_test_ns_mcmc.R create_screenlog.R has_xml_short_closing_tag.R has_xml_opening_tag.R is_mrca_align_id_in_fasta.R get_site_models_n_distrs.R get_site_models_n_params.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 check_site_model.R get_crown_age.R compare_lines.R create_data_xml.R create_tree_priors.R are_tree_priors.R are_ids.R get_clock_models_ids.R get_tree_prior_names.R are_fasta_filenames.R site_models_to_xml_state.R create_test_treelog.R create_test_tracelog.R create_test_screenlog.R is_inference_model.R is_mrca_prior.R site_models_to_xml_prior_distr.R gamma_site_models_to_xml_prior_distr.R get_tree_priors_n_params.R check_site_models.R is_one_int.R check_tree_priors.R tree_priors_to_xml_state.R has_xml_closing_tag.R is_in_patterns.R find_first_regex_line.R check_log_mode.R get_xml_closing_tag.R find_last_regex_line.R tree_priors_to_xml_distr.R check_phylogeny.R get_alignment_ids.R create_site_models_from_names.R get_xml_opening_tag.R site_models_to_xml_operators.R is_one_double.R check_log_sort.R are_site_models.R create_site_models.R get_alignment_id.R tree_priors_to_xml_tracelog.R create_clock_models_from_names.R get_has_non_strict_clock_model.R is_gamma_site_model.R get_log_modes.R get_gamma_site_model_n_distrs.R remove_empty_lines.R create_temp_screenlog_filename.R get_clock_model_name.R check_inference_models.R get_beautier_path.R are_init_tree_priors.R are_init_mrca_priors.R is_init_gamma_site_model.R create_temp_treelog_filename.R are_init_clock_models.R create_temp_tracelog_filename.R phylo_to_xml_state.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 are_mrca_align_ids_in_fasta.R init_param.R get_gamma_site_model_n_params.R get_distr_names.R is_mrca_prior_with_distr.R get_beautier_paths.R is_init_param.R create_clock_models.R find_first_xml_opening_tag_line.R check_is_monophyletic.R has_mrca_prior.R get_taxa_names.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 get_clock_model_names.R is_distr_name.R is_param_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 get_test_filenames.R is_id.R get_file_base_sans_ext.R is_one_bool.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.

1 untracked files changed.
Other files ignored by Codecov
.Rinstignore 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.

3 Commits

Richel Bilderbeek
100.00% ø ø
Merge branch 'develop'
richelbilderbeek
2713f22
CI Failed
richelbilderbeek
Contextual
Add .Rinstignore
richelbilderbeek
b9570f9
Hiding 2 contexual commits
Richel Bilderbeek
100.00% ø ø
Remove 'vignettes/.install_extras' for CRAN build
richelbilderbeek
5ed40f2
CI Passed
Files Coverage
R 100.00%
Project Totals (244 files) 100.00%
Loading