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