ropensci / beautier

Compare 19ec15b ... +3 ... ee3e9db

Coverage Reach
parameter_to_xml.R create_beast2_input_distr.R init_site_models.R distr_to_xml.R site_model_to_xml_subst_model.R create_distr.R create_beast2_input_loggers.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 site_model_to_xml_prior.R create_beast2_input_file.R site_model_to_xml_operators.R site_model_to_xml_state.R create_beast2_input_run.R init_distr.R clock_model_to_xml_lh_distr.R clock_model_to_xml_operators.R is_param.R is_site_model.R create_beast2_input.R check_mcmc.R is_init_distr.R create_clock_model.R mrca_prior_to_xml_prior_distr.R check_inference_model.R create_tree_prior.R check_mrca_prior.R is_init_site_model.R mcmc_to_xml_run.R site_model_to_xml_lh_distr.R tree_prior_to_xml_state.R create_beast2_input_beast.R create_beast2_input_state.R clock_model_to_xml_prior_distr.R taxa_to_xml_tree.R is_tree_prior.R init_inference_model.R create_gamma_site_model.R mrca_prior_to_xml_lh_distr.R site_model_to_xml_tracelog.R get_site_model_n_params.R check_gamma_site_model.R check_beauti_options.R check_fasta_file_and_inference_model.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_data.R create_beast2_input_operators.R are_equal_xml_lines.R clock_model_to_xml_state.R are_mrca_taxa_non_intersecting.R create_beast2_input_data_sequences.R create_beast2_input_from_model.R clock_models_to_xml_state.R get_param_names.R create_beast2_beast_xml.R gamma_site_model_to_xml_prior_distr.R create_beast2_input_map.R check_tracelog.R create_beast2_input_file_from_model.R get_tree_prior_n_params.R check_screenlog.R check_treelog.R clock_model_to_xml_treelogger.R mrca_prior_to_xml_tracelog.R check_clock_models.R create_mcmc_nested_sampling.R clock_model_to_xml_tracelog.R check_mcmc_nested_sampling.R is_init_clock_model.R mrca_priors_to_xml_distr.R phylo_to_xml_state.R tree_prior_to_xml_prior_distr.R rnd_phylo_xml_init.R rln_clock_model_to_xml_mean_rate_prior.R get_site_model_n_distrs.R tree_priors_to_xml_operators.R is_mcmc.R get_tree_prior_n_distrs.R are_mrca_taxa_names_in_fastas.R are_equal_xml_files.R get_operator_id_pre.R freq_equilibrium_to_xml.R clock_models_to_xml_operators.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 check_file_exists.R remove_multiline.R clock_models_to_xml_tracelog.R fasta_to_sequences.R create_beast2_input_init.R init_gamma_site_model.R fastas_to_phylos.R clock_models_to_xml_prior_distr.R create_inference_model.R create_tree_prior_from_name.R mrca_priors_to_xml_tracelog.R are_clock_models.R mrca_priors_to_xml_state.R is_xml.R create_mrca_prior.R create_beauti_options.R fasta_to_phylo.R are_mrca_priors.R create_site_model_from_name.R create_treelog.R create_tracelog.R create_trait_set_string.R tree_models_to_xml_tracelog.R indent.R find_clock_model.R create_screenlog.R is_init_mrca_prior.R has_xml_short_closing_tag.R has_xml_opening_tag.R is_mrca_align_ids_in_fasta.R get_site_models_n_distrs.R get_site_models_n_params.R is_mrca_align_ids_in_fastas.R get_tree_priors_n_distrs.R get_n_taxa.R check_tree_prior.R check_site_model.R get_crown_age.R compare_lines.R create_data_xml.R are_tree_priors.R are_ids.R get_clock_models_ids.R create_tree_priors.R get_tree_prior_names.R are_fasta_filenames.R site_models_to_xml_state.R is_inference_model.R is_mrca_prior.R site_models_to_xml_prior_distr.R tree_priors_to_xml_state.R get_tree_priors_n_params.R init_mrca_prior.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 get_alignment_ids.R is_in_patterns.R find_first_regex_line.R check_log_mode.R get_xml_closing_tag.R extract_xml_operators_from_lines.R find_last_regex_line.R tree_priors_to_xml_distr.R check_phylogeny.R create_tree_priors_from_names.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 tree_priors_to_xml_tracelog.R are_mrca_alignment_ids_in_fastas.R get_has_non_strict_clock_model.R is_gamma_site_model.R create_clock_models_from_names.R get_log_modes.R get_gamma_site_model_n_distrs.R remove_empty_lines.R get_clock_model_name.R files_exist.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 are_init_clock_models.R is_beauti_options.R site_models_to_xml_tracelog.R get_log_sorts.R extract_xml_loggers_from_lines.R get_alignment_id.R are_equal_mcmcs.R count_trailing_spaces.R create_clock_model_from_name.R are_init_site_models.R init_param.R get_gamma_site_model_n_params.R get_distr_names.R is_mrca_prior_with_distr.R are_initial_phylogenies.R get_beautier_paths.R is_init_param.R create_clock_models.R is_one_na.R find_first_xml_opening_tag_line.R has_mrca_prior.R get_taxa_names.R find_last_xml_closing_tag_line.R is_default_mcmc.R create_beast2_input_xml.R is_site_model_name.R is_clock_model_name.R get_clock_model_names.R is_phylo.R is_distr_name.R is_param_name.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

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@@ -27,9 +27,9 @@
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  inference_model
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) {
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  testit::assert(length(input_filename) == 1)
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  check_inference_model(inference_model)
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  beautier::check_inference_model(inference_model)
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  tracelog_text <- create_beast2_input_tracelog(
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  tracelog_text <- beautier::create_beast2_input_tracelog(
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    input_filename = input_filename,
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    inference_model = inference_model
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  )
@@ -124,6 +124,12 @@
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    "logEvery=\"", inference_model$mcmc$tracelog$log_every, "\" ",
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    "model=\"@posterior\""
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  )
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  if (inference_model$mcmc$tracelog$mode != "autodetect") {
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    top_line <- paste0(
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      top_line,
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      " mode=\"", inference_model$mcmc$tracelog$mode, "\""
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    )
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  }
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  if (inference_model$mcmc$tracelog$sanitise_headers == TRUE) {
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    top_line <- paste0(
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      top_line,

@@ -38,7 +38,7 @@
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      tipdates_filename = tipdates_filename
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    )
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  )
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  text <- interspace(text) # nolint beautier function
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  text <- beautier::interspace(text)
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  indent(text, n_spaces = 4) # nolint beautier function
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  beautier::indent(text, n_spaces = 4)
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}

@@ -2,7 +2,7 @@
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#' @param lines lines of text
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#' @return interspaced lines of text
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#' @author Richèl J.C. Bilderbeek
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#' @noRd
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#' @export
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interspace <- function(lines) {
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  if (length(lines) == 0) return(lines)

Learn more Showing 1 files with coverage changes found.

Changes in R/create_beast2_input_loggers.R
-4
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Files Coverage
R 0.09% 99.57%
Project Totals (228 files) 99.57%
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