ropensci / beautier

Compare 19a6753 ... +0 ... 19ec15b

99.48% 50.00% -0.09%

Overview Diff Coverage Changes Files Commits
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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Showing 3 of 5 files from the diff.

@@ -100,7 +100,7 @@
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    "<logger ",
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    "id=\"tracelog\" "
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  )
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  if (inference_model$mcmc$tracelog$filename != "") {
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  if (is.na(inference_model$mcmc$tracelog$filename)) {
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    # Alignment IDs
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    ids <- beautier::get_alignment_id(
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      input_filename,
@@ -112,6 +112,12 @@
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      top_line,
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      "fileName=\"", filename, ".log\" "
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    )
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  } else {
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    testit::assert(!is.na(inference_model$mcmc$tracelog$filename))
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    top_line <- paste0(
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      top_line,
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      "fileName=\"", inference_model$mcmc$tracelog$filename, "\" "
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    )
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  }
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  top_line <- paste0(
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    top_line,

@@ -1,5 +1,8 @@
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1 1 
#' Create a \code{tracelog} object
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#' @param filename name of the file to store the posterior traces
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#' @param filename
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#'   name of the file to store the posterior traces.
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#'   Use \link{NA} to use the filename \code{[alignment_id].log},
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#'   where \code{alignment_id} is obtained using \link{get_alignment_id}
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#' @param log_every number of MCMC states between the logging of that state
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#' phylogenies to. By default, this is \code{$(trace).traces}
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#' @param mode mode how to log.
@@ -10,7 +13,7 @@
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#' Valid values are the ones returned by \link{get_log_sorts}
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#' @export
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create_tracelog <- function(
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  filename = "test_output_0.log",
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  filename = NA,
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  log_every = 1000,
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  mode = "autodetect",
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  sanitise_headers = TRUE,

@@ -44,8 +44,10 @@
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44 44 
#' @noRd
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check_tracelog_list_element_values <- function(tracelog) {
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                            -
                            
  assertive::assert_is_character(tracelog$filename)









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                            -
                            
  assertive::assert_is_a_string(tracelog$filename)











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                            +
                            
  if (!beautier::is_one_na(tracelog$filename)) {











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                            +
                            
    assertive::assert_is_character(tracelog$filename)











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                            +
                            
    assertive::assert_is_a_string(tracelog$filename)











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                            +
                            
  }









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  assertive::assert_is_numeric(tracelog$log_every)










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  assertive::assert_all_are_positive(tracelog$log_every)










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  beautier::check_log_mode(tracelog$mode)







 
 






































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2

Commits






















Richel Bilderbeek


























99.48%




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'create_tracelog' has NA as the filename default, will use '[alignment_id].log' if set to NA











richelbilderbeek














19ec15b





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Richel Bilderbeek


























99.57%




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'inference_model' get more or less used











richelbilderbeek














19a6753





 CI Passed








































































Files






Coverage
























R



















-0.09%






99.48%











Project Totals (228 files)






99.48%
































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