{ "_id": "6a13f14aacfb0bcc41d30ad3", "Package": "beautier", "Title": "'BEAUti' from R", "Version": "2.6.16", "Authors@R": "c(\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"rjcbilderbeek@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1107-7049\")),\nperson(\"Joëlle\", \"Barido-Sottani\", role = \"rev\", comment = \"Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209\"),\nperson(\"David\", \"Winter\", role = \"rev\", comment = \"David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209\"),\nperson(\"Paul\", \"Van Els\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9499-8873\")),\nperson(\"Raphael\", \"Scherrer\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1447-7630\")),\nperson(\"Yacine B.\", \"Chehida\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7269-9082\")),\nperson(\"Katharine S.\", \"Walter\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0065-2204\")),\nperson(\"Gary\", \"Napier\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1077-0055\")),\nperson(\"Jason\", \"Griffiths\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1667-8233\")),\nperson(\"Thijs\", \"Janzen\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4162-1140\")),\nperson(\"Pedro\", \"Taucce\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3088-4543\")),\nperson(\"Olivier\", \"Roy\", role = \"ctb\"),\nperson(\"Jianhui\", \"Wang\", role = \"ctb\"),\nperson(\"Ngoc X.B.\", \"Nguyen\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6802-5509\")),\nperson(\"Jana\", \"Riederer\", role = \"ctb\", comment = c(ORCID = \"0000-0001-6951-9984\")))", "Description": "'BEAST2' () is a widely used\nBayesian phylogenetic tool, that uses DNA/RNA/protein data and\nmany model priors to create a posterior of jointly estimated\nphylogenies and parameters. 'BEAUti 2' (which is part of\n'BEAST2') is a GUI tool that allows users to specify the many\npossible setups and generates the XML file 'BEAST2' needs to\nrun. This package provides a way to create 'BEAST2' input files\nwithout active user input, but using R function calls instead.", "License": "GPL-3", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "https://docs.ropensci.org/beautier/,\nhttps://github.com/ropensci/beautier", "BugReports": "https://github.com/ropensci/beautier/issues", "Language": "en-US", "Encoding": "UTF-8", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-08 18:28:22 UTC", "RemoteUrl": "https://github.com/ropensci/beautier", "RemoteRef": "main", "RemoteSha": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 06:46:44 UTC", "User": "root" }, "Author": "Richèl J.C. Bilderbeek [aut, cre] (ORCID:\n),\nJoëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,\nsee https://github.com/ropensci/onboarding/issues/209),\nDavid Winter [rev] (David reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/onboarding/issues/209),\nPaul Van Els [ctb] (ORCID: ),\nRaphael Scherrer [ctb] (ORCID: ),\nYacine B. Chehida [ctb] (ORCID:\n),\nKatharine S. Walter [ctb] (ORCID:\n),\nGary Napier [ctb] (ORCID: ),\nJason Griffiths [ctb] (ORCID: ),\nThijs Janzen [ctb] (ORCID: ),\nPedro Taucce [ctb] (ORCID: ),\nOlivier Roy [ctb],\nJianhui Wang [ctb],\nNgoc X.B. Nguyen [ctb] (ORCID: ),\nJana Riederer [ctb] (ORCID: )", "Maintainer": "Richèl J.C. 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"init_ccp_tree_prior", "init_cep_tree_prior", "init_clock_models", "init_distr", "init_exp_distr", "init_gamma_distr", "init_gamma_site_model", "init_gtr_site_model", "init_hky_site_model", "init_inference_model", "init_inv_gamma_distr", "init_jc69_site_model", "init_laplace_distr", "init_log_normal_distr", "init_mrca_prior", "init_mrca_priors", "init_normal_distr", "init_one_div_x_distr", "init_param", "init_poisson_distr", "init_rln_clock_model", "init_site_models", "init_strict_clock_model", "init_tn93_site_model", "init_tree_priors", "init_uniform_distr", "init_yule_tree_prior", "interspace", "is_alpha_param", "is_b_pop_sizes_param", "is_bd_tree_prior", "is_beast2_input_file_with_tipdates", "is_beauti_options", "is_beta_distr", "is_beta_param", "is_cbs_tree_prior", "is_ccp_tree_prior", "is_cep_tree_prior", "is_clock_model", "is_clock_model_name", "is_clock_rate_param", "is_default_mcmc", "is_distr", "is_distr_name", "is_exp_distr", "is_freq_equilibrium_name", "is_freq_param", "is_gamma_distr", "is_gamma_site_model", "is_gtr_site_model", "is_hky_site_model", "is_id", "is_in_patterns", "is_inference_model", "is_init_bd_tree_prior", "is_init_beta_distr", "is_init_cbs_tree_prior", "is_init_ccp_tree_prior", "is_init_cep_tree_prior", "is_init_clock_model", "is_init_distr", "is_init_exp_distr", "is_init_gamma_distr", "is_init_gamma_site_model", "is_init_gtr_site_model", "is_init_hky_site_model", "is_init_inv_gamma_distr", "is_init_jc69_site_model", "is_init_laplace_distr", "is_init_log_normal_distr", "is_init_mrca_prior", "is_init_normal_distr", "is_init_one_div_x_distr", "is_init_param", "is_init_poisson_distr", "is_init_rln_clock_model", "is_init_site_model", "is_init_strict_clock_model", "is_init_tn93_site_model", "is_init_tree_prior", "is_init_uniform_distr", "is_init_yule_tree_prior", "is_inv_gamma_distr", "is_jc69_site_model", "is_kappa_1_param", "is_kappa_2_param", "is_kappa_param", "is_lambda_param", "is_laplace_distr", "is_log_normal_distr", "is_m_param", "is_mcmc", "is_mcmc_nested_sampling", "is_mean_param", "is_mrca_align_id_in_fasta", "is_mrca_align_ids_in_fastas", "is_mrca_prior", "is_mrca_prior_with_distr", "is_mu_param", "is_nested_sampling_mcmc", "is_normal_distr", "is_on_appveyor", "is_on_ci", "is_on_github_actions", "is_on_travis", "is_one_bool", "is_one_div_x_distr", "is_one_double", "is_one_empty_string", "is_one_int", "is_one_na", "is_one_string", "is_one_string_that_is_a_number", "is_param", "is_param_name", "is_phylo", "is_poisson_distr", "is_rate_ac_param", "is_rate_ag_param", "is_rate_at_param", "is_rate_cg_param", "is_rate_ct_param", "is_rate_gt_param", "is_rln_clock_model", "is_s_param", "is_scale_param", "is_sigma_param", "is_site_model", "is_site_model_name", "is_strict_clock_model", "is_tn93_site_model", "is_tree_prior", "is_tree_prior_name", "is_uniform_distr", "is_xml", "is_yule_tree_prior", "jc69_site_model_to_xml_state", "kappa_param_to_xml", "m_param_to_xml", "mcmc_to_xml_run", "mcmc_to_xml_run_default", "mcmc_to_xml_run_nested_sampling", "mrca_prior_to_xml_prior_distr", "mrca_prior_to_xml_state", "mrca_prior_to_xml_taxonset", "mrca_prior_to_xml_tracelog", "mrca_priors_to_xml_prior_distr", "needs_trait_set_str", "no_taxa_to_xml_tree", "obj_type_friendly", "parameter_to_xml", "parameter_to_xml_kappa_1", "parameter_to_xml_kappa_2", "parameter_to_xml_lambda", "parameter_to_xml_mean", "parameter_to_xml_mu", "parameter_to_xml_rate_ac", "parameter_to_xml_rate_ag", "parameter_to_xml_rate_at", "parameter_to_xml_rate_cg", "parameter_to_xml_rate_ct", "parameter_to_xml_rate_gt", "parameter_to_xml_scale", "parameter_to_xml_sigma", "read_tipdates_file", "remove_beautier_folder", "remove_empty_lines", "remove_multiline", "rename_inference_model_filenames", "rename_mcmc_filenames", "rln_clock_model_to_xml_mean_rate_prior", "rln_clock_model_to_xml_operators", "rln_clock_model_to_xml_prior_distr", "rln_clock_model_to_xml_state", "rln_clock_model_to_xml_tracelog", "rnd_phylo_to_xml_init", "s_parameter_to_xml", "site_model_to_xml_operators", "site_model_to_xml_prior_distr", "site_model_to_xml_state", "site_model_to_xml_tracelog", "site_models_to_xml_operators", "site_models_to_xml_prior_distr", "site_models_to_xml_tracelog", "stop_input_type", "strict_clock_model_to_xml_operators", "strict_clock_model_to_xml_prior_distr", "strict_clock_model_to_xml_state", "strict_clock_model_to_xml_tracelog", "taxa_to_xml_tree", "tipdate_taxa_to_xml_trait", "tipdate_taxa_to_xml_tree", "tn93_site_model_to_xml_prior_distr", "tn93_site_model_to_xml_state", "tree_model_to_tracelog_xml", "tree_prior_to_xml_operators", "tree_prior_to_xml_prior_distr", "tree_prior_to_xml_state", "tree_prior_to_xml_tracelog", "tree_priors_to_xml_prior_distr", "tree_priors_to_xml_tracelog", "unindent", "yule_tree_prior_to_xml_operators", "yule_tree_prior_to_xml_prior_distr" ], "_help": [ { "page": "alpha_parameter_to_xml", "title": "Internal function", "topics": [ "alpha_parameter_to_xml" ] }, { "page": "are_clock_models", "title": "Determine if x consists out of clock_models objects", "topics": [ "are_clock_models" ] }, { "page": "are_equal_mcmcs", "title": "Determine if two MCMCs are equal.", "topics": [ "are_equal_mcmcs" ] }, { "page": "are_equal_screenlogs", "title": "Determine if two screenlogs are equal.", "topics": [ "are_equal_screenlogs" ] }, { "page": "are_equal_tracelogs", "title": "Determine if two tracelogs are equal.", "topics": [ "are_equal_tracelogs" ] }, { "page": "are_equal_treelogs", "title": "Determine if two treelogs are equal.", "topics": [ "are_equal_treelogs" ] }, { "page": "are_equal_xml_files", "title": "Determine if XML files result in equal trees", "topics": [ "are_equal_xml_files" ] }, { "page": "are_equal_xml_lines", "title": "Determine if XML lines result in equal trees", "topics": [ "are_equal_xml_lines" ] }, { "page": "are_equivalent_xml_files", "title": "Internal function", "topics": [ "are_equivalent_xml_files" ] }, { "page": "are_equivalent_xml_lines", "title": "Determine if XML lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines" ] }, { "page": "are_equivalent_xml_lines_all", "title": "Determine if XML lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_all" ] }, { "page": "are_equivalent_xml_lines_loggers", "title": "Determine if XML operator lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_loggers" ] }, { "page": "are_equivalent_xml_lines_operators", "title": "Determine if XML operator lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_operators" ] }, { "page": "are_equivalent_xml_lines_section", "title": "Determine if XML lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_section" ] }, { "page": "are_fasta_filenames", "title": "Checks if all filenames have a FASTA filename extension", "topics": [ "are_fasta_filenames" ] }, { "page": "are_ids", "title": "Determine if x consists out of IDs", "topics": [ "are_ids" ] }, { "page": "are_init_clock_models", "title": "Determine if x consists out of initialized clock_models objects", "topics": [ "are_init_clock_models" ] }, { "page": "are_init_mrca_priors", "title": "Determine if x consists out of initialized MRCA priors", "topics": [ "are_init_mrca_priors" ] }, { "page": "are_init_site_models", "title": "Determine if x consists out of initialized site_models objects", "topics": [ "are_init_site_models" ] }, { "page": "are_init_tree_priors", "title": "Determine if x consists out of initialized tree_priors objects", "topics": [ "are_init_tree_priors" ] }, { "page": "are_mrca_align_ids_in_fasta", "title": "Determine if the MRCA priors' alignment IDs are present in the FASTA files", "topics": [ "are_mrca_align_ids_in_fasta" ] }, { "page": "are_mrca_priors", "title": "Determine if x consists out of MRCA priors", "topics": [ "are_mrca_priors" ] }, { "page": "are_mrca_taxon_names_in_fasta", "title": "Determine if the MRCA priors' taxa names are present in the FASTA files", "topics": [ "are_mrca_taxon_names_in_fasta" ] }, { "page": "are_rln_clock_models", "title": "Are the clock models Relaxed Log-Normal clock models?", "topics": [ "are_rln_clock_models" ] }, { "page": "are_site_models", "title": "Determine if x consists out of site_models objects", "topics": [ "are_site_models" ] }, { "page": "are_tree_priors", "title": "Determine if x consists out of tree_priors objects", "topics": [ "are_tree_priors" ] }, { "page": "b_pop_sizes_param_to_xml", "title": "Internal function", "topics": [ "b_pop_sizes_param_to_xml" ] }, { "page": "b_pop_sizes_parameter_to_xml", "title": "Internal function", "topics": [ "b_pop_sizes_parameter_to_xml" ] }, { "page": "bd_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior", "topics": [ "bd_tree_prior_to_xml_prior_distr" ] }, { "page": "beta_parameter_to_xml", "title": "Internal function", "topics": [ "beta_parameter_to_xml" ] }, { "page": "cbs_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior", "topics": [ "cbs_tree_prior_to_xml_prior_distr" ] }, { "page": "ccp_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Constant Population tree prior", "topics": [ "ccp_tree_prior_to_xml_prior_distr" ] }, { "page": "ccp_tree_prior_to_xml_state", "title": "Convert a CCP tree prior to the XML as part of the 'state' section", "topics": [ "ccp_tree_prior_to_xml_state" ] }, { "page": "cep_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Exponential Population tree prior", "topics": [ "cep_tree_prior_to_xml_prior_distr" ] }, { "page": "check_alignment_id", "title": "Check if the 'alignment_id' is valid.", "topics": [ "check_alignment_id" ] }, { "page": "check_beauti_options", "title": "Check if the 'beauti_options' is a valid 'beauti_options' object.", "topics": [ "check_beauti_options" ] }, { "page": "check_bool", "title": "Determine if `x` is one boolean", "topics": [ "check_bool" ] }, { "page": "check_clock_model", "title": "Check if the clock model is a valid clock model.", "topics": [ "check_clock_model" ] }, { "page": "check_clock_models", "title": "Check if the object is a list of one or more clock models.", "topics": [ "check_clock_models" ] }, { "page": "check_empty_beautier_folder", "title": "Internal function", "topics": [ "check_empty_beautier_folder" ] }, { "page": "check_false", "title": "Determine if `x` is one FALSE", "topics": [ "check_false" ] }, { "page": "check_file_and_model_agree", "title": "Checks if the input FASTA file and the inference model agree.", "topics": [ "check_file_and_model_agree" ] }, { "page": "check_file_exists", "title": "Function to check if a file exists. Calls 'stop' if the file is absent", "topics": [ "check_file_exists" ] }, { "page": "check_filename", "title": "Check if the `filename` is valid", "topics": [ "check_filename" ] }, { "page": "check_gamma_site_model", "title": "Checks if the parameter is a valid gamma site model", "topics": [ "check_gamma_site_model" ] }, { "page": "check_gamma_site_model_names", "title": "Checks if the gamma site model has the right list elements' names", "topics": [ "check_gamma_site_model_names" ] }, { "page": "check_gtr_site_model", "title": "Check if the 'gtr_site_model' is a valid GTR nucleotide substitution model.", "topics": [ "check_gtr_site_model" ] }, { "page": "check_gtr_site_model_names", "title": "Check if the 'gtr_site_model' has the list elements of a valid 'gtr_site_model' object.", "topics": [ "check_gtr_site_model_names" ] }, { "page": "check_inference_model", "title": "Check if the supplied object is a valid Bayesian phylogenetic inference model.", "topics": [ "check_inference_model" ] }, { "page": "check_inference_models", "title": "Check if the 'inference_model' is a valid BEAUti inference model.", "topics": [ "check_inference_models" ] }, { "page": "check_is_monophyletic", "title": "Check if 'is_monophyletic' has a valid value.", "topics": [ "check_is_monophyletic" ] }, { "page": "check_log_mode", "title": "Check if the supplied 'mode' is a valid logging mode.", "topics": [ "check_log_mode" ] }, { "page": "check_log_sort", "title": "Check if the supplied 'sort' is a valid logging sorting option.", "topics": [ "check_log_sort" ] }, { "page": "check_logical", "title": "Determine if `x` is one logical value", "topics": [ "check_logical" ] }, { "page": "check_mcmc", "title": "Check if the MCMC is a valid MCMC object.", "topics": [ "check_mcmc" ] }, { "page": "check_mcmc_list_element_names", "title": "Check if the MCMC has the list elements of a valid MCMC object.", "topics": [ "check_mcmc_list_element_names" ] }, { "page": "check_mcmc_values", "title": "Check if the MCMC has the list elements with valid values for being a valid MCMC object.", "topics": [ "check_mcmc_values" ] }, { "page": "check_mrca_prior", "title": "Check if the MRCA prior is a valid MRCA prior.", "topics": [ "check_mrca_prior" ] }, { "page": "check_mrca_prior_name", "title": "Check if 'mrca_prior_name' is a valid MRCA prior name.", "topics": [ "check_mrca_prior_name" ] }, { "page": "check_mrca_prior_names", "title": "Check if the MRCA prior, which is a list, has all the named elements.", "topics": [ "check_mrca_prior_names" ] }, { "page": "check_mrca_prior_taxa_names", "title": "Check the MRCA prior's taxon names are valid.", "topics": [ "check_mrca_prior_taxa_names" ] }, { "page": "check_ns_mcmc", "title": "Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.", "topics": [ "check_mcmc_nested_sampling", "check_nested_sampling_mcmc", "check_ns_mcmc" ] }, { "page": "check_number_whole", "title": "Determine if `x` is one whole number", "topics": [ "check_number_whole" ] }, { "page": "check_param", "title": "Check if the parameter is a valid parameter", "topics": [ "check_param" ] }, { "page": "check_param_names", "title": "Check if the 'param' has the list elements of a valid 'param' object.", "topics": [ "check_param_names" ] }, { "page": "check_param_types", "title": "Check if the 'param' has the list elements of the right type for a valid 'param' object.", "topics": [ "check_param_types" ] }, { "page": "check_phylogeny", "title": "Check if the phylogeny is a valid phylogeny object.", "topics": [ "check_phylogeny" ] }, { "page": "check_rename_fun", "title": "Check if the rename function is a valid filename rename function", "topics": [ "check_rename_fun" ] }, { "page": "check_rln_clock_model", "title": "Check if the clock model is a valid clock model.", "topics": [ "check_rln_clock_model" ] }, { "page": "check_screenlog", "title": "Check if a 'screenlog' is valid.", "topics": [ "check_screenlog" ] }, { "page": "check_screenlog_names", "title": "Check if the 'screenlog' has the list elements of a valid 'screenlog' object.", "topics": [ "check_screenlog_names" ] }, { "page": "check_screenlog_values", "title": "Check if the screenlog has the list elements with valid values for being a valid screenlog object.", "topics": [ "check_screenlog_values" ] }, { "page": "check_site_model", "title": "Check if the site model is a valid site model", "topics": [ "check_site_model" ] }, { "page": "check_site_model_names", "title": "Check if the 'site_model' has the list elements of a valid 'site_model' object.", "topics": [ "check_site_model_names" ] }, { "page": "check_site_model_types", "title": "Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object.", "topics": [ "check_site_model_types" ] }, { "page": "check_site_models", "title": "Check if the object is a list of one or more site models.", "topics": [ "check_site_models" ] }, { "page": "check_store_every", "title": "Check if 'store_every' holds a valid value", "topics": [ "check_store_every" ] }, { "page": "check_strict_clock_model", "title": "Check if the clock model is a valid clock model.", "topics": [ "check_strict_clock_model" ] }, { "page": "check_string", "title": "Determine if `x` is one string", "topics": [ "check_string" ] }, { "page": "check_tipdates_file", "title": "Check if the tip dates file is valid", "topics": [ "check_tipdates_file" ] }, { "page": "check_tn93_site_model", "title": "Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model.", "topics": [ "check_tn93_site_model" ] }, { "page": "check_tn93_site_model_names", "title": "Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object.", "topics": [ "check_tn93_site_model_names" ] }, { "page": "check_tracelog", "title": "Check if a 'tracelog' is valid.", "topics": [ "check_tracelog" ] }, { "page": "check_tracelog_names", "title": "Check if the 'tracelog' has the list elements of a valid 'tracelog' object.", "topics": [ "check_tracelog_names" ] }, { "page": "check_tracelog_values", "title": "Check if the tracelog has the list elements with valid values for being a valid tracelog object.", "topics": [ "check_tracelog_values" ] }, { "page": "check_tree_prior", "title": "Check if the tree prior is a valid tree prior", "topics": [ "check_tree_prior" ] }, { "page": "check_tree_priors", "title": "Check if the object is a list of one or more tree priors.", "topics": [ "check_tree_priors" ] }, { "page": "check_treelog", "title": "Check if a 'treelog' is valid.", "topics": [ "check_treelog" ] }, { "page": "check_treelog_names", "title": "Check if the 'treelog' has the list elements of a valid 'treelog' object.", "topics": [ "check_treelog_names" ] }, { "page": "check_treelog_values", "title": "Check if the treelog has the list elements with valid values for being a valid treelog object.", "topics": [ "check_treelog_values" ] }, { "page": "check_true", "title": "Determine if `x` is one TRUE", "topics": [ "check_true" ] }, { "page": "clock_model_to_xml_operators", "title": "Internal function", "topics": [ "clock_model_to_xml_operators" ] }, { "page": "clock_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "clock_model_to_xml_prior_distr" ] }, { "page": "clock_model_to_xml_state", "title": "Internal function", "topics": [ "clock_model_to_xml_state" ] }, { "page": "clock_model_to_xml_tracelog", "title": "Internal function", "topics": [ "clock_model_to_xml_tracelog" ] }, { "page": "clock_model_to_xml_treelogger", "title": "Convert a clock model to the XML of the 'TreeLogger'", "topics": [ "clock_model_to_xml_treelogger" ] }, { "page": "clock_rate_param_to_xml", "title": "Internal function", "topics": [ "clock_rate_param_to_xml" ] }, { "page": "compare_lines", "title": "Internal function", "topics": [ "compare_lines" ] }, { "page": "count_trailing_spaces", "title": "Count the number of spaces before the first character", "topics": [ "count_trailing_spaces" ] }, { "page": "create_alpha_param", "title": "Create a parameter called alpha", "topics": [ "create_alpha_param", "create_param_alpha" ] }, { "page": "create_b_pop_sizes_param", "title": "Create a parameter called `b_pop_sizes`.", "topics": [ "create_b_pop_sizes_param", "create_param_b_pop_sizes" ] }, { "page": "create_bd_tree_prior", "title": "Create a Birth-Death tree prior", "topics": [ "create_bd_tree_prior", "create_tree_prior_bd" ] }, { "page": "create_beast2_beast_xml", "title": "Create the '' XML", "topics": [ "create_beast2_beast_xml" ] }, { "page": "create_beast2_input", "title": "Create a BEAST2 XML input text", "topics": [ "create_beast2_input" ] }, { "page": "create_beast2_input_beast", "title": "Creates the XML text for the 'beast' tag of a BEAST2 parameter file.", "topics": [ "create_beast2_input_beast" ] }, { "page": "create_beast2_input_data", "title": "Creates the 'data' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_data" ] }, { "page": "create_beast2_input_data_sequences", "title": "Creates the data section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_data_sequences" ] }, { "page": "create_beast2_input_distr", "title": "Creates the distribution section of a BEAST2 XML parameter file.", "topics": [ "create_beast2_input_distr" ] }, { "page": "create_beast2_input_distr_lh", "title": "Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file.", "topics": [ "create_beast2_input_distr_lh" ] }, { "page": "create_beast2_input_distr_prior", "title": "Creates the prior section in the distribution section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_distr_prior" ] }, { "page": "create_beast2_input_file", "title": "Create a BEAST2 input file", "topics": [ "create_beast2_input_file" ] }, { "page": "create_beast2_input_file_from_model", "title": "Create a BEAST2 input file from an inference model", "topics": [ "create_beast2_input_file_from_model" ] }, { "page": "create_beast2_input_from_model", "title": "Create a BEAST2 XML input text from an inference model", "topics": [ "create_beast2_input_from_model" ] }, { "page": "create_beast2_input_init", "title": "Creates the 'init' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_init" ] }, { "page": "create_beast2_input_map", "title": "Creates the map section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_map" ] }, { "page": "create_beast2_input_operators", "title": "Creates the operators section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_operators" ] }, { "page": "create_beast2_input_run", "title": "Creates the ''run'' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_run" ] }, { "page": "create_beast2_input_state", "title": "Creates the ''state'' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_state" ] }, { "page": "create_beauti_options", "title": "Function to create a set of `BEAUti` options.", "topics": [ "create_beauti_options" ] }, { "page": "create_beauti_options_v2_4", "title": "Function to create the BEAUti options for version 2.4.", "topics": [ "create_beauti_options_v2_4" ] }, { "page": "create_beauti_options_v2_6", "title": "Function to create the BEAUti options for version 2.6.", "topics": [ "create_beauti_options_v2_6" ] }, { "page": "create_beautier_tempfolder", "title": "Create the default `beautier` temporary folder", "topics": [ "create_beautier_tempfolder" ] }, { "page": "create_beta_distr", "title": "Create a beta distribution", "topics": [ "create_beta_distr", "create_distr_beta" ] }, { "page": "create_beta_param", "title": "Create a parameter called beta", "topics": [ "create_beta_param", "create_param_beta" ] }, { "page": "create_branch_rate_model_xml", "title": "Internal function to create the 'branchRateModel' section of the XML as text.", "topics": [ "create_branch_rate_model_xml" ] }, { "page": "create_cbs_tree_prior", "title": "Create a Coalescent Bayesian Skyline tree prior", "topics": [ "create_cbs_tree_prior", "create_tree_prior_cbs" ] }, { "page": "create_ccp_tree_prior", "title": "Create a Coalescent Constant Population tree prior", "topics": [ "create_ccp_tree_prior", "create_tree_prior_ccp" ] }, { "page": "create_cep_tree_prior", "title": "Create a Coalescent Exponential Population tree prior", "topics": [ "create_cep_tree_prior", "create_tree_prior_cep" ] }, { "page": "create_clock_model", "title": "General function to create a clock model", "topics": [ "create_clock_model" ] }, { "page": "create_clock_model_from_name", "title": "Create a clock model from name", "topics": [ "create_clock_model_from_name" ] }, { "page": "create_clock_models", "title": "Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model'", "topics": [ "create_clock_models" ] }, { "page": "create_clock_models_from_names", "title": "Create clock models from their names", "topics": [ "create_clock_models_from_names" ] }, { "page": "create_clock_rate_param", "title": "Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'", "topics": [ "create_clock_rate_param", "create_param_clock_rate" ] }, { "page": "create_clock_rate_state_node_parameter_xml", "title": "Internal function", "topics": [ "create_clock_rate_state_node_parameter_xml" ] }, { "page": "create_data_xml", "title": "Create the '' XML", "topics": [ "create_data_xml" ] }, { "page": "create_distr", "title": "General function to create a distribution.", "topics": [ "create_distr" ] }, { "page": "create_exp_distr", "title": "Create an exponential distribution", "topics": [ "create_distr_exp", "create_exp_distr" ] }, { "page": "create_freq_param", "title": "Create a parameter called freq", "topics": [ "create_freq_param", "create_param_freq" ] }, { "page": "create_gamma_distr", "title": "Create a gamma distribution", "topics": [ "create_distr_gamma", "create_gamma_distr" ] }, { "page": "create_gamma_site_model", "title": "Create a gamma site model, part of a site model", "topics": [ "create_gamma_site_model" ] }, { "page": "create_gtr_site_model", "title": "Create a GTR site model", "topics": [ "create_gtr_site_model", "create_site_model_gtr" ] }, { "page": "create_gtr_subst_model_xml", "title": "Converts a GTR site model to XML, used in the 'substModel' section", "topics": [ "create_gtr_subst_model_xml" ] }, { "page": "create_hky_site_model", "title": "Create an HKY site model", "topics": [ "create_hky_site_model", "create_site_model_hky" ] }, { "page": "create_hky_subst_model_xml", "title": "Converts a site model to XML, used in the 'substModel' section", "topics": [ "create_hky_subst_model_xml" ] }, { "page": "create_inference_model", "title": "Create a Bayesian phylogenetic inference model.", "topics": [ "create_inference_model" ] }, { "page": "create_inv_gamma_distr", "title": "Create an inverse-gamma distribution", "topics": [ "create_distr_inv_gamma", "create_inv_gamma_distr" ] }, { "page": "create_jc69_site_model", "title": "Create a JC69 site model", "topics": [ "create_jc69_site_model", "create_site_model_jc69" ] }, { "page": "create_jc69_subst_model_xml", "title": "Converts a JC69 site model to XML, used in the 'substModel' section", "topics": [ "create_jc69_subst_model_xml" ] }, { "page": "create_kappa_1_param", "title": "Create a parameter called kappa 1", "topics": [ "create_kappa_1_param", "create_param_kappa_1" ] }, { "page": "create_kappa_2_param", "title": "Create a parameter called kappa 2", "topics": [ "create_kappa_2_param", "create_param_kappa_2" ] }, { "page": "create_kappa_param", "title": "Create a parameter called kappa", "topics": [ "create_kappa_param", "create_param_kappa" ] }, { "page": "create_lambda_param", "title": "Create a parameter called lambda", "topics": [ "create_lambda_param", "create_param_lambda" ] }, { "page": "create_laplace_distr", "title": "Create a Laplace distribution", "topics": [ "create_distr_laplace", "create_laplace_distr" ] }, { "page": "create_log_normal_distr", "title": "Create a log-normal distribution", "topics": [ "create_distr_log_normal", "create_log_normal_distr" ] }, { "page": "create_loggers_xml", "title": "Creates the three logger sections of a BEAST2 XML parameter file", "topics": [ "create_loggers_xml" ] }, { "page": "create_m_param", "title": "Create a parameter called m", "topics": [ "create_m_param", "create_param_m" ] }, { "page": "create_mcmc", "title": "Create an MCMC configuration.", "topics": [ "create_mcmc" ] }, { "page": "create_mean_param", "title": "Create a parameter called mean", "topics": [ "create_mean_param", "create_param_mean" ] }, { "page": "create_mrca_prior", "title": "Create a Most Recent Common Ancestor prior", "topics": [ "create_mrca_prior" ] }, { "page": "create_mu_param", "title": "Create a parameter called mu", "topics": [ "create_mu_param", "create_param_mu" ] }, { "page": "create_normal_distr", "title": "Create an normal distribution", "topics": [ "create_distr_normal", "create_normal_distr" ] }, { "page": "create_ns_inference_model", "title": "Create an inference model to measure the evidence of.", "topics": [ "create_ns_inference_model" ] }, { "page": "create_ns_mcmc", "title": "Create an MCMC object to estimate the marginal likelihood using Nested Sampling.", "topics": [ "create_mcmc_nested_sampling", "create_ns_mcmc" ] }, { "page": "create_one_div_x_distr", "title": "Create a 1/x distribution", "topics": [ "create_distr_one_div_x", "create_one_div_x_distr" ] }, { "page": "create_param", "title": "General function to create a parameter.", "topics": [ "create_param" ] }, { "page": "create_poisson_distr", "title": "Create a Poisson distribution", "topics": [ "create_distr_poisson", "create_poisson_distr" ] }, { "page": "create_rate_ac_param", "title": "Create a parameter called 'rate AC'", "topics": [ "create_param_rate_ac", "create_rate_ac_param" ] }, { "page": "create_rate_ag_param", "title": "Create a parameter called 'rate AG'", "topics": [ "create_param_rate_ag", "create_rate_ag_param" ] }, { "page": "create_rate_at_param", "title": "Create a parameter called 'rate AT'", "topics": [ "create_param_rate_at", "create_rate_at_param" ] }, { "page": "create_rate_categories_state_node_xml", "title": "Internal function", "topics": [ "create_rate_categories_state_node_xml" ] }, { "page": "create_rate_cg_param", "title": "Create a parameter called 'rate CG'", "topics": [ "create_param_rate_cg", "create_rate_cg_param" ] }, { "page": "create_rate_ct_param", "title": "Create a parameter called 'rate CT'", "topics": [ "create_param_rate_ct", "create_rate_ct_param" ] }, { "page": "create_rate_gt_param", "title": "Create a parameter called 'rate GT'", "topics": [ "create_param_rate_gt", "create_rate_gt_param" ] }, { "page": "create_rln_clock_branch_rate_model_xml", "title": "Internal function", "topics": [ "create_rln_clock_branch_rate_model_xml" ] }, { "page": "create_rln_clock_model", "title": "Create a relaxed log-normal clock model", "topics": [ "create_clock_model_rln", "create_rln_clock_model" ] }, { "page": "create_s_param", "title": "Create a parameter called s", "topics": [ "create_param_s", "create_s_param" ] }, { "page": "create_scale_param", "title": "Create a parameter called scale", "topics": [ "create_param_scale", "create_scale_param" ] }, { "page": "create_screenlog", "title": "Create a 'screenlog' object", "topics": [ "create_screenlog" ] }, { "page": "create_screenlog_xml", "title": "Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file", "topics": [ "create_screenlog_xml" ] }, { "page": "create_sigma_param", "title": "Create a parameter called sigma", "topics": [ "create_param_sigma", "create_sigma_param" ] }, { "page": "create_site_model", "title": "General function to create a site model.", "topics": [ "create_site_model" ] }, { "page": "create_site_model_from_name", "title": "Create a site model from name", "topics": [ "create_site_model_from_name" ] }, { "page": "create_site_model_parameters_xml", "title": "Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file.", "topics": [ "create_site_model_parameters_xml" ] }, { "page": "create_site_model_xml", "title": "Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file.", "topics": [ "create_site_model_xml" ] }, { "page": "create_site_models", "title": "Creates all supported site models which is a list of the types returned by 'create_gtr_site_model', 'create_hky_site_model', 'create_jc69_site_model' and 'create_tn93_site_model'", "topics": [ "create_site_models" ] }, { "page": "create_site_models_from_names", "title": "Create site models from their names", "topics": [ "create_site_models_from_names" ] }, { "page": "create_strict_clock_branch_rate_model_xml", "title": "Internal function.", "topics": [ "create_strict_clock_branch_rate_model_xml" ] }, { "page": "create_strict_clock_model", "title": "Create a strict clock model", "topics": [ "create_clock_model_strict", "create_strict_clock_model" ] }, { "page": "create_strict_clock_rate_scaler_operator_xml", "title": "Internal function", "topics": [ "create_strict_clock_rate_scaler_operator_xml" ] }, { "page": "create_subst_model_xml", "title": "Internal function to create the 'substModel' section", "topics": [ "create_subst_model_xml" ] }, { "page": "create_temp_screenlog_filename", "title": "Create a filename for a temporary `screenlog` file", "topics": [ "create_temp_screenlog_filename" ] }, { "page": "create_temp_tracelog_filename", "title": "Create a filename for a temporary `tracelog` file", "topics": [ "create_temp_tracelog_filename" ] }, { "page": "create_temp_treelog_filename", "title": "Create a filename for a temporary `treelog` file", "topics": [ "create_temp_treelog_filename" ] }, { "page": "create_test_inference_model", "title": "Create a testing inference model.", "topics": [ "create_test_inference_model" ] }, { "page": "create_test_mcmc", "title": "Create an MCMC configuration for testing.", "topics": [ "create_test_mcmc" ] }, { "page": "create_test_ns_inference_model", "title": "Create an inference model to be tested by Nested Sampling", "topics": [ "create_test_ns_inference_model" ] }, { "page": "create_test_ns_mcmc", "title": "Create an NS MCMC object for testing", "topics": [ "create_test_ns_mcmc" ] }, { "page": "create_test_screenlog", "title": "Create a 'screenlog' object, to be used in testing", "topics": [ "create_test_screenlog" ] }, { "page": "create_test_tracelog", "title": "Create a 'tracelog' object, as used for testing", "topics": [ "create_test_tracelog" ] }, { "page": "create_test_treelog", "title": "Create a 'treelog' object to be used in testing", "topics": [ "create_test_treelog" ] }, { "page": "create_tn93_site_model", "title": "Create a TN93 site model", "topics": [ "create_site_model_tn93", "create_tn93_site_model" ] }, { "page": "create_tn93_subst_model_xml", "title": "Converts a TN93 site model to XML, used in the 'substModel' section", "topics": [ "create_tn93_subst_model_xml" ] }, { "page": "create_tracelog", "title": "Create a 'tracelog' object", "topics": [ "create_tracelog" ] }, { "page": "create_tracelog_xml", "title": "Internal function", "topics": [ "create_tracelog_xml" ] }, { "page": "create_trait_set_string", "title": "Create a trait set string.", "topics": [ "create_trait_set_string" ] }, { "page": "create_tree_likelihood_distr_xml", "title": "Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file.", "topics": [ "create_tree_likelihood_distr_xml" ] }, { "page": "create_tree_prior", "title": "Internal function to create a tree prior", "topics": [ "create_tree_prior" ] }, { "page": "create_tree_priors", "title": "Creates all supported tree priors, which is a list of the types returned by 'create_bd_tree_prior', 'create_cbs_tree_prior', 'create_ccp_tree_prior', 'create_cep_tree_prior' and 'create_yule_tree_prior'", "topics": [ "create_tree_priors" ] }, { "page": "create_treelog", "title": "Create a 'treelog' object", "topics": [ "create_treelog" ] }, { "page": "create_treelog_xml", "title": "Creates the XML text for the `logger` tag with ID `treelog`. This section has these elements: ``` # nolint indeed long # nolint indeed long ```", "topics": [ "create_treelog_xml" ] }, { "page": "create_ucld_mean_state_node_param_xml", "title": "Internal function", "topics": [ "create_ucld_mean_state_node_param_xml" ] }, { "page": "create_ucld_stdev_state_node_param_xml", "title": "Internal function", "topics": [ "create_ucld_stdev_state_node_param_xml" ] }, { "page": "create_uniform_distr", "title": "Create a uniform distribution", "topics": [ "create_distr_uniform", "create_uniform_distr" ] }, { "page": "create_xml_declaration", "title": "Create the XML declaration of the BEAST2 XML input file", "topics": [ "create_xml_declaration" ] }, { "page": "create_yule_tree_prior", "title": "Create a Yule tree prior", "topics": [ "create_tree_prior_yule", "create_yule_tree_prior" ] }, { "page": "default_parameters_doc", "title": "Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from.", "topics": [ "default_parameters_doc" ] }, { "page": "default_params_doc", "title": "Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.", "topics": [ "default_params_doc" ] }, { "page": "distr_to_xml", "title": "Internal function", "topics": [ "distr_to_xml" ] }, { "page": "distr_to_xml_beta", "title": "Internal function", "topics": [ "distr_to_xml_beta" ] }, { "page": "distr_to_xml_exp", "title": "Internal function", "topics": [ "distr_to_xml_exp" ] }, { "page": "distr_to_xml_inv_gamma", "title": "Internal function", "topics": [ "distr_to_xml_inv_gamma" ] }, { "page": "distr_to_xml_laplace", "title": "Internal function", "topics": [ "distr_to_xml_laplace" ] }, { "page": "distr_to_xml_log_normal", "title": "Internal function", "topics": [ "distr_to_xml_log_normal" ] }, { "page": "distr_to_xml_normal", "title": "Internal function", "topics": [ "distr_to_xml_normal" ] }, { "page": "distr_to_xml_one_div_x", "title": "Internal function", "topics": [ "distr_to_xml_one_div_x" ] }, { "page": "distr_to_xml_poisson", "title": "Internal function", "topics": [ "distr_to_xml_poisson" ] }, { "page": "distr_to_xml_uniform", "title": "Internal function", "topics": [ "distr_to_xml_uniform" ] }, { "page": "extract_xml_loggers_from_lines", "title": "Extract everything between first loggers and last loggers line", "topics": [ "extract_xml_loggers_from_lines" ] }, { "page": "extract_xml_operators_from_lines", "title": "Extract everything between first operators and last operators line", "topics": [ "extract_xml_operators_from_lines" ] }, { "page": "extract_xml_section_from_lines", "title": "Get the lines of an XML section, including the section tags", "topics": [ "extract_xml_section_from_lines" ] }, { "page": "fasta_file_to_sequences", "title": "Convert a FASTA file to a table of sequences", "topics": [ "fasta_file_to_sequences" ] }, { "page": "find_clock_model", "title": "Finds a clock model with a certain ID", "topics": [ "find_clock_model" ] }, { "page": "find_first_regex_line", "title": "Find the first line that satisfies a regex", "topics": [ "find_first_regex_line" ] }, { "page": "find_first_xml_opening_tag_line", "title": "Find the line number of the first section's opening tag", "topics": [ "find_first_xml_opening_tag_line" ] }, { "page": "find_last_regex_line", "title": "Find the index of the last line that matches a regex", "topics": [ "find_last_regex_line" ] }, { "page": "find_last_xml_closing_tag_line", "title": "Find the highest line number of a section's closing tag", "topics": [ "find_last_xml_closing_tag_line" ] }, { "page": "freq_equilibrium_to_xml", "title": "Creates the 'freq_equilibrium' as XML", "topics": [ "freq_equilibrium_to_xml" ] }, { "page": "freq_param_to_xml", "title": "Internal function", "topics": [ "freq_param_to_xml" ] }, { "page": "gamma_distr_to_xml", "title": "Internal function", "topics": [ "gamma_distr_to_xml" ] }, { "page": "gamma_site_model_to_xml_prior_distr", "title": "Internal function.", "topics": [ "gamma_site_model_to_xml_prior_distr" ] }, { "page": "gamma_site_model_to_xml_state", "title": "Converts a gamma site model to XML, used in the 'state' section", "topics": [ "gamma_site_model_to_xml_state" ] }, { "page": "gamma_site_models_to_xml_prior_distr", "title": "Deprecated function", "topics": [ "gamma_site_models_to_xml_prior_distr" ] }, { "page": "get_alignment_id", "title": "Conclude the ID from a FASTA filename.", "topics": [ "get_alignment_id" ] }, { "page": "get_alignment_ids", "title": "Get the alignment IDs from one or more files.", "topics": [ "get_alignment_ids" ] }, { "page": "get_alignment_ids_from_fasta_filenames", "title": "Get the alignment ID from one or more FASTA filenames.", "topics": [ "get_alignment_ids_from_fasta_filenames" ] }, { "page": "get_beautier_folder", "title": "Get the path to the beautier temporary files folder", "topics": [ "get_beautier_folder" ] }, { "page": "get_beautier_path", "title": "Get the full path of a file in the 'inst/extdata' folder", "topics": [ "get_beautier_path" ] }, { "page": "get_beautier_paths", "title": "Get the full paths of files in the 'inst/extdata' folder", "topics": [ "get_beautier_paths" ] }, { "page": "get_beautier_tempfilename", "title": "Get a temporary filename", "topics": [ "get_beautier_tempfilename" ] }, { "page": "get_clock_model_name", "title": "Get the BEAUti name for a clock model", "topics": [ "get_clock_model_name" ] }, { "page": "get_clock_model_names", "title": "Get the clock model names", "topics": [ "get_clock_model_names" ] }, { "page": "get_clock_models_ids", "title": "Collect the IDs of the list of clock models", "topics": [ "get_clock_models_ids" ] }, { "page": "get_crown_age", "title": "Obtain the crown age of a phylogeny.", "topics": [ "get_crown_age" ] }, { "page": "get_default_beast_namespace", "title": "Get the default `namespace` element value of the `beast` XML tag.", "topics": [ "get_default_beast_namespace" ] }, { "page": "get_default_beast_namespace_v2_4", "title": "Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4", "topics": [ "get_default_beast_namespace_v2_4" ] }, { "page": "get_default_beast_namespace_v2_6", "title": "Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6", "topics": [ "get_default_beast_namespace_v2_6" ] }, { "page": "get_distr_n_params", "title": "Get the number of parameters a distribution uses", "topics": [ "get_distr_n_params" ] }, { "page": "get_distr_names", "title": "Get the distribution names", "topics": [ "get_distr_names" ] }, { "page": "get_fasta_filename", "title": "Get the path of a FASTA file used in testing", "topics": [ "get_fasta_filename" ] }, { "page": "get_file_base_sans_ext", "title": "Get the base of the filename base without extension", "topics": [ "get_file_base_sans_ext" ] }, { "page": "get_freq_equilibrium_names", "title": "Returns valid values for the 'freq_equilibrium' argument", "topics": [ "get_freq_equilibrium_names" ] }, { "page": "get_gamma_site_model_n_distrs", "title": "Get the number of distributions in a gamma site model", "topics": [ "get_gamma_site_model_n_distrs" ] }, { "page": "get_gamma_site_model_n_params", "title": "Get the number of distributions a site model has", "topics": [ "get_gamma_site_model_n_params" ] }, { "page": "get_has_non_strict_clock_model", "title": "Determines if there is at least one non-strict clock model in the list of one or more clock models", "topics": [ "get_has_non_strict_clock_model" ] }, { "page": "get_inference_model_filenames", "title": "Get the filenames stored in an inference model.", "topics": [ "get_inference_model_filenames" ] }, { "page": "get_log_modes", "title": "Get the possible log modes", "topics": [ "get_log_modes" ] }, { "page": "get_log_sorts", "title": "Get the possible log sorts", "topics": [ "get_log_sorts" ] }, { "page": "get_mcmc_filenames", "title": "Get the filenames stored in an MCMC.", "topics": [ "get_mcmc_filenames" ] }, { "page": "get_n_taxa", "title": "Extract the number of taxa from a file", "topics": [ "get_n_taxa" ] }, { "page": "get_operator_id_pre", "title": "Get the prefix of operator IDs", "topics": [ "get_operator_id_pre" ] }, { "page": "get_param_names", "title": "Get the parameter names", "topics": [ "get_param_names" ] }, { "page": "get_remove_dir_fun", "title": "Get a function that, from a filename, returns the part without the directory.", "topics": [ "get_remove_dir_fun" ] }, { "page": "get_remove_hex_fun", "title": "Get a function that removes the hex string from filenames.", "topics": [ "get_remove_hex_fun" ] }, { "page": "get_replace_dir_fun", "title": "Get a function to replace the directory of a filename", "topics": [ "get_replace_dir_fun" ] }, { "page": "get_site_model_n_distrs", "title": "Get the number of distributions a site model has", "topics": [ "get_site_model_n_distrs" ] }, { "page": "get_site_model_n_params", "title": "Get the number of distributions a site model has", "topics": [ "get_site_model_n_params" ] }, { "page": "get_site_model_names", "title": "Get the site models' names", "topics": [ "get_site_model_names" ] }, { "page": "get_site_models_n_distrs", "title": "Get the number of distributions a site model has", "topics": [ "get_site_models_n_distrs" ] }, { "page": "get_site_models_n_params", "title": "Get the number of distributions one or more site models have", "topics": [ "get_site_models_n_params" ] }, { "page": "get_taxa_names", "title": "Extract the names of taxa from a file", "topics": [ "get_taxa_names" ] }, { "page": "get_tree_prior_n_distrs", "title": "Get the number of distributions a tree prior has", "topics": [ "get_tree_prior_n_distrs" ] }, { "page": "get_tree_prior_n_params", "title": "Get the number of parameters a tree prior has", "topics": [ "get_tree_prior_n_params" ] }, { "page": "get_tree_prior_names", "title": "Get the tree prior names", "topics": [ "get_tree_prior_names" ] }, { "page": "get_tree_priors_n_distrs", "title": "Get the number of distributions a tree prior has", "topics": [ "get_tree_priors_n_distrs" ] }, { "page": "get_tree_priors_n_params", "title": "Get the number of parameters a list of tree priors has", "topics": [ "get_tree_priors_n_params" ] }, { "page": "get_xml_closing_tag", "title": "Get the XML closing tag", "topics": [ "get_xml_closing_tag" ] }, { "page": "get_xml_opening_tag", "title": "Get the XML opening tag", "topics": [ "get_xml_opening_tag" ] }, { "page": "gtr_site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "gtr_site_model_to_xml_prior_distr" ] }, { "page": "gtr_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "gtr_site_model_to_xml_state" ] }, { "page": "has_mrca_prior", "title": "Determines if the inference model has an MRCA prior.", "topics": [ "has_mrca_prior" ] }, { "page": "has_mrca_prior_with_distr", "title": "See if the inference model has one MRCA prior with a distribution", "topics": [ "has_mrca_prior_with_distr" ] }, { "page": "has_rln_clock_model", "title": "Determine if the 'inference_model' uses a relaxed log-normal clock model.", "topics": [ "has_rln_clock_model" ] }, { "page": "has_strict_clock_model", "title": "Determine if the 'inference_model' uses a strict clock model.", "topics": [ "has_strict_clock_model" ] }, { "page": "has_tip_dating", "title": "Determine if the 'inference_model' uses tip dating.", "topics": [ "has_tip_dating" ] }, { "page": "has_xml_closing_tag", "title": "Is an XML closing tag with the value of 'section' present among the lines of the text?", "topics": [ "has_xml_closing_tag" ] }, { "page": "has_xml_opening_tag", "title": "Is an XML opening tag with value 'section' present among the lines of the text?", "topics": [ "has_xml_opening_tag" ] }, { "page": "has_xml_short_closing_tag", "title": "Is an XML closing tag with short closing text in one of the lines of the text?", "topics": [ "has_xml_short_closing_tag" ] }, { "page": "hky_site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "hky_site_model_to_xml_prior_distr" ] }, { "page": "hky_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "hky_site_model_to_xml_state" ] }, { "page": "indent", "title": "Indent text for a certain number of spaces. If the text is only whitespace, leave it as such", "topics": [ "indent" ] }, { "page": "init_bd_tree_prior", "title": "Initializes a Birth-Death tree prior", "topics": [ "init_bd_tree_prior" ] }, { "page": "init_beta_distr", "title": "Initializes a beta distribution", "topics": [ "init_beta_distr" ] }, { "page": "init_ccp_tree_prior", "title": "Initializes a Coalescent Constant Population tree prior", "topics": [ "init_ccp_tree_prior" ] }, { "page": "init_cep_tree_prior", "title": "Initializes a Coalescent Exponential Population tree prior", "topics": [ "init_cep_tree_prior" ] }, { "page": "init_clock_models", "title": "Initializes all clock models", "topics": [ "init_clock_models" ] }, { "page": "init_distr", "title": "Initializes a distribution", "topics": [ "init_distr" ] }, { "page": "init_exp_distr", "title": "Initializes an exponential distribution", "topics": [ "init_exp_distr" ] }, { "page": "init_gamma_distr", "title": "Initializes a gamma distribution", "topics": [ "init_gamma_distr" ] }, { "page": "init_gamma_site_model", "title": "Initializes a gamma site model", "topics": [ "init_gamma_site_model" ] }, { "page": "init_gtr_site_model", "title": "Initializes a GTR site model", "topics": [ "init_gtr_site_model" ] }, { "page": "init_hky_site_model", "title": "Initializes an HKY site model", "topics": [ "init_hky_site_model" ] }, { "page": "init_inference_model", "title": "Initialize an inference model", "topics": [ "init_inference_model" ] }, { "page": "init_inv_gamma_distr", "title": "Initializes an inverse gamma distribution", "topics": [ "init_inv_gamma_distr" ] }, { "page": "init_jc69_site_model", "title": "Initializes a JC69 site model", "topics": [ "init_jc69_site_model" ] }, { "page": "init_laplace_distr", "title": "Initializes an Laplace distribution", "topics": [ "init_laplace_distr" ] }, { "page": "init_log_normal_distr", "title": "Initializes an log-normal distribution", "topics": [ "init_log_normal_distr" ] }, { "page": "init_mrca_prior", "title": "Initialize the MRCA prior.", "topics": [ "init_mrca_prior" ] }, { "page": "init_mrca_priors", "title": "Initializes all MRCA priors", "topics": [ "init_mrca_priors" ] }, { "page": "init_normal_distr", "title": "Initializes an normal distribution", "topics": [ "init_normal_distr" ] }, { "page": "init_one_div_x_distr", "title": "Initializes an one-divided-by-x distribution", "topics": [ "init_one_div_x_distr" ] }, { "page": "init_param", "title": "Initializes a parameter", "topics": [ "init_param" ] }, { "page": "init_poisson_distr", "title": "Initializes an Poisson distribution", "topics": [ "init_poisson_distr" ] }, { "page": "init_rln_clock_model", "title": "Initializes a Relaxed Log-Normal clock model", "topics": [ "init_rln_clock_model" ] }, { "page": "init_site_models", "title": "Initializes all site models", "topics": [ "init_site_models" ] }, { "page": "init_strict_clock_model", "title": "Initializes a strict clock model", "topics": [ "init_strict_clock_model" ] }, { "page": "init_tn93_site_model", "title": "Initializes a TN93 site model", "topics": [ "init_tn93_site_model" ] }, { "page": "init_tree_priors", "title": "Initializes all tree priors", "topics": [ "init_tree_priors" ] }, { "page": "init_uniform_distr", "title": "Initializes a uniform distribution", "topics": [ "init_uniform_distr" ] }, { "page": "init_yule_tree_prior", "title": "Initializes a Yule tree prior", "topics": [ "init_yule_tree_prior" ] }, { "page": "interspace", "title": "Puts spaces in between the lines", "topics": [ "interspace" ] }, { "page": "is_alpha_param", "title": "Determine if the object is a valid alpha parameter", "topics": [ "is_alpha_param" ] }, { "page": "is_b_pop_sizes_param", "title": "Determine if the object is a valid b_pop_sizes parameter", "topics": [ "is_b_pop_sizes_param" ] }, { "page": "is_bd_tree_prior", "title": "Determine if the object is a valid Birth Death tree prior", "topics": [ "is_bd_tree_prior" ] }, { "page": "is_beast2_input_file_with_tipdates", "title": "Determine if the file is a BEAST2 input file that has tip dating", "topics": [ "is_beast2_input_file_with_tipdates" ] }, { "page": "is_beauti_options", "title": "Determine if the object is a valid 'beauti_options'", "topics": [ "is_beauti_options" ] }, { "page": "is_beta_distr", "title": "Determine if the object is a valid beta distribution, as created by 'create_beta_distr'", "topics": [ "is_beta_distr" ] }, { "page": "is_beta_param", "title": "Determine if the object is a valid beta parameter", "topics": [ "is_beta_param" ] }, { "page": "is_cbs_tree_prior", "title": "Determine if the object is a valid constant coalescent Bayesian skyline prior", "topics": [ "is_cbs_tree_prior" ] }, { "page": "is_ccp_tree_prior", "title": "Determine if the object is a valid constant coalescence population tree prior", "topics": [ "is_ccp_tree_prior" ] }, { "page": "is_cep_tree_prior", "title": "Determine if the object is a valid coalescent exponential population tree prior", "topics": [ "is_cep_tree_prior" ] }, { "page": "is_clock_model", "title": "Determine if the object is a valid clock_model", "topics": [ "is_clock_model" ] }, { "page": "is_clock_model_name", "title": "Determines if the name is a valid clock model name", "topics": [ "is_clock_model_name" ] }, { "page": "is_clock_rate_param", "title": "Determine if the object is a valid clock_rate parameter", "topics": [ "is_clock_rate_param" ] }, { "page": "is_default_mcmc", "title": "Determine if the MCMC is a default MCMC", "topics": [ "is_default_mcmc" ] }, { "page": "is_distr", "title": "Determine if the object is a valid distribution", "topics": [ "is_distr" ] }, { "page": "is_distr_name", "title": "Determines if the name is a valid distribution name", "topics": [ "is_distr_name" ] }, { "page": "is_exp_distr", "title": "Determine if the object is a valid exponential distribution as created by 'create_exp_distr'", "topics": [ "is_exp_distr" ] }, { "page": "is_freq_equilibrium_name", "title": "Checks if 'name' is a valid 'freq_equilibrium' argument value", "topics": [ "is_freq_equilibrium_name" ] }, { "page": "is_freq_param", "title": "Determine if the object is a valid freq parameter", "topics": [ "is_freq_param" ] }, { "page": "is_gamma_distr", "title": "Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr'", "topics": [ "is_gamma_distr" ] }, { "page": "is_gamma_site_model", "title": "Is object x a gamma site model?", "topics": [ "is_gamma_site_model" ] }, { "page": "is_gtr_site_model", "title": "Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model'", "topics": [ "is_gtr_site_model" ] }, { "page": "is_hky_site_model", "title": "Determine if the object is a valid HKY site model, as created by 'create_hky_site_model'", "topics": [ "is_hky_site_model" ] }, { "page": "is_id", "title": "Determine if the object is a valid ID", "topics": [ "is_id" ] }, { "page": "is_in_patterns", "title": "Is there at least one regular expression having a match with the line?", "topics": [ "is_in_patterns" ] }, { "page": "is_inference_model", "title": "Determine if the input is an inference model", "topics": [ "is_inference_model" ] }, { "page": "is_init_bd_tree_prior", "title": "Determine if x is an initialized Birth-Death tree_prior object", "topics": [ "is_init_bd_tree_prior" ] }, { "page": "is_init_beta_distr", "title": "Determine if x is an initialized beta distribution object as created by 'create_beta_distr'", "topics": [ "is_init_beta_distr" ] }, { "page": "is_init_cbs_tree_prior", "title": "Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object", "topics": [ "is_init_cbs_tree_prior" ] }, { "page": "is_init_ccp_tree_prior", "title": "Determine if x is an initialized Coalescent Constant Population tree_prior object", "topics": [ "is_init_ccp_tree_prior" ] }, { "page": "is_init_cep_tree_prior", "title": "Determine if x is an initialized Coalescent Exponential Population tree_prior object", "topics": [ "is_init_cep_tree_prior" ] }, { "page": "is_init_clock_model", "title": "Determine if x is an initialized clock_model object, as created by 'create_clock_model'", "topics": [ "is_init_clock_model" ] }, { "page": "is_init_distr", "title": "Determine if x is an initialized distribution object as created by 'create_distr'", "topics": [ "is_init_distr" ] }, { "page": "is_init_exp_distr", "title": "Determine if x is an initialized exponential distribution object as created by 'create_exp_distr'", "topics": [ "is_init_exp_distr" ] }, { "page": "is_init_gamma_distr", "title": "Determine if x is an initialized gamma distribution object", "topics": [ "is_init_gamma_distr" ] }, { "page": "is_init_gamma_site_model", "title": "Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model'", "topics": [ "is_init_gamma_site_model" ] }, { "page": "is_init_gtr_site_model", "title": "Determine if x is an initialized GTR site model as created by 'create_gtr_site_model'", "topics": [ "is_init_gtr_site_model" ] }, { "page": "is_init_hky_site_model", "title": "Determine if x is an initialized HKY site model as created by 'create_hky_site_model'", "topics": [ "is_init_hky_site_model" ] }, { "page": "is_init_inv_gamma_distr", "title": "Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'", "topics": [ "is_init_inv_gamma_distr" ] }, { "page": "is_init_jc69_site_model", "title": "Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model'", "topics": [ "is_init_jc69_site_model" ] }, { "page": "is_init_laplace_distr", "title": "Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr'", "topics": [ "is_init_laplace_distr" ] }, { "page": "is_init_log_normal_distr", "title": "Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr'", "topics": [ "is_init_log_normal_distr" ] }, { "page": "is_init_mrca_prior", "title": "Determine if x is an initialized MRCA prior", "topics": [ "is_init_mrca_prior" ] }, { "page": "is_init_normal_distr", "title": "Determine if x is an initialized normal distribution object as created by 'create_normal_distr'", "topics": [ "is_init_normal_distr" ] }, { "page": "is_init_one_div_x_distr", "title": "Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr'", "topics": [ "is_init_one_div_x_distr" ] }, { "page": "is_init_param", "title": "Determine if x is an initialized parameter, as created by create_param", "topics": [ "is_init_param" ] }, { "page": "is_init_poisson_distr", "title": "Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'", "topics": [ "is_init_poisson_distr" ] }, { "page": "is_init_rln_clock_model", "title": "Determine if x is an initialized relaxed log-normal clock_model object", "topics": [ "is_init_rln_clock_model" ] }, { "page": "is_init_site_model", "title": "Determine if x is an initialized site model, as created by 'create_site_model'", "topics": [ "is_init_site_model" ] }, { "page": "is_init_strict_clock_model", "title": "Determine if x is an initialized strict clock_model object", "topics": [ "is_init_strict_clock_model" ] }, { "page": "is_init_tn93_site_model", "title": "Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model'", "topics": [ "is_init_tn93_site_model" ] }, { "page": "is_init_tree_prior", "title": "Determine if x is an initialized tree_prior objects", "topics": [ "is_init_tree_prior" ] }, { "page": "is_init_uniform_distr", "title": "Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'", "topics": [ "is_init_uniform_distr" ] }, { "page": "is_init_yule_tree_prior", "title": "Determine if x is an initialized Yule tree_prior object", "topics": [ "is_init_yule_tree_prior" ] }, { "page": "is_inv_gamma_distr", "title": "Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr'", "topics": [ "is_inv_gamma_distr" ] }, { "page": "is_jc69_site_model", "title": "Determine if the object is a valid JC69 site model", "topics": [ "is_jc69_site_model" ] }, { "page": "is_kappa_1_param", "title": "Determine if the object is a valid kappa 1 parameter", "topics": [ "is_kappa_1_param" ] }, { "page": "is_kappa_2_param", "title": "Determine if the object is a valid kappa 2 parameter", "topics": [ "is_kappa_2_param" ] }, { "page": "is_kappa_param", "title": "Determine if the object is a valid kappa parameter", "topics": [ "is_kappa_param" ] }, { "page": "is_lambda_param", "title": "Determine if the object is a valid lambda parameter", "topics": [ "is_lambda_param" ] }, { "page": "is_laplace_distr", "title": "Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr'", "topics": [ "is_laplace_distr" ] }, { "page": "is_log_normal_distr", "title": "Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr'", "topics": [ "is_log_normal_distr" ] }, { "page": "is_m_param", "title": "Determine if the object is a valid m parameter", "topics": [ "is_m_param" ] }, { "page": "is_mcmc", "title": "Determine if the object is a valid MCMC", "topics": [ "is_mcmc" ] }, { "page": "is_mcmc_nested_sampling", "title": "Determine if the object is a valid Nested-Sampling MCMC, as used in [1]", "topics": [ "is_mcmc_nested_sampling", "is_nested_sampling_mcmc" ] }, { "page": "is_mean_param", "title": "Determine if the object is a valid mean parameter", "topics": [ "is_mean_param" ] }, { "page": "is_mrca_align_id_in_fasta", "title": "Determine if an MRCA prior's alignment IDs is present in the FASTA file", "topics": [ "is_mrca_align_id_in_fasta" ] }, { "page": "is_mrca_align_ids_in_fastas", "title": "Determine if an MRCA prior's alignment IDs are present in the FASTA files", "topics": [ "is_mrca_align_ids_in_fastas" ] }, { "page": "is_mrca_prior", "title": "Determine of the object is an empty ('NA') or valid MRCA prior.", "topics": [ "is_mrca_prior" ] }, { "page": "is_mrca_prior_with_distr", "title": "See if x is one MRCA prior with a distribution", "topics": [ "is_mrca_prior_with_distr" ] }, { "page": "is_mu_param", "title": "Determine if the object is a valid mu parameter", "topics": [ "is_mu_param" ] }, { "page": "is_normal_distr", "title": "Determine if the object is a valid normal distribution as created by 'create_normal_distr'", "topics": [ "is_normal_distr" ] }, { "page": "is_on_appveyor", "title": "Determines if the environment is AppVeyor", "topics": [ "is_on_appveyor" ] }, { "page": "is_on_ci", "title": "Determines if the environment is a continuous integration service", "topics": [ "is_on_ci" ] }, { "page": "is_on_github_actions", "title": "Determines if the environment is GitHub Actions", "topics": [ "is_on_github_actions" ] }, { "page": "is_on_travis", "title": "Determines if the environment is Travis CI", "topics": [ "is_on_travis" ] }, { "page": "is_one_bool", "title": "Check if the argument is one boolean", "topics": [ "is_one_bool" ] }, { "page": "is_one_div_x_distr", "title": "Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr'", "topics": [ "is_one_div_x_distr" ] }, { "page": "is_one_double", "title": "Determines if the argument is a double", "topics": [ "is_one_double" ] }, { "page": "is_one_empty_string", "title": "Determine if an object is one empty string", "topics": [ "is_one_empty_string" ] }, { "page": "is_one_int", "title": "Determines if the argument is a whole number", "topics": [ "is_one_int" ] }, { "page": "is_one_na", "title": "Determines if x is one NA", "topics": [ "is_one_na" ] }, { "page": "is_one_string", "title": "Determines if the argument is one string", "topics": [ "is_one_string" ] }, { "page": "is_one_string_that_is_a_number", "title": "General function to create a distribution.", "topics": [ "is_one_string_that_is_a_number" ] }, { "page": "is_param", "title": "Determine if the object is a valid parameter", "topics": [ "is_param" ] }, { "page": "is_param_name", "title": "Determines if the name is a valid parameter name", "topics": [ "is_param_name" ] }, { "page": "is_phylo", "title": "Checks if the input is a phylogeny", "topics": [ "is_phylo" ] }, { "page": "is_poisson_distr", "title": "Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr'", "topics": [ "is_poisson_distr" ] }, { "page": "is_rate_ac_param", "title": "Determine if the object is a valid 'rate AC' parameter", "topics": [ "is_rate_ac_param" ] }, { "page": "is_rate_ag_param", "title": "Determine if the object is a valid 'rate AG' parameter", "topics": [ "is_rate_ag_param" ] }, { "page": "is_rate_at_param", "title": "Determine if the object is a valid 'rate AT' parameter", "topics": [ "is_rate_at_param" ] }, { "page": "is_rate_cg_param", "title": "Determine if the object is a valid 'rate CG' parameter", "topics": [ "is_rate_cg_param" ] }, { "page": "is_rate_ct_param", "title": "Determine if the object is a valid 'rate CT' parameter", "topics": [ "is_rate_ct_param" ] }, { "page": "is_rate_gt_param", "title": "Determine if the object is a valid 'rate GT' parameter", "topics": [ "is_rate_gt_param" ] }, { "page": "is_rln_clock_model", "title": "Determine if the object is a valid relaxed log normal clock model", "topics": [ "is_rln_clock_model" ] }, { "page": "is_s_param", "title": "Determine if the object is a valid s parameter", "topics": [ "is_s_param" ] }, { "page": "is_scale_param", "title": "Determine if the object is a valid scale parameter", "topics": [ "is_scale_param" ] }, { "page": "is_sigma_param", "title": "Determine if the object is a valid sigma parameter", "topics": [ "is_sigma_param" ] }, { "page": "is_site_model", "title": "Determine if the object is a valid site_model", "topics": [ "is_site_model" ] }, { "page": "is_site_model_name", "title": "Determines if the name is a valid site_model name", "topics": [ "is_site_model_name" ] }, { "page": "is_strict_clock_model", "title": "Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model'", "topics": [ "is_strict_clock_model" ] }, { "page": "is_tn93_site_model", "title": "Determine if the object is a valid TN93 site model,", "topics": [ "is_tn93_site_model" ] }, { "page": "is_tree_prior", "title": "Determine if an object is a valid tree prior", "topics": [ "is_tree_prior" ] }, { "page": "is_tree_prior_name", "title": "Determines if the name is a valid tree prior name", "topics": [ "is_tree_prior_name" ] }, { "page": "is_uniform_distr", "title": "Determine if the object is a valid uniform distribution as created by 'create_uniform_distr'", "topics": [ "is_uniform_distr" ] }, { "page": "is_xml", "title": "Checks if the text is a valid XML node, that is, it has a opening and matching closing tag", "topics": [ "is_xml" ] }, { "page": "is_yule_tree_prior", "title": "Determine if the object is a valid Yule tree prior,", "topics": [ "is_yule_tree_prior" ] }, { "page": "jc69_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "jc69_site_model_to_xml_state" ] }, { "page": "kappa_param_to_xml", "title": "Internal function", "topics": [ "kappa_param_to_xml" ] }, { "page": "m_param_to_xml", "title": "Internal function", "topics": [ "m_param_to_xml" ] }, { "page": "mcmc_to_xml_run", "title": "Converts an MCMC object to the run section's XML", "topics": [ "mcmc_to_xml_run" ] }, { "page": "mcmc_to_xml_run_default", "title": "Converts an MCMC object to the run section's XML for a default MCMC", "topics": [ "mcmc_to_xml_run_default" ] }, { "page": "mcmc_to_xml_run_nested_sampling", "title": "Converts an MCMC object to the run section's XML for a Nested-Sampling MCMC", "topics": [ "mcmc_to_xml_run_nested_sampling" ] }, { "page": "mrca_prior_to_xml_prior_distr", "title": "Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "mrca_prior_to_xml_prior_distr" ] }, { "page": "mrca_prior_to_xml_state", "title": "Internal function to create the XML of an MRCA prior, as used in the 'state' section", "topics": [ "mrca_prior_to_xml_state" ] }, { "page": "mrca_prior_to_xml_taxonset", "title": "Creates the 'taxonset' section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "mrca_prior_to_xml_taxonset" ] }, { "page": "mrca_prior_to_xml_tracelog", "title": "Internal function", "topics": [ "mrca_prior_to_xml_tracelog" ] }, { "page": "mrca_priors_to_xml_prior_distr", "title": "Creates the the 'distribution''s prior section (which is part of a posterior distribution section) of a BEAST2 XML parameter file.", "topics": [ "mrca_priors_to_xml_prior_distr" ] }, { "page": "needs_trait_set_str", "title": "Is it needed to add the tip dates as a string to the BEAST2 XML input file?", "topics": [ "needs_trait_set_str" ] }, { "page": "no_taxa_to_xml_tree", "title": "Internal function", "topics": [ "no_taxa_to_xml_tree" ] }, { "page": "obj_type_friendly", "title": "Return English-friendly type", "topics": [ "obj_type_friendly" ] }, { "page": "parameter_to_xml", "title": "Internal function", "topics": [ "parameter_to_xml" ] }, { "page": "parameter_to_xml_kappa_1", "title": "Internal function", "topics": [ "parameter_to_xml_kappa_1" ] }, { "page": "parameter_to_xml_kappa_2", "title": "Internal function", "topics": [ "parameter_to_xml_kappa_2" ] }, { "page": "parameter_to_xml_lambda", "title": "Internal function", "topics": [ "parameter_to_xml_lambda" ] }, { "page": "parameter_to_xml_mean", "title": "Internal function", "topics": [ "parameter_to_xml_mean" ] }, { "page": "parameter_to_xml_mu", "title": "Internal function", "topics": [ "parameter_to_xml_mu" ] }, { "page": "parameter_to_xml_rate_ac", "title": "Internal function", "topics": [ "parameter_to_xml_rate_ac" ] }, { "page": "parameter_to_xml_rate_ag", "title": "Internal function", "topics": [ "parameter_to_xml_rate_ag" ] }, { "page": "parameter_to_xml_rate_at", "title": "Internal function", "topics": [ "parameter_to_xml_rate_at" ] }, { "page": "parameter_to_xml_rate_cg", "title": "Internal function", "topics": [ "parameter_to_xml_rate_cg" ] }, { "page": "parameter_to_xml_rate_ct", "title": "Internal function", "topics": [ "parameter_to_xml_rate_ct" ] }, { "page": "parameter_to_xml_rate_gt", "title": "Internal function", "topics": [ "parameter_to_xml_rate_gt" ] }, { "page": "parameter_to_xml_scale", "title": "Internal function", "topics": [ "parameter_to_xml_scale" ] }, { "page": "parameter_to_xml_sigma", "title": "Internal function", "topics": [ "parameter_to_xml_sigma" ] }, { "page": "read_tipdates_file", "title": "Read a tip dates file", "topics": [ "read_tipdates_file" ] }, { "page": "remove_beautier_folder", "title": "Check there are no files in the default beautier folder", "topics": [ "remove_beautier_folder" ] }, { "page": "remove_empty_lines", "title": "Remove all lines that are only whitespace", "topics": [ "remove_empty_lines" ] }, { "page": "remove_multiline", "title": "Remove consecutive lines", "topics": [ "remove_multiline" ] }, { "page": "rename_inference_model_filenames", "title": "Rename the filenames in an inference model", "topics": [ "rename_inference_model_filenames" ] }, { "page": "rename_mcmc_filenames", "title": "Rename the filenames within an MCMC", "topics": [ "rename_mcmc_filenames" ] }, { "page": "rln_clock_model_to_xml_mean_rate_prior", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_mean_rate_prior" ] }, { "page": "rln_clock_model_to_xml_operators", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_operators" ] }, { "page": "rln_clock_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_prior_distr" ] }, { "page": "rln_clock_model_to_xml_state", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_state" ] }, { "page": "rln_clock_model_to_xml_tracelog", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_tracelog" ] }, { "page": "rnd_phylo_to_xml_init", "title": "Creates the XML of a random phylogeny, as used in the 'init' section", "topics": [ "rnd_phylo_to_xml_init" ] }, { "page": "s_parameter_to_xml", "title": "Internal function", "topics": [ "s_parameter_to_xml" ] }, { "page": "site_model_to_xml_operators", "title": "Converts a site model to XML, used in the 'operators' section", "topics": [ "site_model_to_xml_operators" ] }, { "page": "site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "site_model_to_xml_prior_distr" ] }, { "page": "site_model_to_xml_state", "title": "Internal function to convert a site model to XML, used in the `state` section", "topics": [ "site_model_to_xml_state" ] }, { "page": "site_model_to_xml_tracelog", "title": "Creates the site model's XML for the tracelog section", "topics": [ "site_model_to_xml_tracelog" ] }, { "page": "site_models_to_xml_operators", "title": "Write the XML 'operators' section from the site models.", "topics": [ "site_models_to_xml_operators" ] }, { "page": "site_models_to_xml_prior_distr", "title": "Represent the site models as XML", "topics": [ "site_models_to_xml_prior_distr" ] }, { "page": "site_models_to_xml_tracelog", "title": "Creates the site models' XML for the tracelog section", "topics": [ "site_models_to_xml_tracelog" ] }, { "page": "stop_input_type", "title": "Stops on the input type.", "topics": [ "stop_input_type" ] }, { "page": "strict_clock_model_to_xml_operators", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_operators" ] }, { "page": "strict_clock_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_prior_distr" ] }, { "page": "strict_clock_model_to_xml_state", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_state" ] }, { "page": "strict_clock_model_to_xml_tracelog", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_tracelog" ] }, { "page": "taxa_to_xml_tree", "title": "Internal function", "topics": [ "taxa_to_xml_tree" ] }, { "page": "tipdate_taxa_to_xml_trait", "title": "Internal function", "topics": [ "tipdate_taxa_to_xml_trait" ] }, { "page": "tipdate_taxa_to_xml_tree", "title": "Internal function", "topics": [ "tipdate_taxa_to_xml_tree" ] }, { "page": "tn93_site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "tn93_site_model_to_xml_prior_distr" ] }, { "page": "tn93_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "tn93_site_model_to_xml_state" ] }, { "page": "tree_model_to_tracelog_xml", "title": "Internal function", "topics": [ "tree_model_to_tracelog_xml" ] }, { "page": "tree_prior_to_xml_operators", "title": "Internal function", "topics": [ "tree_prior_to_xml_operators" ] }, { "page": "tree_prior_to_xml_prior_distr", "title": "Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "tree_prior_to_xml_prior_distr" ] }, { "page": "tree_prior_to_xml_state", "title": "Creates the XML of a tree prior, as used in the 'state' section", "topics": [ "tree_prior_to_xml_state" ] }, { "page": "tree_prior_to_xml_tracelog", "title": "Creates the tree prior's XML for the tracelog section", "topics": [ "tree_prior_to_xml_tracelog" ] }, { "page": "tree_priors_to_xml_prior_distr", "title": "Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "tree_priors_to_xml_prior_distr" ] }, { "page": "tree_priors_to_xml_tracelog", "title": "Creates the tree priors' XML for the tracelog section", "topics": [ "tree_priors_to_xml_tracelog" ] }, { "page": "unindent", "title": "Unindents text", "topics": [ "unindent" ] }, { "page": "yule_tree_prior_to_xml_operators", "title": "Internal function", "topics": [ "yule_tree_prior_to_xml_operators" ] }, { "page": "yule_tree_prior_to_xml_prior_distr", "title": "Creates the 'prior' section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Yule tree prior", "topics": [ "yule_tree_prior_to_xml_prior_distr" ] } ], "_readme": "https://github.com/ropensci/beautier/raw/main/README.md", "_rundeps": [ "ade4", "ape", "cli", "digest", "glue", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pixmap", "purrr", "rappdirs", "Rcpp", "RcppArmadillo", "rlang", "segmented", "seqinr", "sp", "stringi", "stringr", "vctrs" ], "_vignettes": [ { "source": "demo.Rmd", "filename": "demo.html", "title": "beautier demo", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Demonstration", "Cleanup" ], "created": "2016-03-11 14:29:40", "modified": "2022-06-01 09:36:07", "commits": 30 }, { "source": "examples.Rmd", "filename": "examples.html", "title": "Examples", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting started", "Example #1: all default", "Example #2: JC69 site model", "Example #3: Relaxed clock log normal", "Example #4: Birth-Death tree prior", "Example #5: Yule tree prior with a normally distributed birth rate", "Example #6: HKY site model with a non-zero proportion of invariants", "Example #7: Strict clock with a known clock rate", "Example #8: Use MRCA prior", "Example #9: Use MRCA prior to specify a close-to-fixed crown age", "Cleanup" ], "created": "2017-11-22 11:10:46", "modified": "2022-06-01 09:36:07", "commits": 34 }, { "source": "inference_models.Rmd", "filename": "inference_models.html", "title": "Inference Models", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting started", "Default inference model", "Site models", "Clock models", "Tree prior", "(optional) MRCA prior: a 'Most Recent Common Ancestor'", "MCMC: the Markov Chain Monte Carlo setup", "(optional) BEAUti options: version-specific options", "(experimental) a tipdates filename: a filename for tip-dating" ], "created": "2020-08-23 14:06:47", "modified": "2022-06-01 09:36:07", "commits": 7 } ], "_score": 8.63137019654351, "_indexed": true, "_nocasepkg": "beautier", "_universes": [ "ropensci", "richelbilderbeek" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.6.16", "date": "2026-05-25T06:49:19.000Z", "distro": "noble", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "1a7e1485d235c56ea5319a4a2016f9d68214438f37715e115d4e24b60d87d77e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.6.0", "os": "linux", "version": "2.6.16", "date": "2026-05-25T06:49:31.000Z", "distro": "noble", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "7f190ac312a0f083266095b32a84ec34e6ede7cbf390422e867ea72dec5ba6b3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.5.3", "os": "mac", "version": "2.6.16", "date": "2026-05-25T06:48:35.000Z", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "5fd0b1b0d953ad9872c7adb8723dbe3d812ec996562c7c477a8a9ddc1e140e8f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.6.0", "os": "mac", "version": "2.6.16", "date": "2026-05-25T06:48:35.000Z", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "b8d24205ffd10a737ffcd78428d3015af34a736cbeccab280088de1bda1a9e0b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.6.0", "os": "wasm", "version": "2.6.16", "date": "2026-05-25T06:49:33.000Z", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "4c803f01ed32f4c16399370413952b317c3d75335982f33d078c979f43d79e43", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.7.0", "os": "win", "version": "2.6.16", "date": "2026-05-25T06:48:42.000Z", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "bf01eb8f6aa3a63d6cc50f9a78457cc720d16af2fb535e3f376d4030d00faf16", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.5.3", "os": "win", "version": "2.6.16", "date": "2026-05-25T06:48:28.000Z", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "a09fa5531a9901233bd4bb3f513d4f03b6d6a299a6a4e90cd25522868ecdcdcd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" }, { "r": "4.6.0", "os": "win", "version": "2.6.16", "date": "2026-05-25T06:48:35.000Z", "commit": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "fileid": "42c97a6d712e977e971cf04392a28d0c30efecc1bfe02b41095c075dc5102434", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26387263862" } ] }