Package: beautier 2.6.12

Richèl J.C. Bilderbeek

beautier: 'BEAUti' from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.

Authors:Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev], David Winter [rev], Paul Van Els [ctb], Raphael Scherrer [ctb], Yacine B. Chehida [ctb], Katharine S. Walter [ctb], Gary Napier [ctb], Jason Griffiths [ctb], Thijs Janzen [ctb], Pedro Taucce [ctb], Olivier Roy [ctb], Jana Riederer [ctb]

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beautier.pdf |beautier.html
beautier/json (API)
NEWS

# Install beautier in R:
install.packages('beautier', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/beautier/issues

On CRAN:

bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics

537 exports 13 stars 3.19 score 22 dependencies 9 dependents

Last updated 3 months agofrom:046635e2788219cf8fe17446d2944186828537a6 (via master)

Exports:alpha_parameter_to_xmlare_clock_modelsare_equal_mcmcsare_equal_screenlogsare_equal_tracelogsare_equal_treelogsare_equal_xml_filesare_equal_xml_linesare_equivalent_xml_filesare_equivalent_xml_linesare_equivalent_xml_lines_allare_equivalent_xml_lines_loggersare_equivalent_xml_lines_operatorsare_equivalent_xml_lines_sectionare_fasta_filenamesare_idsare_init_clock_modelsare_init_mrca_priorsare_init_site_modelsare_init_tree_priorsare_mrca_align_ids_in_fastaare_mrca_priorsare_mrca_taxon_names_in_fastaare_rln_clock_modelsare_site_modelsare_tree_priorsb_pop_sizes_param_to_xmlb_pop_sizes_parameter_to_xmlbd_tree_prior_to_xml_prior_distrbeta_parameter_to_xmlcbs_tree_prior_to_xml_prior_distrccp_tree_prior_to_xml_prior_distrccp_tree_prior_to_xml_statecep_tree_prior_to_xml_prior_distrcheck_alignment_idcheck_beauti_optionscheck_clock_modelcheck_clock_modelscheck_empty_beautier_foldercheck_file_and_model_agreecheck_file_existscheck_filenamecheck_gamma_site_modelcheck_gamma_site_model_namescheck_gtr_site_modelcheck_gtr_site_model_namescheck_inference_modelcheck_inference_modelscheck_is_monophyleticcheck_log_modecheck_log_sortcheck_mcmccheck_mcmc_list_element_namescheck_mcmc_nested_samplingcheck_mcmc_valuescheck_mrca_priorcheck_mrca_prior_namecheck_mrca_prior_namescheck_mrca_prior_taxa_namescheck_nested_sampling_mcmccheck_ns_mcmccheck_paramcheck_param_namescheck_param_typescheck_phylogenycheck_rename_funcheck_rln_clock_modelcheck_screenlogcheck_screenlog_namescheck_screenlog_valuescheck_site_modelcheck_site_model_namescheck_site_model_typescheck_site_modelscheck_store_everycheck_strict_clock_modelcheck_tn93_site_modelcheck_tn93_site_model_namescheck_tracelogcheck_tracelog_namescheck_tracelog_valuescheck_tree_priorcheck_tree_priorscheck_treelogcheck_treelog_namescheck_treelog_valuesclock_model_to_xml_operatorsclock_model_to_xml_prior_distrclock_model_to_xml_stateclock_model_to_xml_tracelogclock_model_to_xml_treeloggerclock_rate_param_to_xmlcompare_linescount_trailing_spacescreate_alpha_paramcreate_b_pop_sizes_paramcreate_bd_tree_priorcreate_beast2_beast_xmlcreate_beast2_inputcreate_beast2_input_beastcreate_beast2_input_datacreate_beast2_input_data_sequencescreate_beast2_input_distrcreate_beast2_input_distr_lhcreate_beast2_input_distr_priorcreate_beast2_input_filecreate_beast2_input_file_from_modelcreate_beast2_input_from_modelcreate_beast2_input_initcreate_beast2_input_mapcreate_beast2_input_operatorscreate_beast2_input_runcreate_beast2_input_statecreate_beauti_optionscreate_beauti_options_v2_4create_beauti_options_v2_6create_beautier_tempfoldercreate_beta_distrcreate_beta_paramcreate_branch_rate_model_xmlcreate_cbs_tree_priorcreate_ccp_tree_priorcreate_cep_tree_priorcreate_clock_modelcreate_clock_model_from_namecreate_clock_model_rlncreate_clock_model_strictcreate_clock_modelscreate_clock_models_from_namescreate_clock_rate_paramcreate_clock_rate_state_node_parameter_xmlcreate_data_xmlcreate_distrcreate_distr_betacreate_distr_expcreate_distr_gammacreate_distr_inv_gammacreate_distr_laplacecreate_distr_log_normalcreate_distr_normalcreate_distr_one_div_xcreate_distr_poissoncreate_distr_uniformcreate_exp_distrcreate_freq_paramcreate_gamma_distrcreate_gamma_site_modelcreate_gtr_site_modelcreate_gtr_subst_model_xmlcreate_hky_site_modelcreate_hky_subst_model_xmlcreate_inference_modelcreate_inv_gamma_distrcreate_jc69_site_modelcreate_jc69_subst_model_xmlcreate_kappa_1_paramcreate_kappa_2_paramcreate_kappa_paramcreate_lambda_paramcreate_laplace_distrcreate_log_normal_distrcreate_loggers_xmlcreate_m_paramcreate_mcmccreate_mcmc_nested_samplingcreate_mean_paramcreate_mrca_priorcreate_mu_paramcreate_normal_distrcreate_ns_inference_modelcreate_ns_mcmccreate_one_div_x_distrcreate_paramcreate_param_alphacreate_param_b_pop_sizescreate_param_betacreate_param_clock_ratecreate_param_freqcreate_param_kappacreate_param_kappa_1create_param_kappa_2create_param_lambdacreate_param_mcreate_param_meancreate_param_mucreate_param_rate_accreate_param_rate_agcreate_param_rate_atcreate_param_rate_cgcreate_param_rate_ctcreate_param_rate_gtcreate_param_screate_param_scalecreate_param_sigmacreate_poisson_distrcreate_rate_ac_paramcreate_rate_ag_paramcreate_rate_at_paramcreate_rate_categories_state_node_xmlcreate_rate_cg_paramcreate_rate_ct_paramcreate_rate_gt_paramcreate_rln_clock_branch_rate_model_xmlcreate_rln_clock_modelcreate_s_paramcreate_scale_paramcreate_screenlogcreate_screenlog_xmlcreate_sigma_paramcreate_site_modelcreate_site_model_from_namecreate_site_model_gtrcreate_site_model_hkycreate_site_model_jc69create_site_model_parameters_xmlcreate_site_model_tn93create_site_model_xmlcreate_site_modelscreate_site_models_from_namescreate_strict_clock_branch_rate_model_xmlcreate_strict_clock_modelcreate_strict_clock_rate_scaler_operator_xmlcreate_subst_model_xmlcreate_temp_screenlog_filenamecreate_temp_tracelog_filenamecreate_temp_treelog_filenamecreate_test_inference_modelcreate_test_mcmccreate_test_ns_inference_modelcreate_test_ns_mcmccreate_test_screenlogcreate_test_tracelogcreate_test_treelogcreate_tn93_site_modelcreate_tn93_subst_model_xmlcreate_tracelogcreate_tracelog_xmlcreate_trait_set_stringcreate_tree_likelihood_distr_xmlcreate_tree_priorcreate_tree_prior_bdcreate_tree_prior_cbscreate_tree_prior_ccpcreate_tree_prior_cepcreate_tree_prior_yulecreate_tree_priorscreate_treelogcreate_treelog_xmlcreate_ucld_mean_state_node_param_xmlcreate_ucld_stdev_state_node_param_xmlcreate_uniform_distrcreate_xml_declarationcreate_yule_tree_priordistr_to_xmldistr_to_xml_betadistr_to_xml_expdistr_to_xml_inv_gammadistr_to_xml_laplacedistr_to_xml_log_normaldistr_to_xml_normaldistr_to_xml_one_div_xdistr_to_xml_poissondistr_to_xml_uniformextract_xml_loggers_from_linesextract_xml_operators_from_linesextract_xml_section_from_linesfasta_file_to_sequencesfind_clock_modelfind_first_regex_linefind_first_xml_opening_tag_linefind_last_regex_linefind_last_xml_closing_tag_linefreq_equilibrium_to_xmlfreq_param_to_xmlgamma_distr_to_xmlgamma_site_model_to_xml_prior_distrgamma_site_model_to_xml_stategamma_site_models_to_xml_prior_distrget_alignment_idget_alignment_idsget_alignment_ids_from_fasta_filenamesget_beautier_folderget_beautier_pathget_beautier_pathsget_beautier_tempfilenameget_clock_model_nameget_clock_model_namesget_clock_models_idsget_crown_ageget_default_beast_namespaceget_default_beast_namespace_v2_4get_default_beast_namespace_v2_6get_distr_n_paramsget_distr_namesget_fasta_filenameget_file_base_sans_extget_freq_equilibrium_namesget_gamma_site_model_n_distrsget_gamma_site_model_n_paramsget_has_non_strict_clock_modelget_inference_model_filenamesget_log_modesget_log_sortsget_mcmc_filenamesget_n_taxaget_operator_id_preget_param_namesget_remove_dir_funget_remove_hex_funget_replace_dir_funget_site_model_n_distrsget_site_model_n_paramsget_site_model_namesget_site_models_n_distrsget_site_models_n_paramsget_taxa_namesget_tree_prior_n_distrsget_tree_prior_n_paramsget_tree_prior_namesget_tree_priors_n_distrsget_tree_priors_n_paramsget_xml_closing_tagget_xml_opening_taggtr_site_model_to_xml_prior_distrgtr_site_model_to_xml_statehas_mrca_priorhas_mrca_prior_with_distrhas_rln_clock_modelhas_strict_clock_modelhas_tip_datinghas_xml_closing_taghas_xml_opening_taghas_xml_short_closing_taghky_site_model_to_xml_prior_distrhky_site_model_to_xml_stateindentinit_bd_tree_priorinit_beta_distrinit_ccp_tree_priorinit_cep_tree_priorinit_clock_modelsinit_distrinit_exp_distrinit_gamma_distrinit_gamma_site_modelinit_gtr_site_modelinit_hky_site_modelinit_inference_modelinit_inv_gamma_distrinit_jc69_site_modelinit_laplace_distrinit_log_normal_distrinit_mrca_priorinit_mrca_priorsinit_normal_distrinit_one_div_x_distrinit_paraminit_poisson_distrinit_rln_clock_modelinit_site_modelsinit_strict_clock_modelinit_tn93_site_modelinit_tree_priorsinit_uniform_distrinit_yule_tree_priorinterspaceis_alpha_paramis_b_pop_sizes_paramis_bd_tree_prioris_beauti_optionsis_beta_distris_beta_paramis_cbs_tree_prioris_ccp_tree_prioris_cep_tree_prioris_clock_modelis_clock_model_nameis_clock_rate_paramis_default_mcmcis_distris_distr_nameis_exp_distris_freq_equilibrium_nameis_freq_paramis_gamma_distris_gamma_site_modelis_gtr_site_modelis_hky_site_modelis_idis_in_patternsis_inference_modelis_init_bd_tree_prioris_init_beta_distris_init_cbs_tree_prioris_init_ccp_tree_prioris_init_cep_tree_prioris_init_clock_modelis_init_distris_init_exp_distris_init_gamma_distris_init_gamma_site_modelis_init_gtr_site_modelis_init_hky_site_modelis_init_inv_gamma_distris_init_jc69_site_modelis_init_laplace_distris_init_log_normal_distris_init_mrca_prioris_init_normal_distris_init_one_div_x_distris_init_paramis_init_poisson_distris_init_rln_clock_modelis_init_site_modelis_init_strict_clock_modelis_init_tn93_site_modelis_init_tree_prioris_init_uniform_distris_init_yule_tree_prioris_inv_gamma_distris_jc69_site_modelis_kappa_1_paramis_kappa_2_paramis_kappa_paramis_lambda_paramis_laplace_distris_log_normal_distris_m_paramis_mcmcis_mcmc_nested_samplingis_mean_paramis_mrca_align_id_in_fastais_mrca_align_ids_in_fastasis_mrca_prioris_mrca_prior_with_distris_mu_paramis_nested_sampling_mcmcis_normal_distris_on_appveyoris_on_ciis_on_github_actionsis_on_travisis_one_boolis_one_div_x_distris_one_doubleis_one_empty_stringis_one_intis_one_nais_one_stringis_one_string_that_is_a_numberis_paramis_param_nameis_phylois_poisson_distris_rate_ac_paramis_rate_ag_paramis_rate_at_paramis_rate_cg_paramis_rate_ct_paramis_rate_gt_paramis_rln_clock_modelis_s_paramis_scale_paramis_sigma_paramis_site_modelis_site_model_nameis_strict_clock_modelis_tn93_site_modelis_tree_prioris_tree_prior_nameis_uniform_distris_xmlis_yule_tree_priorjc69_site_model_to_xml_statekappa_param_to_xmlm_param_to_xmlmcmc_to_xml_runmcmc_to_xml_run_defaultmcmc_to_xml_run_nested_samplingmrca_prior_to_xml_prior_distrmrca_prior_to_xml_statemrca_prior_to_xml_taxonsetmrca_prior_to_xml_tracelogmrca_priors_to_xml_prior_distrno_taxa_to_xml_treeparameter_to_xmlparameter_to_xml_kappa_1parameter_to_xml_kappa_2parameter_to_xml_lambdaparameter_to_xml_meanparameter_to_xml_muparameter_to_xml_rate_acparameter_to_xml_rate_agparameter_to_xml_rate_atparameter_to_xml_rate_cgparameter_to_xml_rate_ctparameter_to_xml_rate_gtparameter_to_xml_scaleparameter_to_xml_sigmaremove_beautier_folderremove_empty_linesremove_multilinerename_inference_model_filenamesrename_mcmc_filenamesrln_clock_model_to_xml_mean_rate_priorrln_clock_model_to_xml_operatorsrln_clock_model_to_xml_prior_distrrln_clock_model_to_xml_staterln_clock_model_to_xml_tracelogrnd_phylo_to_xml_inits_parameter_to_xmlsite_model_to_xml_operatorssite_model_to_xml_prior_distrsite_model_to_xml_statesite_model_to_xml_tracelogsite_models_to_xml_operatorssite_models_to_xml_prior_distrsite_models_to_xml_tracelogstrict_clock_model_to_xml_operatorsstrict_clock_model_to_xml_prior_distrstrict_clock_model_to_xml_statestrict_clock_model_to_xml_tracelogtaxa_to_xml_treetipdate_taxa_to_xml_traittipdate_taxa_to_xml_treetn93_site_model_to_xml_prior_distrtn93_site_model_to_xml_statetree_model_to_tracelog_xmltree_prior_to_xml_operatorstree_prior_to_xml_prior_distrtree_prior_to_xml_statetree_prior_to_xml_tracelogtree_priors_to_xml_prior_distrtree_priors_to_xml_tracelogunindentyule_tree_prior_to_xml_operatorsyule_tree_prior_to_xml_prior_distr

Dependencies:ade4apeclidigestgluelatticelifecyclemagrittrMASSnlmepixmappurrrrappdirsRcppRcppArmadillorlangsegmentedseqinrspstringistringrvctrs

beautier demo

Rendered fromdemo.Rmdusingknitr::rmarkdownon May 25 2024.

Last update: 2022-06-01
Started: 2016-03-11

Examples

Rendered fromexamples.Rmdusingknitr::rmarkdownon May 25 2024.

Last update: 2022-06-01
Started: 2017-11-22

Inference Models

Rendered frominference_models.Rmdusingknitr::rmarkdownon May 25 2024.

Last update: 2022-06-01
Started: 2020-08-23

Readme and manuals

Help Manual

Help pageTopics
Internal functionalpha_parameter_to_xml
Determine if x consists out of clock_models objectsare_clock_models
Determine if two MCMCs are equal.are_equal_mcmcs
Determine if two screenlogs are equal.are_equal_screenlogs
Determine if two tracelogs are equal.are_equal_tracelogs
Determine if two treelogs are equal.are_equal_treelogs
Determine if XML files result in equal treesare_equal_xml_files
Determine if XML lines result in equal treesare_equal_xml_lines
Internal functionare_equivalent_xml_files
Determine if XML lines result in equivalent treesare_equivalent_xml_lines
Determine if XML lines result in equivalent treesare_equivalent_xml_lines_all
Determine if XML operator lines result in equivalent treesare_equivalent_xml_lines_loggers
Determine if XML operator lines result in equivalent treesare_equivalent_xml_lines_operators
Determine if XML lines result in equivalent treesare_equivalent_xml_lines_section
Checks if all filenames have a FASTA filename extensionare_fasta_filenames
Determine if x consists out of IDsare_ids
Determine if x consists out of initialized clock_models objectsare_init_clock_models
Determine if x consists out of initialized MRCA priorsare_init_mrca_priors
Determine if x consists out of initialized site_models objectsare_init_site_models
Determine if x consists out of initialized tree_priors objectsare_init_tree_priors
Determine if the MRCA priors' alignment IDs are present in the FASTA filesare_mrca_align_ids_in_fasta
Determine if x consists out of MRCA priorsare_mrca_priors
Determine if the MRCA priors' taxa names are present in the FASTA filesare_mrca_taxon_names_in_fasta
Are the clock models Relaxed Log-Normal clock models?are_rln_clock_models
Determine if x consists out of site_models objectsare_site_models
Determine if x consists out of tree_priors objectsare_tree_priors
Internal functionb_pop_sizes_param_to_xml
Internal functionb_pop_sizes_parameter_to_xml
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 priorbd_tree_prior_to_xml_prior_distr
Internal functionbeta_parameter_to_xml
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 priorcbs_tree_prior_to_xml_prior_distr
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 priorccp_tree_prior_to_xml_prior_distr
Convert a CCP tree prior to the XML as part of the 'state' sectionccp_tree_prior_to_xml_state
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 priorcep_tree_prior_to_xml_prior_distr
Check if the 'alignment_id' is valid.check_alignment_id
Check if the 'beauti_options' is a valid 'beauti_options' object.check_beauti_options
Check if the clock model is a valid clock model.check_clock_model
Check if the object is a list of one or more clock models.check_clock_models
Internal functioncheck_empty_beautier_folder
Checks if the input FASTA file and the inference model agree.check_file_and_model_agree
Function to check if a file exists. Calls 'stop' if the file is absentcheck_file_exists
Check if the `filename` is validcheck_filename
Checks if the parameter is a valid gamma site modelcheck_gamma_site_model
Checks if the gamma site model has the right list elements' namescheck_gamma_site_model_names
Check if the 'gtr_site_model' is a valid GTR nucleotide substitution model.check_gtr_site_model
Check if the 'gtr_site_model' has the list elements of a valid 'gtr_site_model' object.check_gtr_site_model_names
Check if the supplied object is a valid Bayesian phylogenetic inference model.check_inference_model
Check if the 'inference_model' is a valid BEAUti inference model.check_inference_models
Check if 'is_monophyletic' has a valid value.check_is_monophyletic
Check if the supplied 'mode' is a valid logging mode.check_log_mode
Check if the supplied 'sort' is a valid logging sorting option.check_log_sort
Check if the MCMC is a valid MCMC object.check_mcmc
Check if the MCMC has the list elements of a valid MCMC object.check_mcmc_list_element_names
Check if the MCMC has the list elements with valid values for being a valid MCMC object.check_mcmc_values
Check if the MRCA prior is a valid MRCA prior.check_mrca_prior
Check if 'mrca_prior_name' is a valid MRCA prior name.check_mrca_prior_name
Check if the MRCA prior, which is a list, has all the named elements.check_mrca_prior_names
Check the MRCA prior's taxon names are valid.check_mrca_prior_taxa_names
Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.check_mcmc_nested_sampling check_nested_sampling_mcmc check_ns_mcmc
Check if the parameter is a valid parametercheck_param
Check if the 'param' has the list elements of a valid 'param' object.check_param_names
Check if the 'param' has the list elements of the right type for a valid 'param' object.check_param_types
Check if the phylogeny is a valid phylogeny object.check_phylogeny
Check if the rename function is a valid filename rename functioncheck_rename_fun
Check if the clock model is a valid clock model.check_rln_clock_model
Check if a 'screenlog' is valid.check_screenlog
Check if the 'screenlog' has the list elements of a valid 'screenlog' object.check_screenlog_names
Check if the screenlog has the list elements with valid values for being a valid screenlog object.check_screenlog_values
Check if the site model is a valid site modelcheck_site_model
Check if the 'site_model' has the list elements of a valid 'site_model' object.check_site_model_names
Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object.check_site_model_types
Check if the object is a list of one or more site models.check_site_models
Check if 'store_every' holds a valid valuecheck_store_every
Check if the clock model is a valid clock model.check_strict_clock_model
Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model.check_tn93_site_model
Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object.check_tn93_site_model_names
Check if a 'tracelog' is valid.check_tracelog
Check if the 'tracelog' has the list elements of a valid 'tracelog' object.check_tracelog_names
Check if the tracelog has the list elements with valid values for being a valid tracelog object.check_tracelog_values
Check if the tree prior is a valid tree priorcheck_tree_prior
Check if the object is a list of one or more tree priors.check_tree_priors
Check if a 'treelog' is valid.check_treelog
Check if the 'treelog' has the list elements of a valid 'treelog' object.check_treelog_names
Check if the treelog has the list elements with valid values for being a valid treelog object.check_treelog_values
Internal functionclock_model_to_xml_operators
Internal functionclock_model_to_xml_prior_distr
Internal functionclock_model_to_xml_state
Internal functionclock_model_to_xml_tracelog
Convert a clock model to the XML of the 'TreeLogger'clock_model_to_xml_treelogger
Internal functionclock_rate_param_to_xml
Internal functioncompare_lines
Count the number of spaces before the first charactercount_trailing_spaces
Create a parameter called alphacreate_alpha_param create_param_alpha
Create a parameter called `b_pop_sizes`.create_b_pop_sizes_param create_param_b_pop_sizes
Create a Birth-Death tree priorcreate_bd_tree_prior create_tree_prior_bd
Create the '<beast ...>' XMLcreate_beast2_beast_xml
Create a BEAST2 XML input textcreate_beast2_input
Creates the XML text for the 'beast' tag of a BEAST2 parameter file.create_beast2_input_beast
Creates the 'data' section of a BEAST2 XML parameter filecreate_beast2_input_data
Creates the data section of a BEAST2 XML parameter filecreate_beast2_input_data_sequences
Creates the distribution section of a BEAST2 XML parameter file.create_beast2_input_distr
Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file.create_beast2_input_distr_lh
Creates the prior section in the distribution section of a BEAST2 XML parameter filecreate_beast2_input_distr_prior
Create a BEAST2 input filecreate_beast2_input_file
Create a BEAST2 input file from an inference modelcreate_beast2_input_file_from_model
Create a BEAST2 XML input text from an inference modelcreate_beast2_input_from_model
Creates the 'init' section of a BEAST2 XML parameter filecreate_beast2_input_init
Creates the map section of a BEAST2 XML parameter filecreate_beast2_input_map
Creates the operators section of a BEAST2 XML parameter filecreate_beast2_input_operators
Creates the ''run'' section of a BEAST2 XML parameter filecreate_beast2_input_run
Creates the ''state'' section of a BEAST2 XML parameter filecreate_beast2_input_state
Function to create a set of `BEAUti` options.create_beauti_options
Function to create the BEAUti options for version 2.4.create_beauti_options_v2_4
Function to create the BEAUti options for version 2.6.create_beauti_options_v2_6
Create the default `beautier` temporary foldercreate_beautier_tempfolder
Create a beta distributioncreate_beta_distr create_distr_beta
Create a parameter called betacreate_beta_param create_param_beta
Internal function to create the 'branchRateModel' section of the XML as text.create_branch_rate_model_xml
Create a Coalescent Bayesian Skyline tree priorcreate_cbs_tree_prior create_tree_prior_cbs
Create a Coalescent Constant Population tree priorcreate_ccp_tree_prior create_tree_prior_ccp
Create a Coalescent Exponential Population tree priorcreate_cep_tree_prior create_tree_prior_cep
General function to create a clock modelcreate_clock_model
Create a clock model from namecreate_clock_model_from_name
Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model'create_clock_models
Create clock models from their namescreate_clock_models_from_names
Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'create_clock_rate_param create_param_clock_rate
Internal functioncreate_clock_rate_state_node_parameter_xml
Create the '<data ..>' XMLcreate_data_xml
General function to create a distribution.create_distr
Create an exponential distributioncreate_distr_exp create_exp_distr
Create a parameter called freqcreate_freq_param create_param_freq
Create a gamma distributioncreate_distr_gamma create_gamma_distr
Create a gamma site model, part of a site modelcreate_gamma_site_model
Create a GTR site modelcreate_gtr_site_model create_site_model_gtr
Converts a GTR site model to XML, used in the 'substModel' sectioncreate_gtr_subst_model_xml
Create an HKY site modelcreate_hky_site_model create_site_model_hky
Converts a site model to XML, used in the 'substModel' sectioncreate_hky_subst_model_xml
Create a Bayesian phylogenetic inference model.create_inference_model
Create an inverse-gamma distributioncreate_distr_inv_gamma create_inv_gamma_distr
Create a JC69 site modelcreate_jc69_site_model create_site_model_jc69
Converts a JC69 site model to XML, used in the 'substModel' sectioncreate_jc69_subst_model_xml
Create a parameter called kappa 1create_kappa_1_param create_param_kappa_1
Create a parameter called kappa 2create_kappa_2_param create_param_kappa_2
Create a parameter called kappacreate_kappa_param create_param_kappa
Create a parameter called lambdacreate_lambda_param create_param_lambda
Create a Laplace distributioncreate_distr_laplace create_laplace_distr
Create a log-normal distributioncreate_distr_log_normal create_log_normal_distr
Creates the three logger sections of a BEAST2 XML parameter filecreate_loggers_xml
Create a parameter called mcreate_m_param create_param_m
Create an MCMC configuration.create_mcmc
Create a parameter called meancreate_mean_param create_param_mean
Create a Most Recent Common Ancestor priorcreate_mrca_prior
Create a parameter called mucreate_mu_param create_param_mu
Create an normal distributioncreate_distr_normal create_normal_distr
Create an inference model to measure the evidence of.create_ns_inference_model
Create an MCMC object to estimate the marginal likelihood using Nested Sampling.create_mcmc_nested_sampling create_ns_mcmc
Create a 1/x distributioncreate_distr_one_div_x create_one_div_x_distr
General function to create a parameter.create_param
Create a Poisson distributioncreate_distr_poisson create_poisson_distr
Create a parameter called 'rate AC'create_param_rate_ac create_rate_ac_param
Create a parameter called 'rate AG'create_param_rate_ag create_rate_ag_param
Create a parameter called 'rate AT'create_param_rate_at create_rate_at_param
Internal functioncreate_rate_categories_state_node_xml
Create a parameter called 'rate CG'create_param_rate_cg create_rate_cg_param
Create a parameter called 'rate CT'create_param_rate_ct create_rate_ct_param
Create a parameter called 'rate GT'create_param_rate_gt create_rate_gt_param
Internal functioncreate_rln_clock_branch_rate_model_xml
Create a relaxed log-normal clock modelcreate_clock_model_rln create_rln_clock_model
Create a parameter called screate_param_s create_s_param
Create a parameter called scalecreate_param_scale create_scale_param
Create a 'screenlog' objectcreate_screenlog
Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter filecreate_screenlog_xml
Create a parameter called sigmacreate_param_sigma create_sigma_param
General function to create a site model.create_site_model
Create a site model from namecreate_site_model_from_name
Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file.create_site_model_parameters_xml
Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file.create_site_model_xml
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'create_site_models
Create site models from their namescreate_site_models_from_names
Internal function.create_strict_clock_branch_rate_model_xml
Create a strict clock modelcreate_clock_model_strict create_strict_clock_model
Internal functioncreate_strict_clock_rate_scaler_operator_xml
Internal function to create the 'substModel' sectioncreate_subst_model_xml
Create a filename for a temporary `screenlog` filecreate_temp_screenlog_filename
Create a filename for a temporary `tracelog` filecreate_temp_tracelog_filename
Create a filename for a temporary `treelog` filecreate_temp_treelog_filename
Create a testing inference model.create_test_inference_model
Create an MCMC configuration for testing.create_test_mcmc
Create an inference model to be tested by Nested Samplingcreate_test_ns_inference_model
Create an NS MCMC object for testingcreate_test_ns_mcmc
Create a 'screenlog' object, to be used in testingcreate_test_screenlog
Create a 'tracelog' object, as used for testingcreate_test_tracelog
Create a 'treelog' object to be used in testingcreate_test_treelog
Create a TN93 site modelcreate_site_model_tn93 create_tn93_site_model
Converts a TN93 site model to XML, used in the 'substModel' sectioncreate_tn93_subst_model_xml
Create a 'tracelog' objectcreate_tracelog
Internal functioncreate_tracelog_xml
Create a trait set string.create_trait_set_string
Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file.create_tree_likelihood_distr_xml
Internal function to create a tree priorcreate_tree_prior
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'create_tree_priors
Create a 'treelog' objectcreate_treelog
Creates the XML text for the `logger` tag with ID `treelog`. This section has these elements: ``` <logger id="treelog.t:test_output_0" spec="Logger" fileName="my_treelog.trees" logEvery="345000" mode="tree" sanitiseHeaders="true" sort="smart"> # nolint indeed long <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test_output_0"/> # nolint indeed long </logger> ```create_treelog_xml
Internal functioncreate_ucld_mean_state_node_param_xml
Internal functioncreate_ucld_stdev_state_node_param_xml
Create a uniform distributioncreate_distr_uniform create_uniform_distr
Create the XML declaration of the BEAST2 XML input filecreate_xml_declaration
Create a Yule tree priorcreate_tree_prior_yule create_yule_tree_prior
Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from.default_parameters_doc
Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.default_params_doc
Internal functiondistr_to_xml
Internal functiondistr_to_xml_beta
Internal functiondistr_to_xml_exp
Internal functiondistr_to_xml_inv_gamma
Internal functiondistr_to_xml_laplace
Internal functiondistr_to_xml_log_normal
Internal functiondistr_to_xml_normal
Internal functiondistr_to_xml_one_div_x
Internal functiondistr_to_xml_poisson
Internal functiondistr_to_xml_uniform
Extract everything between first loggers and last loggers lineextract_xml_loggers_from_lines
Extract everything between first operators and last operators lineextract_xml_operators_from_lines
Get the lines of an XML section, including the section tagsextract_xml_section_from_lines
Convert a FASTA file to a table of sequencesfasta_file_to_sequences
Finds a clock model with a certain IDfind_clock_model
Find the first line that satisfies a regexfind_first_regex_line
Find the line number of the first section's opening tagfind_first_xml_opening_tag_line
Find the index of the last line that matches a regexfind_last_regex_line
Find the highest line number of a section's closing tagfind_last_xml_closing_tag_line
Creates the 'freq_equilibrium' as XMLfreq_equilibrium_to_xml
Internal functionfreq_param_to_xml
Internal functiongamma_distr_to_xml
Internal function.gamma_site_model_to_xml_prior_distr
Converts a gamma site model to XML, used in the 'state' sectiongamma_site_model_to_xml_state
Deprecated functiongamma_site_models_to_xml_prior_distr
Conclude the ID from a FASTA filename.get_alignment_id
Get the alignment IDs from one or more files.get_alignment_ids
Get the alignment ID from one or more FASTA filenames.get_alignment_ids_from_fasta_filenames
Get the path to the beautier temporary files folderget_beautier_folder
Get the full path of a file in the 'inst/extdata' folderget_beautier_path
Get the full paths of files in the 'inst/extdata' folderget_beautier_paths
Get a temporary filenameget_beautier_tempfilename
Get the BEAUti name for a clock modelget_clock_model_name
Get the clock model namesget_clock_model_names
Collect the IDs of the list of clock modelsget_clock_models_ids
Obtain the crown age of a phylogeny.get_crown_age
Get the default `namespace` element value of the `beast` XML tag.get_default_beast_namespace
Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4get_default_beast_namespace_v2_4
Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6get_default_beast_namespace_v2_6
Get the number of parameters a distribution usesget_distr_n_params
Get the distribution namesget_distr_names
Get the path of a FASTA file used in testingget_fasta_filename
Get the base of the filename base without extensionget_file_base_sans_ext
Returns valid values for the 'freq_equilibrium' argumentget_freq_equilibrium_names
Get the number of distributions in a gamma site modelget_gamma_site_model_n_distrs
Get the number of distributions a site model hasget_gamma_site_model_n_params
Determines if there is at least one non-strict clock model in the list of one or more clock modelsget_has_non_strict_clock_model
Get the filenames stored in an inference model.get_inference_model_filenames
Get the possible log modesget_log_modes
Get the possible log sortsget_log_sorts
Get the filenames stored in an MCMC.get_mcmc_filenames
Extract the number of taxa from a fileget_n_taxa
Get the prefix of operator IDsget_operator_id_pre
Get the parameter namesget_param_names
Get a function that, from a filename, returns the part without the directory.get_remove_dir_fun
Get a function that removes the hex string from filenames.get_remove_hex_fun
Get a function to replace the directory of a filenameget_replace_dir_fun
Get the number of distributions a site model hasget_site_model_n_distrs
Get the number of distributions a site model hasget_site_model_n_params
Get the site models' namesget_site_model_names
Get the number of distributions a site model hasget_site_models_n_distrs
Get the number of distributions one or more site models haveget_site_models_n_params
Extract the names of taxa from a fileget_taxa_names
Get the number of distributions a tree prior hasget_tree_prior_n_distrs
Get the number of parameters a tree prior hasget_tree_prior_n_params
Get the tree prior namesget_tree_prior_names
Get the number of distributions a tree prior hasget_tree_priors_n_distrs
Get the number of parameters a list of tree priors hasget_tree_priors_n_params
Get the XML closing tagget_xml_closing_tag
Get the XML opening tagget_xml_opening_tag
Internal functiongtr_site_model_to_xml_prior_distr
Converts a site model to XML, used in the 'state' sectiongtr_site_model_to_xml_state
Determines if the inference model has an MRCA prior.has_mrca_prior
See if the inference model has one MRCA prior with a distributionhas_mrca_prior_with_distr
Determine if the 'inference_model' uses a relaxed log-normal clock model.has_rln_clock_model
Determine if the 'inference_model' uses a strict clock model.has_strict_clock_model
Determine if the 'inference_model' uses tip dating.has_tip_dating
Is an XML closing tag with the value of 'section' present among the lines of the text?has_xml_closing_tag
Is an XML opening tag with value 'section' present among the lines of the text?has_xml_opening_tag
Is an XML closing tag with short closing text in one of the lines of the text?has_xml_short_closing_tag
Internal functionhky_site_model_to_xml_prior_distr
Converts a site model to XML, used in the 'state' sectionhky_site_model_to_xml_state
Indent text for a certain number of spaces. If the text is only whitespace, leave it as suchindent
Initializes a Birth-Death tree priorinit_bd_tree_prior
Initializes a beta distributioninit_beta_distr
Initializes a Coalescent Constant Population tree priorinit_ccp_tree_prior
Initializes a Coalescent Exponential Population tree priorinit_cep_tree_prior
Initializes all clock modelsinit_clock_models
Initializes a distributioninit_distr
Initializes an exponential distributioninit_exp_distr
Initializes a gamma distributioninit_gamma_distr
Initializes a gamma site modelinit_gamma_site_model
Initializes a GTR site modelinit_gtr_site_model
Initializes an HKY site modelinit_hky_site_model
Initialize an inference modelinit_inference_model
Initializes an inverse gamma distributioninit_inv_gamma_distr
Initializes a JC69 site modelinit_jc69_site_model
Initializes an Laplace distributioninit_laplace_distr
Initializes an log-normal distributioninit_log_normal_distr
Initialize the MRCA prior.init_mrca_prior
Initializes all MRCA priorsinit_mrca_priors
Initializes an normal distributioninit_normal_distr
Initializes an one-divided-by-x distributioninit_one_div_x_distr
Initializes a parameterinit_param
Initializes an Poisson distributioninit_poisson_distr
Initializes a Relaxed Log-Normal clock modelinit_rln_clock_model
Initializes all site modelsinit_site_models
Initializes a strict clock modelinit_strict_clock_model
Initializes a TN93 site modelinit_tn93_site_model
Initializes all tree priorsinit_tree_priors
Initializes a uniform distributioninit_uniform_distr
Initializes a Yule tree priorinit_yule_tree_prior
Puts spaces in between the linesinterspace
Determine if the object is a valid alpha parameteris_alpha_param
Determine if the object is a valid b_pop_sizes parameteris_b_pop_sizes_param
Determine if the object is a valid Birth Death tree prioris_bd_tree_prior
Determine if the object is a valid 'beauti_options'is_beauti_options
Determine if the object is a valid beta distribution, as created by 'create_beta_distr'is_beta_distr
Determine if the object is a valid beta parameteris_beta_param
Determine if the object is a valid constant coalescent Bayesian skyline prioris_cbs_tree_prior
Determine if the object is a valid constant coalescence population tree prioris_ccp_tree_prior
Determine if the object is a valid coalescent exponential population tree prioris_cep_tree_prior
Determine if the object is a valid clock_modelis_clock_model
Determines if the name is a valid clock model nameis_clock_model_name
Determine if the object is a valid clock_rate parameteris_clock_rate_param
Determine if the MCMC is a default MCMCis_default_mcmc
Determine if the object is a valid distributionis_distr
Determines if the name is a valid distribution nameis_distr_name
Determine if the object is a valid exponential distribution as created by 'create_exp_distr'is_exp_distr
Checks if 'name' is a valid 'freq_equilibrium' argument valueis_freq_equilibrium_name
Determine if the object is a valid freq parameteris_freq_param
Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr'is_gamma_distr
Is object x a gamma site model?is_gamma_site_model
Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model'is_gtr_site_model
Determine if the object is a valid HKY site model, as created by 'create_hky_site_model'is_hky_site_model
Determine if the object is a valid IDis_id
Is there at least one regular expression having a match with the line?is_in_patterns
Determine if the input is an inference modelis_inference_model
Determine if x is an initialized Birth-Death tree_prior objectis_init_bd_tree_prior
Determine if x is an initialized beta distribution object as created by 'create_beta_distr'is_init_beta_distr
Determine if x is an initialized Coalescent Bayesian Skyline tree_prior objectis_init_cbs_tree_prior
Determine if x is an initialized Coalescent Constant Population tree_prior objectis_init_ccp_tree_prior
Determine if x is an initialized Coalescent Exponential Population tree_prior objectis_init_cep_tree_prior
Determine if x is an initialized clock_model object, as created by 'create_clock_model'is_init_clock_model
Determine if x is an initialized distribution object as created by 'create_distr'is_init_distr
Determine if x is an initialized exponential distribution object as created by 'create_exp_distr'is_init_exp_distr
Determine if x is an initialized gamma distribution objectis_init_gamma_distr
Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model'is_init_gamma_site_model
Determine if x is an initialized GTR site model as created by 'create_gtr_site_model'is_init_gtr_site_model
Determine if x is an initialized HKY site model as created by 'create_hky_site_model'is_init_hky_site_model
Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'is_init_inv_gamma_distr
Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model'is_init_jc69_site_model
Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr'is_init_laplace_distr
Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr'is_init_log_normal_distr
Determine if x is an initialized MRCA prioris_init_mrca_prior
Determine if x is an initialized normal distribution object as created by 'create_normal_distr'is_init_normal_distr
Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr'is_init_one_div_x_distr
Determine if x is an initialized parameter, as created by create_paramis_init_param
Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'is_init_poisson_distr
Determine if x is an initialized relaxed log-normal clock_model objectis_init_rln_clock_model
Determine if x is an initialized site model, as created by 'create_site_model'is_init_site_model
Determine if x is an initialized strict clock_model objectis_init_strict_clock_model
Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model'is_init_tn93_site_model
Determine if x is an initialized tree_prior objectsis_init_tree_prior
Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'is_init_uniform_distr
Determine if x is an initialized Yule tree_prior objectis_init_yule_tree_prior
Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr'is_inv_gamma_distr
Determine if the object is a valid JC69 site modelis_jc69_site_model
Determine if the object is a valid kappa 1 parameteris_kappa_1_param
Determine if the object is a valid kappa 2 parameteris_kappa_2_param
Determine if the object is a valid kappa parameteris_kappa_param
Determine if the object is a valid lambda parameteris_lambda_param
Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr'is_laplace_distr
Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr'is_log_normal_distr
Determine if the object is a valid m parameteris_m_param
Determine if the object is a valid MCMCis_mcmc
Determine if the object is a valid Nested-Sampling MCMC, as used in [1]is_mcmc_nested_sampling is_nested_sampling_mcmc
Determine if the object is a valid mean parameteris_mean_param
Determine if an MRCA prior's alignment IDs is present in the FASTA fileis_mrca_align_id_in_fasta
Determine if an MRCA prior's alignment IDs are present in the FASTA filesis_mrca_align_ids_in_fastas
Determine of the object is an empty ('NA') or valid MRCA prior.is_mrca_prior
See if x is one MRCA prior with a distributionis_mrca_prior_with_distr
Determine if the object is a valid mu parameteris_mu_param
Determine if the object is a valid normal distribution as created by 'create_normal_distr'is_normal_distr
Determines if the environment is AppVeyoris_on_appveyor
Determines if the environment is a continuous integration serviceis_on_ci
Determines if the environment is GitHub Actionsis_on_github_actions
Determines if the environment is Travis CIis_on_travis
Check if the argument is one booleanis_one_bool
Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr'is_one_div_x_distr
Determines if the argument is a doubleis_one_double
Determine if an object is one empty stringis_one_empty_string
Determines if the argument is a whole numberis_one_int
Determines if x is one NAis_one_na
Determines if the argument is one stringis_one_string
General function to create a distribution.is_one_string_that_is_a_number
Determine if the object is a valid parameteris_param
Determines if the name is a valid parameter nameis_param_name
Checks if the input is a phylogenyis_phylo
Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr'is_poisson_distr
Determine if the object is a valid 'rate AC' parameteris_rate_ac_param
Determine if the object is a valid 'rate AG' parameteris_rate_ag_param
Determine if the object is a valid 'rate AT' parameteris_rate_at_param
Determine if the object is a valid 'rate CG' parameteris_rate_cg_param
Determine if the object is a valid 'rate CT' parameteris_rate_ct_param
Determine if the object is a valid 'rate GT' parameteris_rate_gt_param
Determine if the object is a valid relaxed log normal clock modelis_rln_clock_model
Determine if the object is a valid s parameteris_s_param
Determine if the object is a valid scale parameteris_scale_param
Determine if the object is a valid sigma parameteris_sigma_param
Determine if the object is a valid site_modelis_site_model
Determines if the name is a valid site_model nameis_site_model_name
Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model'is_strict_clock_model
Determine if the object is a valid TN93 site model,is_tn93_site_model
Determine if an object is a valid tree prioris_tree_prior
Determines if the name is a valid tree prior nameis_tree_prior_name
Determine if the object is a valid uniform distribution as created by 'create_uniform_distr'is_uniform_distr
Checks if the text is a valid XML node, that is, it has a opening and matching closing tagis_xml
Determine if the object is a valid Yule tree prior,is_yule_tree_prior
Converts a site model to XML, used in the 'state' sectionjc69_site_model_to_xml_state
Internal functionkappa_param_to_xml
Internal functionm_param_to_xml
Converts an MCMC object to the run section's XMLmcmc_to_xml_run
Converts an MCMC object to the run section's XML for a default MCMCmcmc_to_xml_run_default
Converts an MCMC object to the run section's XML for a Nested-Sampling MCMCmcmc_to_xml_run_nested_sampling
Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.mrca_prior_to_xml_prior_distr
Internal function to create the XML of an MRCA prior, as used in the 'state' sectionmrca_prior_to_xml_state
Creates the 'taxonset' section in the prior section of the distribution section of a BEAST2 XML parameter file.mrca_prior_to_xml_taxonset
Internal functionmrca_prior_to_xml_tracelog
Creates the the 'distribution''s prior section (which is part of a posterior distribution section) of a BEAST2 XML parameter file.mrca_priors_to_xml_prior_distr
Internal functionno_taxa_to_xml_tree
Internal functionparameter_to_xml
Internal functionparameter_to_xml_kappa_1
Internal functionparameter_to_xml_kappa_2
Internal functionparameter_to_xml_lambda
Internal functionparameter_to_xml_mean
Internal functionparameter_to_xml_mu
Internal functionparameter_to_xml_rate_ac
Internal functionparameter_to_xml_rate_ag
Internal functionparameter_to_xml_rate_at
Internal functionparameter_to_xml_rate_cg
Internal functionparameter_to_xml_rate_ct
Internal functionparameter_to_xml_rate_gt
Internal functionparameter_to_xml_scale
Internal functionparameter_to_xml_sigma
Check there are no files in the default beautier folderremove_beautier_folder
Remove all lines that are only whitespaceremove_empty_lines
Remove consecutive linesremove_multiline
Rename the filenames in an inference modelrename_inference_model_filenames
Rename the filenames within an MCMCrename_mcmc_filenames
Internal functionrln_clock_model_to_xml_mean_rate_prior
Internal functionrln_clock_model_to_xml_operators
Internal functionrln_clock_model_to_xml_prior_distr
Internal functionrln_clock_model_to_xml_state
Internal functionrln_clock_model_to_xml_tracelog
Creates the XML of a random phylogeny, as used in the 'init' sectionrnd_phylo_to_xml_init
Internal functions_parameter_to_xml
Converts a site model to XML, used in the 'operators' sectionsite_model_to_xml_operators
Internal functionsite_model_to_xml_prior_distr
Internal function to convert a site model to XML, used in the `state` sectionsite_model_to_xml_state
Creates the site model's XML for the tracelog sectionsite_model_to_xml_tracelog
Write the XML 'operators' section from the site models.site_models_to_xml_operators
Represent the site models as XMLsite_models_to_xml_prior_distr
Creates the site models' XML for the tracelog sectionsite_models_to_xml_tracelog
Internal functionstrict_clock_model_to_xml_operators
Internal functionstrict_clock_model_to_xml_prior_distr
Internal functionstrict_clock_model_to_xml_state
Internal functionstrict_clock_model_to_xml_tracelog
Internal functiontaxa_to_xml_tree
Internal functiontipdate_taxa_to_xml_trait
Internal functiontipdate_taxa_to_xml_tree
Internal functiontn93_site_model_to_xml_prior_distr
Converts a site model to XML, used in the 'state' sectiontn93_site_model_to_xml_state
Internal functiontree_model_to_tracelog_xml
Internal functiontree_prior_to_xml_operators
Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.tree_prior_to_xml_prior_distr
Creates the XML of a tree prior, as used in the 'state' sectiontree_prior_to_xml_state
Creates the tree prior's XML for the tracelog sectiontree_prior_to_xml_tracelog
Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.tree_priors_to_xml_prior_distr
Creates the tree priors' XML for the tracelog sectiontree_priors_to_xml_tracelog
Unindents textunindent
Internal functionyule_tree_prior_to_xml_operators
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 prioryule_tree_prior_to_xml_prior_distr