Files in beautier

'BEAUti' from R

R/find_first_xml_opening_tag_line.R R/s_parameter_to_xml.R R/taxa_to_xml_tree.R R/create_clock_model.R R/get_mcmc_filenames.R R/m_param_to_xml.R R/check_site_models.R R/mrca_priors_to_xml_distr.R R/create_clock_model_from_name.R R/create_treelog.R R/get_n_taxa.R R/get_tree_prior_n_params.R R/create_beauti_options_v2_4.R R/is_gamma_site_model.R R/is_on_ci.R R/create_rate_categories_state_node_xml.R R/strict_clock_model_to_xml_operators.R R/has_strict_clock_model.R R/create_tracelog.R R/create_clock_models.R R/create_site_model_from_name.R R/check_gamma_site_model.R R/is_mrca_align_id_in_fasta.R R/is_in_patterns.R R/are_fasta_filenames.R R/create_strict_clock_rate_scaler_operator_xml.R R/create_tree_priors.R R/is_param_name.R R/get_beautier_path.R R/check_is_monophyletic.R R/rename_inference_model_filenames.R R/has_xml_opening_tag.R R/get_remove_hex_fun.R R/get_site_models_n_distrs.R R/create_temp_screenlog_filename.R R/find_first_regex_line.R R/init_clock_models.R R/are_clock_models.R R/beta_parameter_to_xml.R R/create_data_xml.R R/create_test_ns_mcmc.R R/is_param.R R/is_init_mrca_prior.R R/check_screenlog.R R/get_tree_prior_n_distrs.R R/rln_clock_model_to_xml_mean_rate_prior.R R/create_test_tracelog.R R/fasta_to_sequences.R R/create_clock_models_from_names.R R/get_gamma_site_model_n_distrs.R R/are_site_models.R R/create_ucld_mean_state_node_param_xml.R R/tree_prior_to_xml_state.R R/get_beautier_tempfilename.R R/check_mrca_prior_taxa_names.R R/compare_lines.R R/create_beast2_input_data_sequences.R R/clock_model_to_xml_tracelog.R R/is_tree_prior.R R/interspace.R R/create_beast2_input.R R/check_tracelog.R R/import-standalone-types-check.R R/is_xml.R R/is_init_gamma_site_model.R R/mrca_prior_to_xml_prior_distr.R R/freq_equilibrium_to_xml.R R/are_mrca_priors.R R/site_models_to_xml_prior_distr.R R/get_file_base_sans_ext.R R/create_beauti_options.R R/tree_priors_to_xml_tracelog.R R/tipdate_taxa_to_xml_trait.R R/create_trait_set_string.R R/get_xml_closing_tag.R R/create_beast2_input_xml.R R/are_init_tree_priors.R R/are_mrca_align_ids_in_fasta.R R/get_taxa_names.R R/gamma_distr_to_xml.R R/check_tree_priors.R R/rename_mcmc_filenames.R R/create_beast2_beast_xml.R R/has_mrca_prior_with_distr.R R/get_site_model_names.R R/is_beauti_options.R R/check_empty_beautier_folder.R R/is_one_empty_string.R R/create_treelog_xml.R R/clock_model_to_xml_operators.R R/create_subst_model_xml.R R/get_default_beast_namespace.R R/site_models_to_xml_tracelog.R R/check_file_and_model_agree.R R/check_mrca_prior.R R/create_test_screenlog.R R/are_equal_tracelogs.R R/check_tree_prior.R R/get_log_modes.R R/remove_empty_lines.R R/has_tip_dating.R R/is_mcmc.R R/create_distr.R R/create_beast2_input_file_from_model.R R/check_filename.R R/get_beautier_paths.R R/create_strict_clock_branch_rate_model_xml.R R/import-standalone-obj-type.R R/strict_clock_model_to_xml_state.R R/create_site_models_from_names.R R/kappa_param_to_xml.R R/are_tree_priors.R R/get_clock_model_names.R R/get_site_models_n_params.R R/remove_beautier_folder.R R/create_loggers_xml.R R/are_equal_screenlogs.R R/create_temp_treelog_filename.R R/has_mrca_prior.R R/check_clock_models.R R/get_clock_models_ids.R R/check_tn93_site_model.R R/are_mrca_taxon_names_in_fasta.R R/check_phylogeny.R R/create_tracelog_xml.R R/default_params_doc.R R/get_tree_priors_n_params.R R/get_distr_names.R R/is_phylo.R R/check_mcmc_nested_sampling.R R/tn93_site_model_to_xml_state.R R/check_treelog.R R/are_equal_xml_files.R R/check_mcmc.R R/find_clock_model.R R/init_gamma_site_model.R R/get_test_filenames.R R/create_site_model.R R/beautier-package.R R/is_clock_model_name.R R/create_tree_prior.R R/find_last_xml_closing_tag_line.R R/gamma_site_model_to_xml_state.R R/get_distr_n_params.R R/count_trailing_spaces.R R/rln_clock_model_to_xml_operators.R R/tree_prior_to_xml_operators.R R/create_screenlog_xml.R R/are_ids.R R/check_log_sort.R R/b_pop_sizes_param_to_xml.R R/is_distr_name.R R/is_init_distr.R R/clock_rate_param_to_xml.R R/mrca_prior_to_xml_taxonset.R R/jc69_site_model_to_xml_state.R R/gamma_site_model_to_xml_prior_distr.R R/are_equal_treelogs.R R/mcmc_to_xml_run.R R/unindent.R R/is_inference_model.R R/init_distr.R R/extract_xml_operators_from_lines.R R/create_test_ns_inference_model.R R/rln_clock_model_to_xml_tracelog.R R/clock_model_to_xml_treelogger.R R/init_inference_model.R R/check_gtr_site_model.R R/create_beast2_input_run.R R/create_beast2_input_distr.R R/create_gamma_site_model.R R/create_branch_rate_model_stuff_xml.R R/create_site_model_xml.R R/is_mrca_align_ids_in_fastas.R R/rnd_phylo_xml_init.R R/init_mrca_priors.R R/is_m_param.R R/create_beast2_input_operators.R R/check_true_false.R R/get_operator_id_pre.R R/create_site_model_parameters_xml.R R/is_id.R R/get_gamma_site_model_n_params.R R/yule_tree_prior_to_xml_operators.R R/has_xml_closing_tag.R R/create_param.R R/check_inference_model.R R/init_param.R R/create_mcmc.R R/hky_site_model_to_xml_state.R R/tree_prior_to_xml_tracelog.R R/is_one_string_that_is_a_number.R R/indent.R R/are_init_site_models.R R/create_beast2_input_state.R R/has_xml_short_closing_tag.R R/is_default_mcmc.R R/get_replace_dir_fun.R R/is_one_na.R R/create_rln_clock_branch_rate_model_xml.R R/distr_to_xml.R R/create_beast2_input_beast.R R/create_beast2_input_from_model.R R/check_mrca_prior_name.R R/get_xml_opening_tag.R R/check_site_model.R R/gtr_site_model_to_xml_state.R R/clock_model_to_xml_prior_distr.R R/hky_site_model_to_xml_prior_distr.R R/create_test_treelog.R R/get_param_names.R R/is_distr.R R/get_freq_equilibrium_names.R R/is_site_model.R R/check_beauti_options.R R/find_last_regex_line.R R/create_mrca_prior.R R/is_mrca_prior_with_distr.R R/get_crown_age.R R/check_alignment_id.R R/site_model_to_xml_operators.R R/check_file_exists.R R/is_tree_prior_name.R R/create_beast2_input_map.R R/is_init_clock_model.R R/get_tree_prior_names.R R/get_log_sorts.R R/are_equal_mcmcs.R R/check_rename_fun.R R/get_alignment_ids.R R/create_mcmc_nested_sampling.R R/get_site_model_n_params.R R/create_ucld_stdev_state_node_param_xml.R R/strict_clock_model_to_xml_prior_distr.R R/are_init_mrca_priors.R R/create_tree_likelihood_distr_xml.R R/parameter_to_xml.R R/get_tree_priors_n_distrs.R R/is_site_model_name.R R/check_store_every.R R/create_branch_rate_model_xml.R R/get_beautier_folder.R R/clock_model_to_xml_state.R R/are_equal_xml_lines.R R/is_one_bool.R R/create_site_models.R R/freq_param_to_xml.R R/strict_clock_model_to_xml_tracelog.R R/is_mrca_prior.R R/is_init_site_model.R R/ccp_tree_prior_to_xml_state.R R/site_model_to_xml_state.R R/tn93_site_model_to_xml_prior_distr.R R/has_rln_clock_model.R R/create_beast2_input_init.R R/rln_clock_model_to_xml_prior_distr.R R/are_init_clock_models.R R/get_has_non_strict_clock_model.R R/gtr_site_model_to_xml_prior.R R/are_equivalent_xmls.R R/check_param.R R/init_mrca_prior.R R/is_one_int.R R/get_alignment_id.R R/get_site_model_n_distrs.R R/mrca_prior_to_xml_tracelog.R R/create_inference_model.R R/is_one_string.R R/check_inference_models.R R/get_inference_model_filenames.R R/extract_xml_section_from_lines.R R/get_clock_model_name.R R/tree_prior_to_xml_prior_distr.R R/create_ns_inference_model.R R/gamma_site_models_to_xml_prior_distr.R R/alpha_parameter_to_xml.R R/site_model_to_xml_tracelog.R R/create_temp_tracelog_filename.R R/is_init_param.R R/site_model_to_xml_prior.R R/create_screenlog.R R/create_test_inference_model.R R/extract_xml_loggers_from_lines.R R/is_init_tree_prior.R R/site_models_to_xml_operators.R R/mrca_prior_to_xml_state.R R/is_freq_equilibrium_name.R R/remove_multiline.R R/init_tree_priors.R R/tree_model_to_tracelog_xml.R R/create_test_mcmc.R R/rln_clock_model_to_xml_state.R R/is_clock_model.R R/create_beast2_input_data.R R/create_clock_rate_state_node_parameter_xml.R R/get_remove_dir_fun.R R/create_beast2_input_file.R R/create_beauti_options_v2_6.R R/is_one_double.R R/tree_priors_to_xml_distr.R R/init_site_models.R R/b_pop_sizes_parameter_to_xml.R R/check_log_mode.R R/check_clock_model.R R/create_beautier_tempfolder.R inst/doc/examples.Rmd inst/doc/demo.Rmd inst/doc/inference_models.R inst/doc/demo.R inst/doc/inference_models.Rmd inst/doc/examples.R vignettes/examples.Rmd vignettes/demo.Rmd vignettes/inference_models.Rmd man/is_init_hky_site_model.Rd man/create_laplace_distr.Rd man/create_data_xml.Rd man/get_site_model_n_distrs.Rd man/is_clock_model_name.Rd man/create_ucld_mean_state_node_param_xml.Rd man/create_inv_gamma_distr.Rd man/check_log_mode.Rd man/is_rate_at_param.Rd man/init_inv_gamma_distr.Rd man/parameter_to_xml_rate_ac.Rd man/is_init_exp_distr.Rd man/is_init_tn93_site_model.Rd man/are_equal_xml_lines.Rd man/init_bd_tree_prior.Rd man/parameter_to_xml_mu.Rd man/get_tree_prior_n_distrs.Rd man/create_subst_model_xml.Rd man/check_tracelog.Rd man/tn93_site_model_to_xml_prior_distr.Rd man/rln_clock_model_to_xml_state.Rd man/site_models_to_xml_operators.Rd man/is_mcmc_nested_sampling.Rd man/create_mean_param.Rd man/create_mu_param.Rd man/get_alignment_ids_from_fasta_filenames.Rd man/is_tree_prior_name.Rd man/get_fasta_filename.Rd man/get_log_modes.Rd man/yule_tree_prior_to_xml_operators.Rd man/s_parameter_to_xml.Rd man/is_init_strict_clock_model.Rd man/mcmc_to_xml_run_default.Rd man/ccp_tree_prior_to_xml_state.Rd man/check_tn93_site_model.Rd man/init_one_div_x_distr.Rd man/init_hky_site_model.Rd man/create_b_pop_sizes_param.Rd man/is_one_empty_string.Rd man/create_beauti_options_v2_6.Rd man/tree_priors_to_xml_prior_distr.Rd man/gtr_site_model_to_xml_prior_distr.Rd man/create_rate_categories_state_node_xml.Rd man/is_gtr_site_model.Rd man/is_init_laplace_distr.Rd man/create_test_tracelog.Rd man/check_inference_model.Rd man/is_init_beta_distr.Rd man/rln_clock_model_to_xml_tracelog.Rd man/create_xml_declaration.Rd man/check_mrca_prior_names.Rd man/get_distr_n_params.Rd man/get_clock_models_ids.Rd man/parameter_to_xml_kappa_1.Rd man/find_last_xml_closing_tag_line.Rd man/get_default_beast_namespace.Rd man/check_ns_mcmc.Rd man/are_equal_tracelogs.Rd man/is_beauti_options.Rd man/is_normal_distr.Rd man/clock_model_to_xml_prior_distr.Rd man/get_tree_prior_names.Rd man/create_tree_likelihood_distr_xml.Rd man/create_screenlog_xml.Rd man/is_phylo.Rd man/create_beauti_options.Rd man/parameter_to_xml_rate_gt.Rd man/check_param.Rd man/init_clock_models.Rd man/freq_equilibrium_to_xml.Rd man/get_param_names.Rd man/create_screenlog.Rd man/distr_to_xml_laplace.Rd man/parameter_to_xml_kappa_2.Rd man/is_init_param.Rd man/are_equivalent_xml_lines_loggers.Rd man/is_init_jc69_site_model.Rd man/is_tree_prior.Rd man/check_log_sort.Rd man/check_gamma_site_model_names.Rd man/create_lambda_param.Rd man/is_kappa_param.Rd man/is_one_na.Rd man/strict_clock_model_to_xml_state.Rd man/tipdate_taxa_to_xml_trait.Rd man/site_model_to_xml_prior_distr.Rd man/create_distr.Rd man/is_kappa_2_param.Rd man/create_gamma_distr.Rd man/create_rate_at_param.Rd man/create_beast2_input_distr_prior.Rd man/get_log_sorts.Rd man/create_clock_model_from_name.Rd man/init_param.Rd man/is_mu_param.Rd man/tree_prior_to_xml_state.Rd man/clock_rate_param_to_xml.Rd man/create_gamma_site_model.Rd man/is_rate_gt_param.Rd man/remove_empty_lines.Rd man/check_tree_prior.Rd man/init_laplace_distr.Rd man/init_jc69_site_model.Rd man/is_rate_cg_param.Rd man/distr_to_xml_uniform.Rd man/is_lambda_param.Rd man/is_rate_ac_param.Rd man/distr_to_xml_inv_gamma.Rd man/is_init_uniform_distr.Rd man/clock_model_to_xml_treelogger.Rd man/check_screenlog.Rd man/create_beta_param.Rd man/check_param_names.Rd man/check_treelog.Rd man/check_rln_clock_model.Rd man/create_strict_clock_rate_scaler_operator_xml.Rd man/alpha_parameter_to_xml.Rd man/is_alpha_param.Rd man/are_tree_priors.Rd man/clock_model_to_xml_operators.Rd man/create_beast2_input_map.Rd man/is_cep_tree_prior.Rd man/create_tree_prior.Rd man/gamma_site_model_to_xml_state.Rd man/create_test_ns_inference_model.Rd man/is_distr_name.Rd man/create_test_mcmc.Rd man/is_log_normal_distr.Rd man/create_beautier_tempfolder.Rd man/distr_to_xml_log_normal.Rd man/check_inference_models.Rd man/create_site_models_from_names.Rd man/is_beta_param.Rd man/are_init_site_models.Rd man/mcmc_to_xml_run_nested_sampling.Rd man/create_param.Rd man/is_gamma_site_model.Rd man/extract_xml_operators_from_lines.Rd man/is_gamma_distr.Rd man/get_site_model_n_params.Rd man/create_normal_distr.Rd man/is_mrca_align_ids_in_fastas.Rd man/check_filename.Rd man/tree_prior_to_xml_tracelog.Rd man/create_jc69_site_model.Rd man/create_yule_tree_prior.Rd man/is_kappa_1_param.Rd man/is_mcmc.Rd man/distr_to_xml_poisson.Rd man/are_equal_treelogs.Rd man/is_mrca_prior.Rd man/init_tree_priors.Rd man/create_site_model.Rd man/strict_clock_model_to_xml_prior_distr.Rd man/get_beautier_folder.Rd man/create_poisson_distr.Rd man/is_one_string_that_is_a_number.Rd man/rename_inference_model_filenames.Rd man/are_equivalent_xml_lines_operators.Rd man/create_ccp_tree_prior.Rd man/find_first_xml_opening_tag_line.Rd man/check_file_exists.Rd man/create_cbs_tree_prior.Rd man/hky_site_model_to_xml_prior_distr.Rd man/mrca_prior_to_xml_taxonset.Rd man/is_init_bd_tree_prior.Rd man/create_kappa_param.Rd man/init_rln_clock_model.Rd man/check_store_every.Rd man/init_log_normal_distr.Rd man/check_mrca_prior_name.Rd man/check_strict_clock_model.Rd man/is_init_gamma_distr.Rd man/create_test_treelog.Rd man/get_beautier_path.Rd man/check_site_model.Rd man/extract_xml_section_from_lines.Rd man/init_normal_distr.Rd man/create_branch_rate_model_xml.Rd man/yule_tree_prior_to_xml_prior_distr.Rd man/is_xml.Rd man/check_clock_model.Rd man/is_init_mrca_prior.Rd man/create_mcmc.Rd man/create_uniform_distr.Rd man/remove_beautier_folder.Rd man/is_param_name.Rd man/create_tracelog_xml.Rd man/check_alignment_id.Rd man/is_ccp_tree_prior.Rd man/check_mcmc_values.Rd man/is_init_inv_gamma_distr.Rd man/tree_prior_to_xml_prior_distr.Rd man/create_beast2_input_distr_lh.Rd man/is_tn93_site_model.Rd man/rln_clock_model_to_xml_operators.Rd man/create_tracelog.Rd man/freq_param_to_xml.Rd man/check_treelog_values.Rd man/check_mrca_prior.Rd man/check_mcmc.Rd man/ccp_tree_prior_to_xml_prior_distr.Rd man/get_beautier_tempfilename.Rd man/is_freq_param.Rd man/create_beast2_input_distr.Rd man/parameter_to_xml_scale.Rd man/is_site_model.Rd man/check_screenlog_names.Rd man/are_rln_clock_models.Rd man/check_site_model_types.Rd man/is_default_mcmc.Rd man/create_test_screenlog.Rd man/is_yule_tree_prior.Rd man/are_init_tree_priors.Rd man/check_beauti_options.Rd man/has_xml_closing_tag.Rd man/check_mrca_prior_taxa_names.Rd man/is_mean_param.Rd man/rnd_phylo_to_xml_init.Rd man/has_xml_short_closing_tag.Rd man/is_clock_rate_param.Rd man/clock_model_to_xml_tracelog.Rd man/find_clock_model.Rd man/init_beta_distr.Rd man/are_equal_screenlogs.Rd man/distr_to_xml_exp.Rd man/create_rate_ag_param.Rd man/beautier-package.Rd man/check_tracelog_names.Rd man/is_init_poisson_distr.Rd man/create_test_ns_mcmc.Rd man/is_in_patterns.Rd man/create_rate_ct_param.Rd man/is_init_clock_model.Rd man/create_m_param.Rd man/hky_site_model_to_xml_state.Rd man/are_equal_xml_files.Rd man/is_init_distr.Rd man/rename_mcmc_filenames.Rd man/mcmc_to_xml_run.Rd man/check_tn93_site_model_names.Rd man/parameter_to_xml_sigma.Rd man/is_rln_clock_model.Rd man/b_pop_sizes_param_to_xml.Rd man/create_beast2_input_operators.Rd man/cbs_tree_prior_to_xml_prior_distr.Rd man/indent.Rd man/is_mrca_align_id_in_fasta.Rd man/default_parameters_doc.Rd man/strict_clock_model_to_xml_tracelog.Rd man/is_one_bool.Rd man/are_equivalent_xml_lines_all.Rd man/is_init_tree_prior.Rd man/get_tree_priors_n_params.Rd man/init_poisson_distr.Rd man/create_beast2_input_run.Rd man/is_init_gamma_site_model.Rd man/create_log_normal_distr.Rd man/clock_model_to_xml_state.Rd man/is_poisson_distr.Rd man/is_distr.Rd man/parameter_to_xml_lambda.Rd man/count_trailing_spaces.Rd man/create_clock_models_from_names.Rd man/init_cep_tree_prior.Rd man/check_clock_models.Rd man/is_one_div_x_distr.Rd man/create_exp_distr.Rd man/is_sigma_param.Rd man/mrca_priors_to_xml_prior_distr.Rd man/no_taxa_to_xml_tree.Rd man/get_clock_model_names.Rd man/init_gtr_site_model.Rd man/beta_parameter_to_xml.Rd man/has_tip_dating.Rd man/check_mcmc_list_element_names.Rd man/create_ns_inference_model.Rd man/create_beast2_input_state.Rd man/create_beast2_input_beast.Rd man/unindent.Rd man/get_site_model_names.Rd man/has_rln_clock_model.Rd man/site_models_to_xml_prior_distr.Rd man/is_b_pop_sizes_param.Rd man/parameter_to_xml_rate_cg.Rd man/interspace.Rd man/create_kappa_1_param.Rd man/mrca_prior_to_xml_prior_distr.Rd man/is_on_github_actions.Rd man/get_xml_opening_tag.Rd man/is_on_ci.Rd man/is_rate_ct_param.Rd man/create_temp_treelog_filename.Rd man/get_gamma_site_model_n_params.Rd man/get_n_taxa.Rd man/has_strict_clock_model.Rd man/get_distr_names.Rd man/has_mrca_prior_with_distr.Rd man/are_init_mrca_priors.Rd man/is_init_ccp_tree_prior.Rd man/create_temp_screenlog_filename.Rd man/check_file_and_model_agree.Rd man/init_distr.Rd man/bd_tree_prior_to_xml_prior_distr.Rd man/create_hky_subst_model_xml.Rd man/check_gtr_site_model_names.Rd man/is_id.Rd man/distr_to_xml_beta.Rd man/check_phylogeny.Rd man/is_rate_ag_param.Rd man/check_screenlog_values.Rd man/create_clock_model.Rd man/get_tree_priors_n_distrs.Rd man/check_param_types.Rd man/create_loggers_xml.Rd man/is_cbs_tree_prior.Rd man/tn93_site_model_to_xml_state.Rd man/are_equivalent_xml_lines_section.Rd man/create_mrca_prior.Rd man/init_uniform_distr.Rd man/check_is_monophyletic.Rd man/create_site_model_parameters_xml.Rd man/get_site_models_n_params.Rd man/get_inference_model_filenames.Rd man/check_gamma_site_model.Rd man/create_freq_param.Rd man/create_cep_tree_prior.Rd man/create_gtr_subst_model_xml.Rd man/create_site_model_xml.Rd man/is_inv_gamma_distr.Rd man/init_mrca_priors.Rd man/find_first_regex_line.Rd man/create_clock_rate_state_node_parameter_xml.Rd man/site_models_to_xml_tracelog.Rd man/create_rln_clock_model.Rd man/is_freq_equilibrium_name.Rd man/is_param.Rd man/create_beast2_input_file_from_model.Rd man/is_inference_model.Rd man/get_has_non_strict_clock_model.Rd man/check_rename_fun.Rd man/create_gtr_site_model.Rd man/is_beta_distr.Rd man/is_init_one_div_x_distr.Rd man/is_init_yule_tree_prior.Rd man/init_exp_distr.Rd man/create_ns_mcmc.Rd man/default_params_doc.Rd man/create_beast2_beast_xml.Rd man/create_beauti_options_v2_4.Rd man/kappa_param_to_xml.Rd man/is_strict_clock_model.Rd man/extract_xml_loggers_from_lines.Rd man/create_treelog.Rd man/create_clock_models.Rd man/is_init_normal_distr.Rd man/create_bd_tree_prior.Rd man/is_init_cbs_tree_prior.Rd man/create_clock_rate_param.Rd man/distr_to_xml_one_div_x.Rd man/get_default_beast_namespace_v2_4.Rd man/is_init_site_model.Rd man/is_scale_param.Rd man/create_inference_model.Rd man/are_init_clock_models.Rd man/are_equivalent_xml_lines.Rd man/is_init_log_normal_distr.Rd man/create_tn93_subst_model_xml.Rd man/create_hky_site_model.Rd man/is_on_appveyor.Rd man/create_site_models.Rd man/check_site_models.Rd man/are_site_models.Rd man/init_mrca_prior.Rd man/is_s_param.Rd man/get_clock_model_name.Rd man/is_on_travis.Rd man/create_sigma_param.Rd man/parameter_to_xml_mean.Rd man/create_beast2_input_init.Rd man/check_treelog_names.Rd man/create_kappa_2_param.Rd man/distr_to_xml.Rd man/is_init_gtr_site_model.Rd man/create_alpha_param.Rd man/gtr_site_model_to_xml_state.Rd man/parameter_to_xml.Rd man/find_last_regex_line.Rd man/site_model_to_xml_tracelog.Rd man/parameter_to_xml_rate_ct.Rd man/create_beast2_input.Rd man/get_alignment_ids.Rd man/remove_multiline.Rd man/create_jc69_subst_model_xml.Rd man/create_rate_cg_param.Rd man/is_one_string.Rd man/create_treelog_xml.Rd man/mrca_prior_to_xml_tracelog.Rd man/init_strict_clock_model.Rd man/check_site_model_names.Rd man/create_beast2_input_file.Rd man/site_model_to_xml_state.Rd man/get_operator_id_pre.Rd man/check_tracelog_values.Rd man/init_gamma_distr.Rd man/create_beta_distr.Rd man/create_temp_tracelog_filename.Rd man/create_beast2_input_data.Rd man/is_init_cep_tree_prior.Rd man/mrca_prior_to_xml_state.Rd man/get_site_models_n_distrs.Rd man/are_ids.Rd man/tipdate_taxa_to_xml_tree.Rd man/init_tn93_site_model.Rd man/check_empty_beautier_folder.Rd man/strict_clock_model_to_xml_operators.Rd man/is_site_model_name.Rd man/is_hky_site_model.Rd man/create_beast2_input_from_model.Rd man/get_taxa_names.Rd man/get_alignment_id.Rd man/check_gtr_site_model.Rd man/fasta_file_to_sequences.Rd man/gamma_site_models_to_xml_prior_distr.Rd man/create_rln_clock_branch_rate_model_xml.Rd man/create_ucld_stdev_state_node_param_xml.Rd man/get_xml_closing_tag.Rd man/create_site_model_from_name.Rd man/jc69_site_model_to_xml_state.Rd man/create_rate_gt_param.Rd man/get_remove_dir_fun.Rd man/site_model_to_xml_operators.Rd man/is_m_param.Rd man/tree_priors_to_xml_tracelog.Rd man/has_xml_opening_tag.Rd man/init_yule_tree_prior.Rd man/create_test_inference_model.Rd man/is_exp_distr.Rd man/get_tree_prior_n_params.Rd man/compare_lines.Rd man/are_mrca_taxon_names_in_fasta.Rd man/parameter_to_xml_rate_ag.Rd man/init_site_models.Rd man/create_tn93_site_model.Rd man/tree_model_to_tracelog_xml.Rd man/get_replace_dir_fun.Rd man/are_mrca_align_ids_in_fasta.Rd man/is_one_double.Rd man/is_clock_model.Rd man/is_bd_tree_prior.Rd man/create_strict_clock_branch_rate_model_xml.Rd man/init_ccp_tree_prior.Rd man/is_jc69_site_model.Rd man/m_param_to_xml.Rd man/is_uniform_distr.Rd man/create_beast2_input_data_sequences.Rd man/taxa_to_xml_tree.Rd man/is_init_rln_clock_model.Rd man/check_tree_priors.Rd man/gamma_distr_to_xml.Rd man/is_mrca_prior_with_distr.Rd man/init_gamma_site_model.Rd man/get_freq_equilibrium_names.Rd man/has_mrca_prior.Rd man/are_mrca_priors.Rd man/are_equal_mcmcs.Rd man/get_mcmc_filenames.Rd man/create_one_div_x_distr.Rd man/is_one_int.Rd man/rln_clock_model_to_xml_mean_rate_prior.Rd man/cep_tree_prior_to_xml_prior_distr.Rd man/b_pop_sizes_parameter_to_xml.Rd man/get_gamma_site_model_n_distrs.Rd man/get_beautier_paths.Rd man/are_fasta_filenames.Rd man/gamma_site_model_to_xml_prior_distr.Rd man/create_strict_clock_model.Rd man/get_file_base_sans_ext.Rd man/init_inference_model.Rd man/distr_to_xml_normal.Rd man/create_s_param.Rd man/create_scale_param.Rd man/rln_clock_model_to_xml_prior_distr.Rd man/parameter_to_xml_rate_at.Rd man/get_default_beast_namespace_v2_6.Rd man/get_remove_hex_fun.Rd man/get_crown_age.Rd man/tree_prior_to_xml_operators.Rd man/create_trait_set_string.Rd man/create_tree_priors.Rd man/are_clock_models.Rd man/create_rate_ac_param.Rd man/are_equivalent_xml_files.Rd man/is_laplace_distr.Rd