# Generated by roxygen2: do not edit by hand

export(alpha_parameter_to_xml)
export(are_clock_models)
export(are_equal_mcmcs)
export(are_equal_screenlogs)
export(are_equal_tracelogs)
export(are_equal_treelogs)
export(are_equal_xml_files)
export(are_equal_xml_lines)
export(are_equivalent_xml_files)
export(are_equivalent_xml_lines)
export(are_equivalent_xml_lines_all)
export(are_equivalent_xml_lines_loggers)
export(are_equivalent_xml_lines_operators)
export(are_equivalent_xml_lines_section)
export(are_fasta_filenames)
export(are_ids)
export(are_init_clock_models)
export(are_init_mrca_priors)
export(are_init_site_models)
export(are_init_tree_priors)
export(are_mrca_align_ids_in_fasta)
export(are_mrca_priors)
export(are_mrca_taxon_names_in_fasta)
export(are_rln_clock_models)
export(are_site_models)
export(are_tree_priors)
export(b_pop_sizes_param_to_xml)
export(b_pop_sizes_parameter_to_xml)
export(bd_tree_prior_to_xml_prior_distr)
export(beta_parameter_to_xml)
export(cbs_tree_prior_to_xml_prior_distr)
export(ccp_tree_prior_to_xml_prior_distr)
export(ccp_tree_prior_to_xml_state)
export(cep_tree_prior_to_xml_prior_distr)
export(check_alignment_id)
export(check_beauti_options)
export(check_clock_model)
export(check_clock_models)
export(check_empty_beautier_folder)
export(check_file_and_model_agree)
export(check_file_exists)
export(check_filename)
export(check_gamma_site_model)
export(check_gamma_site_model_names)
export(check_gtr_site_model)
export(check_gtr_site_model_names)
export(check_inference_model)
export(check_inference_models)
export(check_is_monophyletic)
export(check_log_mode)
export(check_log_sort)
export(check_mcmc)
export(check_mcmc_list_element_names)
export(check_mcmc_nested_sampling)
export(check_mcmc_values)
export(check_mrca_prior)
export(check_mrca_prior_name)
export(check_mrca_prior_names)
export(check_mrca_prior_taxa_names)
export(check_nested_sampling_mcmc)
export(check_ns_mcmc)
export(check_param)
export(check_param_names)
export(check_param_types)
export(check_phylogeny)
export(check_rename_fun)
export(check_rln_clock_model)
export(check_screenlog)
export(check_screenlog_names)
export(check_screenlog_values)
export(check_site_model)
export(check_site_model_names)
export(check_site_model_types)
export(check_site_models)
export(check_store_every)
export(check_strict_clock_model)
export(check_tn93_site_model)
export(check_tn93_site_model_names)
export(check_tracelog)
export(check_tracelog_names)
export(check_tracelog_values)
export(check_tree_prior)
export(check_tree_priors)
export(check_treelog)
export(check_treelog_names)
export(check_treelog_values)
export(clock_model_to_xml_operators)
export(clock_model_to_xml_prior_distr)
export(clock_model_to_xml_state)
export(clock_model_to_xml_tracelog)
export(clock_model_to_xml_treelogger)
export(clock_rate_param_to_xml)
export(compare_lines)
export(count_trailing_spaces)
export(create_alpha_param)
export(create_b_pop_sizes_param)
export(create_bd_tree_prior)
export(create_beast2_beast_xml)
export(create_beast2_input)
export(create_beast2_input_beast)
export(create_beast2_input_data)
export(create_beast2_input_data_sequences)
export(create_beast2_input_distr)
export(create_beast2_input_distr_lh)
export(create_beast2_input_distr_prior)
export(create_beast2_input_file)
export(create_beast2_input_file_from_model)
export(create_beast2_input_from_model)
export(create_beast2_input_init)
export(create_beast2_input_map)
export(create_beast2_input_operators)
export(create_beast2_input_run)
export(create_beast2_input_state)
export(create_beauti_options)
export(create_beauti_options_v2_4)
export(create_beauti_options_v2_6)
export(create_beautier_tempfolder)
export(create_beta_distr)
export(create_beta_param)
export(create_branch_rate_model_xml)
export(create_cbs_tree_prior)
export(create_ccp_tree_prior)
export(create_cep_tree_prior)
export(create_clock_model)
export(create_clock_model_from_name)
export(create_clock_model_rln)
export(create_clock_model_strict)
export(create_clock_models)
export(create_clock_models_from_names)
export(create_clock_rate_param)
export(create_clock_rate_state_node_parameter_xml)
export(create_data_xml)
export(create_distr)
export(create_distr_beta)
export(create_distr_exp)
export(create_distr_gamma)
export(create_distr_inv_gamma)
export(create_distr_laplace)
export(create_distr_log_normal)
export(create_distr_normal)
export(create_distr_one_div_x)
export(create_distr_poisson)
export(create_distr_uniform)
export(create_exp_distr)
export(create_freq_param)
export(create_gamma_distr)
export(create_gamma_site_model)
export(create_gtr_site_model)
export(create_gtr_subst_model_xml)
export(create_hky_site_model)
export(create_hky_subst_model_xml)
export(create_inference_model)
export(create_inv_gamma_distr)
export(create_jc69_site_model)
export(create_jc69_subst_model_xml)
export(create_kappa_1_param)
export(create_kappa_2_param)
export(create_kappa_param)
export(create_lambda_param)
export(create_laplace_distr)
export(create_log_normal_distr)
export(create_loggers_xml)
export(create_m_param)
export(create_mcmc)
export(create_mcmc_nested_sampling)
export(create_mean_param)
export(create_mrca_prior)
export(create_mu_param)
export(create_normal_distr)
export(create_ns_inference_model)
export(create_ns_mcmc)
export(create_one_div_x_distr)
export(create_param)
export(create_param_alpha)
export(create_param_b_pop_sizes)
export(create_param_beta)
export(create_param_clock_rate)
export(create_param_freq)
export(create_param_kappa)
export(create_param_kappa_1)
export(create_param_kappa_2)
export(create_param_lambda)
export(create_param_m)
export(create_param_mean)
export(create_param_mu)
export(create_param_rate_ac)
export(create_param_rate_ag)
export(create_param_rate_at)
export(create_param_rate_cg)
export(create_param_rate_ct)
export(create_param_rate_gt)
export(create_param_s)
export(create_param_scale)
export(create_param_sigma)
export(create_poisson_distr)
export(create_rate_ac_param)
export(create_rate_ag_param)
export(create_rate_at_param)
export(create_rate_categories_state_node_xml)
export(create_rate_cg_param)
export(create_rate_ct_param)
export(create_rate_gt_param)
export(create_rln_clock_branch_rate_model_xml)
export(create_rln_clock_model)
export(create_s_param)
export(create_scale_param)
export(create_screenlog)
export(create_screenlog_xml)
export(create_sigma_param)
export(create_site_model)
export(create_site_model_from_name)
export(create_site_model_gtr)
export(create_site_model_hky)
export(create_site_model_jc69)
export(create_site_model_parameters_xml)
export(create_site_model_tn93)
export(create_site_model_xml)
export(create_site_models)
export(create_site_models_from_names)
export(create_strict_clock_branch_rate_model_xml)
export(create_strict_clock_model)
export(create_strict_clock_rate_scaler_operator_xml)
export(create_subst_model_xml)
export(create_temp_screenlog_filename)
export(create_temp_tracelog_filename)
export(create_temp_treelog_filename)
export(create_test_inference_model)
export(create_test_mcmc)
export(create_test_ns_inference_model)
export(create_test_ns_mcmc)
export(create_test_screenlog)
export(create_test_tracelog)
export(create_test_treelog)
export(create_tn93_site_model)
export(create_tn93_subst_model_xml)
export(create_tracelog)
export(create_tracelog_xml)
export(create_trait_set_string)
export(create_tree_likelihood_distr_xml)
export(create_tree_prior)
export(create_tree_prior_bd)
export(create_tree_prior_cbs)
export(create_tree_prior_ccp)
export(create_tree_prior_cep)
export(create_tree_prior_yule)
export(create_tree_priors)
export(create_treelog)
export(create_treelog_xml)
export(create_ucld_mean_state_node_param_xml)
export(create_ucld_stdev_state_node_param_xml)
export(create_uniform_distr)
export(create_xml_declaration)
export(create_yule_tree_prior)
export(distr_to_xml)
export(distr_to_xml_beta)
export(distr_to_xml_exp)
export(distr_to_xml_inv_gamma)
export(distr_to_xml_laplace)
export(distr_to_xml_log_normal)
export(distr_to_xml_normal)
export(distr_to_xml_one_div_x)
export(distr_to_xml_poisson)
export(distr_to_xml_uniform)
export(extract_xml_loggers_from_lines)
export(extract_xml_operators_from_lines)
export(extract_xml_section_from_lines)
export(fasta_file_to_sequences)
export(find_clock_model)
export(find_first_regex_line)
export(find_first_xml_opening_tag_line)
export(find_last_regex_line)
export(find_last_xml_closing_tag_line)
export(freq_equilibrium_to_xml)
export(freq_param_to_xml)
export(gamma_distr_to_xml)
export(gamma_site_model_to_xml_prior_distr)
export(gamma_site_model_to_xml_state)
export(gamma_site_models_to_xml_prior_distr)
export(get_alignment_id)
export(get_alignment_ids)
export(get_alignment_ids_from_fasta_filenames)
export(get_beautier_folder)
export(get_beautier_path)
export(get_beautier_paths)
export(get_beautier_tempfilename)
export(get_clock_model_name)
export(get_clock_model_names)
export(get_clock_models_ids)
export(get_crown_age)
export(get_default_beast_namespace)
export(get_default_beast_namespace_v2_4)
export(get_default_beast_namespace_v2_6)
export(get_distr_n_params)
export(get_distr_names)
export(get_fasta_filename)
export(get_file_base_sans_ext)
export(get_freq_equilibrium_names)
export(get_gamma_site_model_n_distrs)
export(get_gamma_site_model_n_params)
export(get_has_non_strict_clock_model)
export(get_inference_model_filenames)
export(get_log_modes)
export(get_log_sorts)
export(get_mcmc_filenames)
export(get_n_taxa)
export(get_operator_id_pre)
export(get_param_names)
export(get_remove_dir_fun)
export(get_remove_hex_fun)
export(get_replace_dir_fun)
export(get_site_model_n_distrs)
export(get_site_model_n_params)
export(get_site_model_names)
export(get_site_models_n_distrs)
export(get_site_models_n_params)
export(get_taxa_names)
export(get_tree_prior_n_distrs)
export(get_tree_prior_n_params)
export(get_tree_prior_names)
export(get_tree_priors_n_distrs)
export(get_tree_priors_n_params)
export(get_xml_closing_tag)
export(get_xml_opening_tag)
export(gtr_site_model_to_xml_prior_distr)
export(gtr_site_model_to_xml_state)
export(has_mrca_prior)
export(has_mrca_prior_with_distr)
export(has_rln_clock_model)
export(has_strict_clock_model)
export(has_tip_dating)
export(has_xml_closing_tag)
export(has_xml_opening_tag)
export(has_xml_short_closing_tag)
export(hky_site_model_to_xml_prior_distr)
export(hky_site_model_to_xml_state)
export(indent)
export(init_bd_tree_prior)
export(init_beta_distr)
export(init_ccp_tree_prior)
export(init_cep_tree_prior)
export(init_clock_models)
export(init_distr)
export(init_exp_distr)
export(init_gamma_distr)
export(init_gamma_site_model)
export(init_gtr_site_model)
export(init_hky_site_model)
export(init_inference_model)
export(init_inv_gamma_distr)
export(init_jc69_site_model)
export(init_laplace_distr)
export(init_log_normal_distr)
export(init_mrca_prior)
export(init_mrca_priors)
export(init_normal_distr)
export(init_one_div_x_distr)
export(init_param)
export(init_poisson_distr)
export(init_rln_clock_model)
export(init_site_models)
export(init_strict_clock_model)
export(init_tn93_site_model)
export(init_tree_priors)
export(init_uniform_distr)
export(init_yule_tree_prior)
export(interspace)
export(is_alpha_param)
export(is_b_pop_sizes_param)
export(is_bd_tree_prior)
export(is_beauti_options)
export(is_beta_distr)
export(is_beta_param)
export(is_cbs_tree_prior)
export(is_ccp_tree_prior)
export(is_cep_tree_prior)
export(is_clock_model)
export(is_clock_model_name)
export(is_clock_rate_param)
export(is_default_mcmc)
export(is_distr)
export(is_distr_name)
export(is_exp_distr)
export(is_freq_equilibrium_name)
export(is_freq_param)
export(is_gamma_distr)
export(is_gamma_site_model)
export(is_gtr_site_model)
export(is_hky_site_model)
export(is_id)
export(is_in_patterns)
export(is_inference_model)
export(is_init_bd_tree_prior)
export(is_init_beta_distr)
export(is_init_cbs_tree_prior)
export(is_init_ccp_tree_prior)
export(is_init_cep_tree_prior)
export(is_init_clock_model)
export(is_init_distr)
export(is_init_exp_distr)
export(is_init_gamma_distr)
export(is_init_gamma_site_model)
export(is_init_gtr_site_model)
export(is_init_hky_site_model)
export(is_init_inv_gamma_distr)
export(is_init_jc69_site_model)
export(is_init_laplace_distr)
export(is_init_log_normal_distr)
export(is_init_mrca_prior)
export(is_init_normal_distr)
export(is_init_one_div_x_distr)
export(is_init_param)
export(is_init_poisson_distr)
export(is_init_rln_clock_model)
export(is_init_site_model)
export(is_init_strict_clock_model)
export(is_init_tn93_site_model)
export(is_init_tree_prior)
export(is_init_uniform_distr)
export(is_init_yule_tree_prior)
export(is_inv_gamma_distr)
export(is_jc69_site_model)
export(is_kappa_1_param)
export(is_kappa_2_param)
export(is_kappa_param)
export(is_lambda_param)
export(is_laplace_distr)
export(is_log_normal_distr)
export(is_m_param)
export(is_mcmc)
export(is_mcmc_nested_sampling)
export(is_mean_param)
export(is_mrca_align_id_in_fasta)
export(is_mrca_align_ids_in_fastas)
export(is_mrca_prior)
export(is_mrca_prior_with_distr)
export(is_mu_param)
export(is_nested_sampling_mcmc)
export(is_normal_distr)
export(is_on_appveyor)
export(is_on_ci)
export(is_on_github_actions)
export(is_on_travis)
export(is_one_bool)
export(is_one_div_x_distr)
export(is_one_double)
export(is_one_empty_string)
export(is_one_int)
export(is_one_na)
export(is_one_string)
export(is_one_string_that_is_a_number)
export(is_param)
export(is_param_name)
export(is_phylo)
export(is_poisson_distr)
export(is_rate_ac_param)
export(is_rate_ag_param)
export(is_rate_at_param)
export(is_rate_cg_param)
export(is_rate_ct_param)
export(is_rate_gt_param)
export(is_rln_clock_model)
export(is_s_param)
export(is_scale_param)
export(is_sigma_param)
export(is_site_model)
export(is_site_model_name)
export(is_strict_clock_model)
export(is_tn93_site_model)
export(is_tree_prior)
export(is_tree_prior_name)
export(is_uniform_distr)
export(is_xml)
export(is_yule_tree_prior)
export(jc69_site_model_to_xml_state)
export(kappa_param_to_xml)
export(m_param_to_xml)
export(mcmc_to_xml_run)
export(mcmc_to_xml_run_default)
export(mcmc_to_xml_run_nested_sampling)
export(mrca_prior_to_xml_prior_distr)
export(mrca_prior_to_xml_state)
export(mrca_prior_to_xml_taxonset)
export(mrca_prior_to_xml_tracelog)
export(mrca_priors_to_xml_prior_distr)
export(no_taxa_to_xml_tree)
export(parameter_to_xml)
export(parameter_to_xml_kappa_1)
export(parameter_to_xml_kappa_2)
export(parameter_to_xml_lambda)
export(parameter_to_xml_mean)
export(parameter_to_xml_mu)
export(parameter_to_xml_rate_ac)
export(parameter_to_xml_rate_ag)
export(parameter_to_xml_rate_at)
export(parameter_to_xml_rate_cg)
export(parameter_to_xml_rate_ct)
export(parameter_to_xml_rate_gt)
export(parameter_to_xml_scale)
export(parameter_to_xml_sigma)
export(remove_beautier_folder)
export(remove_empty_lines)
export(remove_multiline)
export(rename_inference_model_filenames)
export(rename_mcmc_filenames)
export(rln_clock_model_to_xml_mean_rate_prior)
export(rln_clock_model_to_xml_operators)
export(rln_clock_model_to_xml_prior_distr)
export(rln_clock_model_to_xml_state)
export(rln_clock_model_to_xml_tracelog)
export(rnd_phylo_to_xml_init)
export(s_parameter_to_xml)
export(site_model_to_xml_operators)
export(site_model_to_xml_prior_distr)
export(site_model_to_xml_state)
export(site_model_to_xml_tracelog)
export(site_models_to_xml_operators)
export(site_models_to_xml_prior_distr)
export(site_models_to_xml_tracelog)
export(strict_clock_model_to_xml_operators)
export(strict_clock_model_to_xml_prior_distr)
export(strict_clock_model_to_xml_state)
export(strict_clock_model_to_xml_tracelog)
export(taxa_to_xml_tree)
export(tipdate_taxa_to_xml_trait)
export(tipdate_taxa_to_xml_tree)
export(tn93_site_model_to_xml_prior_distr)
export(tn93_site_model_to_xml_state)
export(tree_model_to_tracelog_xml)
export(tree_prior_to_xml_operators)
export(tree_prior_to_xml_prior_distr)
export(tree_prior_to_xml_state)
export(tree_prior_to_xml_tracelog)
export(tree_priors_to_xml_prior_distr)
export(tree_priors_to_xml_tracelog)
export(unindent)
export(yule_tree_prior_to_xml_operators)
export(yule_tree_prior_to_xml_prior_distr)
import(rlang)
