# Generated by roxygen2: do not edit by hand

export(add_quotes_if_has_spaces)
export(are_beast2_input_lines)
export(are_beast2_input_lines_deep)
export(are_beast2_input_lines_fast)
export(are_identical_alignments)
export(beast2_options_to_table)
export(beastier_report)
export(check_beast2)
export(check_beast2_options)
export(check_beast2_options_data_types)
export(check_beast2_options_do_not_overwrite_existing_files)
export(check_beast2_options_filenames_differ)
export(check_beast2_options_names)
export(check_beast2_optionses)
export(check_beast2_path)
export(check_can_create_dir_for_state_output_file)
export(check_can_create_file)
export(check_can_create_screenlog_file)
export(check_can_create_state_output_file)
export(check_can_create_tracelog_file)
export(check_can_create_treelog_file)
export(check_empty_beastier_folder)
export(check_empty_beaustier_folders)
export(check_input_filename)
export(check_input_filename_validity)
export(check_n_threads)
export(check_os)
export(check_rng_seed)
export(continue_beast2)
export(create_beast2_continue_cmd_from_options)
export(create_beast2_input_file_folder)
export(create_beast2_options)
export(create_beast2_run_cmd)
export(create_beast2_run_cmd_from_options)
export(create_beast2_screenlog_folder)
export(create_beast2_state_output_file_folder)
export(create_beast2_tracelog_folder)
export(create_beast2_treelog_folder)
export(create_beast2_validate_cmd)
export(create_beast2_validate_cmd_bin)
export(create_beast2_validate_cmd_jar)
export(create_beast2_version_cmd)
export(create_beast2_version_cmd_bin)
export(create_beast2_version_cmd_jar)
export(create_beastier_tempfolder)
export(create_mcbette_beast2_options)
export(create_random_alignment)
export(create_random_fasta)
export(create_random_phylogeny)
export(create_temp_input_filename)
export(create_temp_state_filename)
export(do_minimal_run)
export(extract_screenlog_filename_from_beast2_input_file)
export(extract_tracelog_filename_from_beast2_input_file)
export(extract_treelog_filename_from_beast2_input_file)
export(get_alignment_ids_from_xml_filename)
export(get_beast2_example_filename)
export(get_beast2_example_filenames)
export(get_beast2_main_class_name)
export(get_beast2_options_filenames)
export(get_beast2_version)
export(get_beastier_folder)
export(get_beastier_path)
export(get_beastier_paths)
export(get_beastier_tempfilename)
export(get_default_beast2_bin_path)
export(get_default_beast2_download_url)
export(get_default_beast2_download_url_linux)
export(get_default_beast2_download_url_win)
export(get_default_beast2_folder)
export(get_default_beast2_jar_path)
export(get_default_beast2_path)
export(get_default_beast2_version)
export(get_default_java_path)
export(get_duplicate_param_ids)
export(get_java_version)
export(get_trees_filenames)
export(gives_beast2_warning)
export(has_unique_ids)
export(install_beast2)
export(is_alignment)
export(is_beast2_input_file)
export(is_beast2_installed)
export(is_bin_path)
export(is_jar_path)
export(is_on_appveyor)
export(is_on_ci)
export(is_on_travis)
export(is_win_bin_path)
export(print_beast2_options)
export(remove_beastier_folder)
export(remove_beaustier_folders)
export(remove_file_if_present)
export(rename_beast2_options_filenames)
export(run_beast2)
export(run_beast2_from_options)
export(save_lines)
export(save_nexus_as_fasta)
export(uninstall_beast2)
import(rlang)
importFrom(beautier,check_rename_fun)
importFrom(beautier,create_alpha_param)
importFrom(beautier,create_bd_tree_prior)
importFrom(beautier,create_beast2_input)
importFrom(beautier,create_beast2_input_file)
importFrom(beautier,create_beast2_input_file_from_model)
importFrom(beautier,create_beast2_input_from_model)
importFrom(beautier,create_beta_distr)
importFrom(beautier,create_beta_param)
importFrom(beautier,create_cbs_tree_prior)
importFrom(beautier,create_ccp_tree_prior)
importFrom(beautier,create_cep_tree_prior)
importFrom(beautier,create_clock_model)
importFrom(beautier,create_clock_model_from_name)
importFrom(beautier,create_clock_model_rln)
importFrom(beautier,create_clock_model_strict)
importFrom(beautier,create_clock_models)
importFrom(beautier,create_clock_models_from_names)
importFrom(beautier,create_clock_rate_param)
importFrom(beautier,create_distr)
importFrom(beautier,create_distr_beta)
importFrom(beautier,create_distr_exp)
importFrom(beautier,create_distr_gamma)
importFrom(beautier,create_distr_inv_gamma)
importFrom(beautier,create_distr_laplace)
importFrom(beautier,create_distr_log_normal)
importFrom(beautier,create_distr_normal)
importFrom(beautier,create_distr_one_div_x)
importFrom(beautier,create_distr_poisson)
importFrom(beautier,create_distr_uniform)
importFrom(beautier,create_exp_distr)
importFrom(beautier,create_gamma_distr)
importFrom(beautier,create_gamma_site_model)
importFrom(beautier,create_gtr_site_model)
importFrom(beautier,create_hky_site_model)
importFrom(beautier,create_inference_model)
importFrom(beautier,create_inv_gamma_distr)
importFrom(beautier,create_jc69_site_model)
importFrom(beautier,create_kappa_1_param)
importFrom(beautier,create_kappa_2_param)
importFrom(beautier,create_lambda_param)
importFrom(beautier,create_laplace_distr)
importFrom(beautier,create_log_normal_distr)
importFrom(beautier,create_m_param)
importFrom(beautier,create_mcmc)
importFrom(beautier,create_mcmc_nested_sampling)
importFrom(beautier,create_mean_param)
importFrom(beautier,create_mrca_prior)
importFrom(beautier,create_mu_param)
importFrom(beautier,create_normal_distr)
importFrom(beautier,create_ns_mcmc)
importFrom(beautier,create_one_div_x_distr)
importFrom(beautier,create_param)
importFrom(beautier,create_param_alpha)
importFrom(beautier,create_param_beta)
importFrom(beautier,create_param_clock_rate)
importFrom(beautier,create_param_kappa_1)
importFrom(beautier,create_param_kappa_2)
importFrom(beautier,create_param_lambda)
importFrom(beautier,create_param_m)
importFrom(beautier,create_param_mean)
importFrom(beautier,create_param_mu)
importFrom(beautier,create_param_rate_ac)
importFrom(beautier,create_param_rate_ag)
importFrom(beautier,create_param_rate_at)
importFrom(beautier,create_param_rate_cg)
importFrom(beautier,create_param_rate_ct)
importFrom(beautier,create_param_rate_gt)
importFrom(beautier,create_param_s)
importFrom(beautier,create_param_scale)
importFrom(beautier,create_param_sigma)
importFrom(beautier,create_poisson_distr)
importFrom(beautier,create_rate_ac_param)
importFrom(beautier,create_rate_ag_param)
importFrom(beautier,create_rate_at_param)
importFrom(beautier,create_rate_cg_param)
importFrom(beautier,create_rate_ct_param)
importFrom(beautier,create_rate_gt_param)
importFrom(beautier,create_rln_clock_model)
importFrom(beautier,create_s_param)
importFrom(beautier,create_scale_param)
importFrom(beautier,create_screenlog)
importFrom(beautier,create_sigma_param)
importFrom(beautier,create_site_model)
importFrom(beautier,create_site_model_from_name)
importFrom(beautier,create_site_model_gtr)
importFrom(beautier,create_site_model_hky)
importFrom(beautier,create_site_model_jc69)
importFrom(beautier,create_site_model_tn93)
importFrom(beautier,create_site_models)
importFrom(beautier,create_site_models_from_names)
importFrom(beautier,create_strict_clock_model)
importFrom(beautier,create_temp_screenlog_filename)
importFrom(beautier,create_temp_tracelog_filename)
importFrom(beautier,create_temp_treelog_filename)
importFrom(beautier,create_test_inference_model)
importFrom(beautier,create_test_mcmc)
importFrom(beautier,create_test_ns_inference_model)
importFrom(beautier,create_test_ns_mcmc)
importFrom(beautier,create_test_screenlog)
importFrom(beautier,create_test_tracelog)
importFrom(beautier,create_test_treelog)
importFrom(beautier,create_tn93_site_model)
importFrom(beautier,create_tracelog)
importFrom(beautier,create_tree_prior)
importFrom(beautier,create_tree_prior_bd)
importFrom(beautier,create_tree_prior_cbs)
importFrom(beautier,create_tree_prior_ccp)
importFrom(beautier,create_tree_prior_cep)
importFrom(beautier,create_tree_prior_yule)
importFrom(beautier,create_tree_priors)
importFrom(beautier,create_treelog)
importFrom(beautier,create_uniform_distr)
importFrom(beautier,create_xml_declaration)
importFrom(beautier,create_yule_tree_prior)
importFrom(beautier,get_remove_dir_fun)
importFrom(beautier,get_remove_hex_fun)
importFrom(beautier,get_replace_dir_fun)
