R/beastier-package.R

In beastier: Call 'BEAST2'

#' \code{beastier}: A package to call BEAST2.
#'
#' \code{beastier} allows to call BEAST2, a popular
#' Bayesian phylogenetics tool, using
#' an R interface. 'beastier' closely follows the interface
#' of BEAST2, including its default settings.
#'
#' @examples
#' check_empty_beaustier_folders()
#'
#' beast2_options <- create_beast2_options(
#'   input_filename = get_beastier_path("2_4.xml")
#' )
#'
#' if (is_beast2_installed() && beautier::is_on_ci()) {
#'   run_beast2_from_options(beast2_options)
#'   file.remove(beast2_options$output_state_filename)
#'   remove_beaustier_folders()
#' }
#' @seealso
#' These are packages associated with \code{beastier}:
#' \itemize{
#'   \item{
#'     The package \code{beautier} can create
#'     BEAST2 input files from R
#'   }
#'   \item{
#'     The package \code{tracerer} can parse
#'     BEAST2 output files from R
#'   }
#'   \item{
#'     The package \code{babette} combines the
#'     functionality of \code{beautier},
#'     \code{beastier} and \code{tracerer}
#'     into a single workflow
#'   }
#' }
#'
#' @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
#' @author Richèl J.C. Bilderbeek
#' @keywords internal
"_PACKAGE"

## usethis namespace: start
#' @import rlang
## usethis namespace: end
NULL