R/get_tree_prior_n_params.R

In beautier: 'BEAUti' from R

#' Get the number of parameters a tree prior has
#' @param tree_prior a tree_prior,
#'   as created by \code{\link{create_tree_prior}}
#' @return the number of parameters a tree prior has
#' @author Richèl J.C. Bilderbeek
#' @examples
#' check_empty_beautier_folder()
#'
#' # birth_rate_distr is uniform, which has zero parameters
#' # death_rate_distr is uniform, which has zero parameters
#' get_tree_prior_n_params(create_bd_tree_prior())
#'
#' # no distributions, no parameters
#' get_tree_prior_n_params(create_cbs_tree_prior())
#'
#' # pop_size_distr is 1/x, which has zero parameters
#' get_tree_prior_n_params(create_ccp_tree_prior())
#'
#' # pop_size_distr is 1/x, which has zero parameters
#' # growth_rate_distr is Laplace, which has two parameters
#' get_tree_prior_n_params(create_cep_tree_prior())
#'
#' # birth_rate_distr is uniform, which has zero parameters
#' get_tree_prior_n_params(create_yule_tree_prior())
#'
#' check_empty_beautier_folder()
#' @export
get_tree_prior_n_params <- function(
  tree_prior
) {
  if (!is_tree_prior(tree_prior)) {
    stop("'tree_prior' must be a tree prior")
  }
  if (is_bd_tree_prior(tree_prior)) {
    return(
      get_distr_n_params(tree_prior$birth_rate_distr) +
        get_distr_n_params(tree_prior$death_rate_distr)
    )
  } else if (is_cbs_tree_prior(tree_prior)) {
    return(0)
  } else if (is_ccp_tree_prior(tree_prior)) {
    return(get_distr_n_params(tree_prior$pop_size_distr))
  } else if (is_cep_tree_prior(tree_prior)) {
    return(
      get_distr_n_params(tree_prior$pop_size_distr) +
        get_distr_n_params(tree_prior$growth_rate_distr)
    )
  } else {
    check_true(is_yule_tree_prior(tree_prior))
    return(
      get_distr_n_params(tree_prior$birth_rate_distr)
    )
  }
}