R/gamma_distr_to_xml.R

In richelbilderbeek/beastscriptr: 'BEAUti' from R

#' Internal function
#'
#' Converts a gamma distribution to XML
#' @inheritParams default_params_doc
#' @return the distribution as XML text
#' @author Richèl J.C. Bilderbeek
#' @examples
#' check_empty_beautier_folder()
#'
#' # gamma distribution must be initialized
#' gamma_distr_to_xml(
#'   gamma_distr = create_gamma_distr(
#'     id = "0",
#'     alpha = create_alpha_param(id = "2", value = "0.5396"),
#'     beta = create_beta_param(id = "3", value = "0.3819")
#'   )
#' )
#'
#' check_empty_beautier_folder()
#' @export
gamma_distr_to_xml <- function(
  gamma_distr,
  beauti_options = create_beauti_options()
) {
  # Don't be smart yet
  distr <- gamma_distr

  check_true(is_gamma_distr(distr))
  check_beauti_options(beauti_options)
  id <- distr$id
  check_true(is_id(id))

  text <- NULL
  text <- c(
    text,
    paste0("<Gamma ", "id=\"Gamma.", id, "\" name=\"distr\">")
  )
  text <- c(text,
    indent(
      alpha_parameter_to_xml(
        alpha_parameter = distr$alpha,
        beauti_options = beauti_options
      )
    )
  )
  text <- c(text,
    indent(
      parameter_to_xml(
        parameter = distr$beta,
        beauti_options = beauti_options
      )
    )
  )
  text <- c(text, paste0("</Gamma>"))
  text
}