R/check_beast2_options.R

In richelbilderbeek/beastier: Call 'BEAST2'

#' Check if the \code{beast2_options} is a valid BEAST2 options object.
#'
#' Calls \code{stop} if the BEAST2 option object is invalid
#' @inheritParams default_params_doc
#' @return nothing
#' Will \code{stop} if the BEAST2 option object is invalid
#' @seealso Use \link{create_beast2_options} to create a valid
#'   BEAST2 options object
#' @examples
#' check_empty_beaustier_folders()
#'
#' check_beast2_options(create_beast2_options())
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
check_beast2_options <- function(
  beast2_options
) {
  check_beast2_options_names(beast2_options)
  check_beast2_options_data_types(beast2_options)
  # Do not check if the BEAST2 path already/still exist.
  # It shouldn't be checked by here, only when actually running BEAST2.
  # By doing so, data with beast2_options can be analysed on different computers
  check_beast2_options_filenames_differ(beast2_options)
}

#' Check if the \code{beast2_options}, which is a list,
#' has all the elements needed.
#'
#' Calls \code{stop} if not.
#' @inheritParams default_params_doc
#' @return nothing
#' @seealso Use \link{check_beast2_options} to check
#'   the entire \code{beast2_options} object
#' @author Richèl J.C. Bilderbeek
#' @export
check_beast2_options_names <- function( # nolint long function name indeed, which is fine for an internal function
  beast2_options
) {
  argument_names <- c(
    "input_filename",
    "output_state_filename",
    "rng_seed", "n_threads", "use_beagle", "overwrite",
    "beast2_path", "verbose"
  )
  for (arg_name in argument_names) {
    if (!arg_name %in% names(beast2_options)) {
      stop(
        "'", arg_name, "' must be an element of an 'beast2_options'. ",
        "Tip: use 'create_beast2_options'"
      )
    }
  }
}

#' Check if the \code{beast2_options}, which is a list,
#' has all elements of the right data types
#'
#' Calls \code{stop} if not.
#' @inheritParams default_params_doc
#' @return nothing
#' @seealso Use \link{check_beast2_options} to check
#'   the entire \code{beast2_options} object
#' @author Richèl J.C. Bilderbeek
#' @export
check_beast2_options_data_types <- function( # nolint long function name indeed, which is fine for an internal function
  beast2_options
) {
  check_true(beautier::is_one_string(beast2_options$input_filename))
  check_true(beautier::is_one_string(beast2_options$output_state_filename))
  check_rng_seed(beast2_options$rng_seed)
  check_n_threads(beast2_options$n_threads)
  if (!beautier::is_one_bool(beast2_options$use_beagle)) {
    stop("'use_beagle' must be one boolean")
  }
  if (!beautier::is_one_bool(beast2_options$overwrite)) {
    stop("'overwrite' must be one boolean")
  }
  check_true(beautier::is_one_string(beast2_options$beast2_path))
  if (!beautier::is_one_bool(beast2_options$verbose)) {
    stop("'verbose' must be one boolean")
  }
  # Isse 60, Issue #60
  # Hi Jeff, I suggest to add 'check_stack_size_kb' here.
  # I have written the tests for you at 'test-check_stack_size_kb' :-)
}

#' Check if the filenames in \code{beast2_options} differ
#'
#' Calls \code{stop} if not.
#' @inheritParams default_params_doc
#' @return nothing
#' @seealso Use \link{check_beast2_options} to check
#'   the entire \code{beast2_options} object
#' @author Richèl J.C. Bilderbeek
#' @export
check_beast2_options_filenames_differ <- function( # nolint long function name indeed, which is fine for an internal function
  beast2_options
) {
  if (beast2_options$input_filename == beast2_options$output_state_filename) {
    stop("'input_filename' and 'output_state_filename' must differ")
  }
}