#' Function to create a set of BEAST2 options.
#'
#' These BEAST2 options are the R equivalent of the command-line options.
#' @inheritParams default_params_doc
#' @return a BEAST2 options structure,
#' which is a \link{list} of all function arguments,
#' of which all elements are checked (by \link{check_beast2_options})
#' @examples
#' check_empty_beaustier_folders()
#'
#' beast2_options <- create_beast2_options()
#' check_beast2_options(beast2_options)
#'
#' check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_options <- function(
input_filename = create_temp_input_filename(),
output_state_filename = create_temp_state_filename(),
rng_seed = NA,
n_threads = NA,
use_beagle = FALSE,
overwrite = TRUE,
beast2_path = get_default_beast2_path(),
verbose = FALSE
) {
beast2_options <- list(
input_filename = input_filename,
output_state_filename = output_state_filename,
rng_seed = rng_seed,
n_threads = n_threads,
use_beagle = use_beagle,
overwrite = overwrite,
beast2_path = beast2_path,
verbose = verbose
)
check_beast2_options(beast2_options)
beast2_options
}
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