R/create_test_mcmc.R

In richelbilderbeek/beastscriptr: 'BEAUti' from R

#' Create an MCMC configuration for testing.
#' @inheritParams default_params_doc
#' @return an MCMC configuration
#' @seealso
#' Use \code{\link{create_mcmc}} to create a default BEAST2 MCMC
#' @author Richèl J.C. Bilderbeek
#' @examples
#' if (is_on_ci()) {
#'
#'   # Create an MCMC chain with 50 states
#'   mcmc <- create_test_mcmc()
#'
#'   beast2_input_file <- get_beautier_tempfilename()
#'   create_beast2_input_file(
#'     get_fasta_filename(),
#'     beast2_input_file,
#'     mcmc = mcmc
#'   )
#'   file.remove(beast2_input_file)
#'
#'   remove_beautier_folder()
#' }
#' @export
create_test_mcmc <- function(
  chain_length = 3000,
  store_every = 1000,
  pre_burnin = 0,
  n_init_attempts = 10,
  sample_from_prior = FALSE,
  tracelog = create_test_tracelog(),
  screenlog = create_test_screenlog(),
  treelog = create_test_treelog()
) {
  create_mcmc(
    chain_length = chain_length,
    store_every = store_every,
    pre_burnin = pre_burnin,
    n_init_attempts = n_init_attempts,
    sample_from_prior = sample_from_prior,
    tracelog = tracelog,
    screenlog = screenlog,
    treelog = treelog
  )
}