R/create_test_pff_gen_experiment.R

In richelbilderbeek/peregrine: Work With The Groninger Peregrine Computer Cluster

#' Creates a Peregrine-friendly generative experiment for testing
#' @inheritParams default_params_doc
#' @author Richèl J.C. Bilderbeek
#' @export
create_test_pff_gen_experiment <- function(
  mrca_prior = beautier::create_mrca_prior(
    mrca_distr = beautier::create_normal_distr(
      mean = 15.0,
      sigma = 0.001
    ),
    is_monophyletic = TRUE
  ),
  mcmc = peregrine::create_pff_mcmc(
    chain_length = 2000,
    store_every = 1000
  ),
  beast2_options = peregrine::create_pff_beast2_options()
) {
  experiment <- pirouette::create_test_gen_experiment(
    inference_model = beautier::create_inference_model(
      mrca_prior = mrca_prior,
      mcmc = mcmc
    ),
    beast2_options = beast2_options
  )
  experiment$errors_filename <- peregrine::get_pff_tempfile(
    pattern = "errors_", fileext = ".csv"
  )
  experiment
}