R/create_razzo_cand_experiments.R

In richelbilderbeek/razzo: The Error if Nature is MBD

#' Create the candidate experiments
#'
#' It needs to know what the generative experiment is,
#' to exclude it from the created candidate experiments.
#' @inheritParams default_params_doc
#' @param gen_experiment the generative experiment
#' @return a list of experiments
#' @author Richèl J.C. Bilderbeek
#' @export
create_razzo_cand_experiments <- function(
  gen_experiment,
  folder_name = peregrine::get_pff_tempfile(),
  rng_seed = 1
) {
  testit::assert(gen_experiment$inference_conditions$model_type == "generative")

  cand_experiments <- NA

  cand_experiments <- pirouette::create_all_experiments(
    site_models = list(
      beautier::create_jc69_site_model(),
      beautier::create_hky_site_model()
    ),
    clock_models = list(beautier::create_strict_clock_model()),
    tree_priors = list(
      beautier::create_yule_tree_prior(),
      beautier::create_bd_tree_prior()
    ),
    exclude_model = gen_experiment$inference_model
  )

  testit::assert(!beautier::is_one_na(cand_experiments))

  # Adapt to razzo
  for (i in seq_along(cand_experiments)) {
    cand_experiments[[i]]$inference_model$mcmc <- razzo::get_razzo_mcmc(
      model_type = "candidate",
      folder_name = folder_name
    )
    cand_experiments[[i]]$est_evidence_mcmc <-
      razzo::create_razzo_ns_mcmc(
        folder_name =  folder_name,
        model_type = "candidate",
        index = i
      )
    cand_experiments[[i]]$inference_model$mrca_prior <-
      razzo::create_razzo_mrca_prior()
    cand_experiments[[i]]$beast2_options <-
      razzo::create_razzo_beast2_options(
        model_type = "candidate",
        folder_name = folder_name,
        rng_seed = rng_seed
      )
  }
  for (experiment in cand_experiments) {
    testit::assert(experiment$inference_model$mcmc$tracelog$filename ==
        file.path(folder_name, "mbd_best.log")
    )
    testit::assert(
      experiment$inference_model$mcmc$tracelog$log_every ==
      get_razzo_mcmc_store_every()
    )
    testit::assert(
      experiment$inference_model$mcmc$treelog$log_every ==
      get_razzo_mcmc_store_every()
    )
  }
  cand_experiments
}