R/create_inference_conditions.R

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

#' @title Create the inference conditions
#' @description Create the parameters to determine how to choose
#' a model for the inference
#' @inheritParams default_params_doc
#' @return the inference conditions
#' @author Giovanni Laudanno, Richèl J.C. Bilderbeek
#' @examples
#' if (beautier::is_on_ci()) {
#'
#'   # Create the inference conditions parameter set
#'   if (rappdirs::app_dir()$os != "win") {
#'     # it does not work on Windows
#'
#'     # Model type can be 'generative' or 'candidate'
#'     model_type <- "candidate"
#'     # Run condition can be 'always' or 'best_candidate'
#'     run_if <- "best_candidate"
#'     # Evidence (aka marginal likelihood) can be measured yes or no
#'     do_measure_evidence <- TRUE
#'   } else {
#'     # Model type can be 'generative' or 'candidate'
#'     model_type <- "generative"
#'     # Run condition can be 'always' or 'best_candidate'
#'     run_if <- "always"
#'     # Evidence (aka marginal likelihood) can be measured yes or no
#'     do_measure_evidence <- FALSE
#'   }
#'
#'   inference_conditions <- create_inference_conditions(
#'     model_type = model_type,
#'     run_if = run_if,
#'     do_measure_evidence = do_measure_evidence
#'   )
#'
#'   # Using the inference conditions, create a testing candidate experiment
#'   experiment <- create_test_cand_experiment(
#'     inference_conditions = inference_conditions
#'   )
#'
#'   evidence_filename <- NA
#'   if (do_measure_evidence) evidence_filename <- get_temp_evidence_filename()
#'
#'   # Use the experiment to create the full pirouette parameter set
#'   pir_params <- create_pir_params(
#'     alignment_params = create_test_alignment_params(),
#'     experiments = list(experiment),
#'     evidence_filename = evidence_filename
#'   )
#'
#'   # Run that experiment on a continuous integration service,
#'   # only when BEAST2 is installed
#'   if (beautier::is_on_ci() &&
#'     beastier::is_beast2_installed() &&
#'     is_beast2_ns_pkg_installed()
#'   ) {
#'     pir_out <- pir_run(
#'       phylogeny = ape::read.tree(text = "((A:2, B:2):1, C:3);"),
#'       pir_params = pir_params
#'     )
#'     pir_plot(pir_out)
#'   }
#' }
#' @export
create_inference_conditions <- function(
  model_type = "generative",
  run_if = "always",
  do_measure_evidence = FALSE,
  os = rappdirs::app_dir()$os
) {
  beastier::check_os(os)
  if (os == "win" && do_measure_evidence == TRUE) {
    stop("This configuration cannot run on windows")
  }
  inference_conditions <- list(
    model_type = model_type,
    run_if = run_if,
    do_measure_evidence = do_measure_evidence
  )
  pirouette::check_inference_conditions(inference_conditions)
  inference_conditions
}