scripts/test_brute_force_2_unlinked.R

In richelbilderbeek/babetter: Check babette

test_that("all combinations, 2 model, unlinked", {

  skip("Support for 2 models deprecated")
  input_filenames <- beautier::get_paths(
    c("anthus_aco.fas", "anthus_nd2.fas"))

  n_fail <- 0

  # Crown ages estimated
  for (site_model_1 in beautier::create_site_models()) {
    for (site_model_2 in beautier::create_site_models()) {
      for (clock_model_1 in beautier::create_clock_models()) {
        for (clock_model_2 in beautier::create_clock_models()) {
          for (tree_prior in beautier::create_tree_priors()) {
            cat(".")
            output_filename <- "~/invalid.xml"
            create_beast2_input_file(
              input_filename = input_filenames,
              site_models = list(site_model_1, site_model_2),
              clock_models = list(clock_model_1, clock_model_2),
              tree_priors = list(tree_prior, tree_prior),
              output_filename = output_filename
            )
            is_ok <- beastier::is_beast2_input_file(output_filename)
            if (!is_ok) {
              print(paste(site_model_1$name, site_model_2$name,
                clock_model_1$name, clock_model_2$name, tree_prior$name))
              beautier::is_beast2_input_file(output_filename,
                verbose = TRUE)
              n_fail <- n_fail + 1
            }
          }
        }
      }
    }
  }

  # Crown ages all fixed
  for (site_model_1 in beautier::create_site_models()) {
    for (site_model_2 in beautier::create_site_models()) {
      for (clock_model_1 in beautier::create_clock_models()) {
        for (clock_model_2 in beautier::create_clock_models()) {
          for (tree_prior in beautier::create_tree_priors()) {
            if (runif(n = 1) < 0.9) next
            cat(".")
            output_filename <- "~/invalid.xml"
            create_beast2_input_file(
              input_filename = input_filenames,
              site_models = list(site_model_1, site_model_2),
              clock_models = list(clock_model_1, clock_model_2),
              tree_priors = list(tree_prior, tree_prior),
              output_filename = output_filename
            )
            is_ok <- beastier::is_beast2_input_file(output_filename)
            if (!is_ok) {
              print(paste(site_model_1$name, site_model_2$name,
                clock_model_1$name, clock_model_2$name, tree_prior$name))
              beautier::is_beast2_input_file(output_filename,
                verbose = TRUE)
              n_fail <- n_fail + 1
            }
          }
        }
      }
    }
  }

  quit(status = n_fail, save = "no")
})