tests/testthat/test-gamma_site_model_to_xml_prior_distr.R

In richelbilderbeek/beastscriptr: 'BEAUti' from R

test_that("use", {
  expect_silent(
    gamma_site_model_to_xml_prior_distr(
      create_inference_model(
        site_model = create_jc69_site_model(id = 1),
        beauti_options = create_beauti_options_v2_4()
      )
    )
  )
  expect_silent(
    gamma_site_model_to_xml_prior_distr(
      create_inference_model(
        site_model = create_jc69_site_model(id = 1),
        beauti_options = create_beauti_options_v2_6()
      )
    )
  )

  expect_silent(
    gamma_site_model_to_xml_prior_distr(
      create_inference_model(
        site_model = create_hky_site_model(
          id = 1,
          kappa_prior_distr = create_uniform_distr(id = 2)
        ),
        beauti_options = create_beauti_options_v2_4()
      )
    )
  )
  expect_silent(
    gamma_site_model_to_xml_prior_distr(
      create_inference_model(
        site_model = create_hky_site_model(
          id = 1,
          kappa_prior_distr = create_uniform_distr(id = 2)
        ),
        beauti_options = create_beauti_options_v2_6()
      )
    )
  )
})

test_that("use", {
  # v2.6 has a FrequenciesPrior section (see below), where v2.4 does not.
  freq_prior_regex <- "FrequenciesPrior.s"
  expect_equal(
    0,
    length(
      stringr::str_subset(
        readr::read_lines(get_beautier_path("hky_2_4.xml")),
        freq_prior_regex
      )
    )
  )
  expect_equal(
    1,
    length(
      stringr::str_subset(
        readr::read_lines(get_beautier_path("hky_2_6.xml")),
        freq_prior_regex
      )
    )
  )

  site_model <- create_hky_site_model(
    id = 1,
    kappa_prior_distr = create_uniform_distr(id = 2)
  )

  expect_equal(
    0,
    length(
      stringr::str_subset(
        gamma_site_model_to_xml_prior_distr(
          create_inference_model(
            site_model = site_model,
            beauti_options = create_beauti_options_v2_4()
          )
        ),
        pattern = freq_prior_regex
      )
    )
  )
  expect_equal(
    1,
    length(
      stringr::str_subset(
        gamma_site_model_to_xml_prior_distr(
          create_inference_model(
            site_model = site_model,
            beauti_options = create_beauti_options_v2_6()
          )
        ),
        pattern = freq_prior_regex
      )
    )
  )
})