tests/testthat/test-create_beast2_beast_xml.R

In richelbilderbeek/beautier: 'BEAUti' from R

test_that("use, v2.6", {
  created <- create_beast2_beast_xml(
    create_beauti_options_v2_6()
  )
  expected <- r"(<beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.6">)"
  expect_equal(created, expected)

})

test_that("use, v2.6.2", {

  beauti_options <- create_beauti_options_v2_6(
    namespace = paste0(
      "beast.core:beast.evolution.alignment:",
      "beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:",
      "beast.evolution.operators:beast.evolution.sitemodel:",
      "beast.evolution.substitutionmodel:beast.evolution.likelihood"
    )
  )
  created <- create_beast2_beast_xml(
    beauti_options
  )
  expected <- paste0(
    "<beast ",
    "beautitemplate='Standard' ",
    "beautistatus='' ",
    "namespace=\"beast.core:beast.evolution.alignment:",
    "beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:",
    "beast.evolution.operators:beast.evolution.sitemodel:",
    "beast.evolution.substitutionmodel:beast.evolution.likelihood\" ",
    "required=\"\" ",
    "version=\"2.6\">"
  )
  expect_equal(created, expected)
})

test_that("use, v2.6, with status", {

  beauti_options <- create_beauti_options_v2_6(
    namespace = paste0(
      "beast.core:beast.evolution.alignment:",
      "beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:",
      "beast.evolution.operators:beast.evolution.sitemodel:",
      "beast.evolution.substitutionmodel:beast.evolution.likelihood"
    ),
    status = "noAutoSetClockRate"
  )
  created <- create_beast2_beast_xml(
    beauti_options
  )
  expected <- paste0(
    "<beast ",
    "beautitemplate='Standard' ",
    "beautistatus='noAutoSetClockRate' ",
    "namespace=\"beast.core:beast.evolution.alignment:",
    "beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:",
    "beast.evolution.operators:beast.evolution.sitemodel:",
    "beast.evolution.substitutionmodel:beast.evolution.likelihood\" ",
    "required=\"\" ",
    "version=\"2.6\">"
  )
  expect_equal(created, expected)
})