tests/testthat/test-create_beast2_input.R

In richelbilderbeek/beautier: 'BEAUti' from R

test_that("use", {

  expect_silent(
    create_beast2_input(
      input_filename = get_fasta_filename()
    )
  )

})

test_that("use with calibration node", {

  fasta_filename <- get_fasta_filename()
  expect_silent(
    create_beast2_input(
      input_filename = fasta_filename,
      mrca_prior = create_mrca_prior(
        alignment_id = get_alignment_id(fasta_filename),
        taxa_names = get_taxa_names(fasta_filename)
      )
    )
  )

})

test_that("Run MRCA, need one branchRateModel, beautier issue #26", {

  fasta_filename <- get_fasta_filename()
  lines <- create_beast2_input(
    input_filename = fasta_filename,
    site_model = create_jc69_site_model(),
    clock_model = create_rln_clock_model(),
    tree_prior = create_cep_tree_prior(),
    mrca_prior = create_mrca_prior(
      alignment_id = get_alignment_id(fasta_filename),
      taxa_names = get_taxa_names(fasta_filename),
      is_monophyletic = TRUE
    )
  )
  expect_equal(
    1,
    sum(grepl(x = lines, pattern = " *<branchRateModel.*"))
  )
})

test_that("Run with default MRCA, beautier issue #75", {

  expect_silent(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      site_model = create_jc69_site_model(),
      clock_model = create_rln_clock_model(),
      tree_prior = create_cep_tree_prior(),
      mrca_prior = create_mrca_prior()
    )
  )
})

test_that("abuse: one alignment", {

  expect_silent(
    create_beast2_input(
      input_filename = get_fasta_filename()
    )
  )

  # 1 input_filename
  expect_error(
    create_beast2_input(
      input_filename = "nonexisting" # Error
    ),
    "'input_filename' not found"
  )
  # 2 site_model
  expect_error(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      site_model = "nonsense"
    ),
    "'site_model' must be a valid site model"
  )
  # 3 clock_models
  expect_error(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      clock_model = "nonsense"
    ),
    "'clock_model' must be a valid clock model"
  )
  # 4 tree_prior
  expect_error(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      tree_prior = "nonsense"
    ),
    "'tree_prior' must be a valid tree prior"
  )
  # mrca_prior
  expect_error(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      mrca_prior = "nonsense"
    ),
    "'mrca_prior' must be a valid MRCA prior"
  )
  # 5 mcmc, tested in-depth by 'check_mcmc'
  expect_error(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      mcmc = "nonsense"
    ),
    "mcmc"
  )

  # 6 beauti_options
  expect_error(
    create_beast2_input(
      input_filename = get_fasta_filename(),
      beauti_options = "nonsense"
    ),
    "'beauti_options' must be a valid BEAUti options"
  )
  # Higher-level abuse
  # Tested by 'check_file_and_model_agree'
})

test_that("abuse: two alignments", {

  input_filenames <- beautier::get_beautier_paths(
    c("anthus_aco.fas", "anthus_nd2.fas")
  )
  ids <- get_alignment_ids(input_filenames)

  # Two filenames, one site model
  expect_error(
    create_beast2_input(
      input_filename = input_filenames
    ),
    "Must use one alignment, site model, clock model and tree prior"
  )
})