test_that("strict", {
expected <- c(
"<distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">", # nolint XML
" <distribution id=\"treeLikelihood.test_output_0\" spec=\"ThreadedTreeLikelihood\" data=\"@test_output_0\" tree=\"@Tree.t:test_output_0\">", # nolint XML
" <siteModel id=\"SiteModel.s:test_output_0\" spec=\"SiteModel\">", # nolint XML
" <parameter id=\"mutationRate.s:test_output_0\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>", # nolint XML
" <parameter id=\"gammaShape.s:test_output_0\" estimate=\"false\" name=\"shape\">1.0</parameter>", # nolint XML
" <parameter id=\"proportionInvariant.s:test_output_0\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>", # nolint XML
" <substModel id=\"JC69.s:test_output_0\" spec=\"JukesCantor\"/>", # nolint XML
" </siteModel>",
" <branchRateModel id=\"StrictClock.c:test_output_0\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">", # nolint XML
" <parameter id=\"clockRate.c:test_output_0\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>", # nolint XML
" </branchRateModel>",
" </distribution>",
"</distribution>"
)
inference_model <- init_inference_model(
input_filename = get_fasta_filename(),
inference_model = create_inference_model(
beauti_options = create_beauti_options_v2_4()
)
)
created <- create_beast2_input_distr_lh(
inference_model = inference_model
)
expect_equal(created, expected)
})
test_that("RLN, v2.4", {
expected <- unindent(
remove_empty_lines(
extract_xml_section_from_lines(
lines = readr::read_lines(get_beautier_path("rln_2_4.xml")),
section = "distribution"
)
)[14:29]
)
inference_model <- init_inference_model(
input_filename = get_fasta_filename(),
inference_model = create_inference_model(
clock_model = create_rln_clock_model(
ucldstdev_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 2, value = "0.5396"),
beta = create_beta_param(id = 3, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 1),
mparam_id = 1
),
beauti_options = create_beauti_options_v2_4()
)
)
created <- create_beast2_input_distr_lh(
inference_model = inference_model
)
expect_equal(created, expected)
})
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