test_that("RLN", {
expected <- c(
"<distribution id=\"prior\" spec=\"util.CompoundDistribution\">",
" <distribution id=\"YuleModel.t:test_output_0\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:test_output_0\" tree=\"@Tree.t:test_output_0\"/>", # nolint XML
" <prior id=\"YuleBirthRatePrior.t:test_output_0\" name=\"distribution\" x=\"@birthRate.t:test_output_0\">", # nolint XML
" <Uniform id=\"Uniform.1\" name=\"distr\" upper=\"Infinity\"/>", # nolint this is no absolute path
" </prior>",
" <prior id=\"ucldStdevPrior.c:test_output_0\" name=\"distribution\" x=\"@ucldStdev.c:test_output_0\">", # nolint XML
" <Gamma id=\"Gamma.0\" name=\"distr\">",
" <parameter id=\"RealParameter.2\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.3\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
" </prior>",
"</distribution>"
)
inference_model <- init_inference_model(
input_filename = get_fasta_filename(),
inference_model = create_test_inference_model(
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
clock_model = create_rln_clock_model(
ucldstdev_distr = create_gamma_distr(
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 = 100),
mparam_id = 1
)
)
)
created <- create_beast2_input_distr_prior(
inference_model = inference_model
)
expect_equal(created, expected)
})
test_that("Yule", {
expected <- c(
"<distribution id=\"prior\" spec=\"util.CompoundDistribution\">",
" <distribution id=\"YuleModel.t:test_output_0\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:test_output_0\" tree=\"@Tree.t:test_output_0\"/>", # nolint long line indeed
" <prior id=\"YuleBirthRatePrior.t:test_output_0\" name=\"distribution\" x=\"@birthRate.t:test_output_0\">", # nolint long line indeed
" <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>",
" </prior>",
"</distribution>"
)
inference_model <- init_inference_model(
input_filename = get_fasta_filename(),
inference_model = create_test_inference_model()
)
created <- create_beast2_input_distr_prior(
inference_model = inference_model
)
expect_equal(created, expected)
})
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