################################################################################
# Clock model: RLN + tipdates
################################################################################
test_that("#99: RLN + tipdates, v2.6", {
inference_model <- create_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")
),
mparam_id = 1,
dimension = 8,
mean_rate_prior_distr = create_uniform_distr(id = "3")
),
tipdates_filename = get_beautier_path("test_output_0_tipdates.tsv"),
beauti_options = create_beauti_options_v2_6(
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"
)
)
created <- create_beast2_input_from_model(
input_filename = get_beautier_path("test_output_0.fas"),
inference_model = inference_model
)
expected <- readLines(get_beautier_path("rln_tipdates_2_6.xml"))
expected_line <- r"(<operator id="YuleBirthRateScaler.t:test_output_0" spec="ScaleOperator" parameter="@birthRate.t:test_output_0" scaleFactor="0.75" weight="3.0"/>)"
testthat::expect_equal(1, sum(stringr::str_detect(expected, expected_line)))
testthat::expect_equal(1, sum(stringr::str_detect(created, expected_line)))
expected_line <- r"(<prior id="MeanRatePrior.c:test_output_0" name="distribution" x="@ucldMean.c:test_output_0">)"
testthat::expect_equal(1, sum(stringr::str_detect(expected, expected_line)))
testthat::expect_equal(1, sum(stringr::str_detect(created, expected_line)))
expected_line <- r"(<Uniform id="Uniform.3" name="distr" upper="Infinity"/>)"
testthat::expect_equal(1, sum(stringr::str_detect(expected, expected_line)))
testthat::expect_equal(1, sum(stringr::str_detect(created, expected_line)))
expected_line <- r"(<operator id="ucldMeanScaler.c:test_output_0" spec="ScaleOperator" parameter="@ucldMean.c:test_output_0" scaleFactor="0.5" weight="1.0"/>)"
testthat::expect_equal(1, sum(stringr::str_detect(expected, expected_line)))
testthat::expect_equal(1, sum(stringr::str_detect(created, expected_line)))
expected_line <- r"(<operator id="relaxedUpDownOperator.c:test_output_0" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">)"
testthat::expect_equal(1, sum(stringr::str_detect(expected, expected_line)))
testthat::expect_equal(1, sum(stringr::str_detect(created, expected_line)))
if (1 == 2) {
compare_lines(
lines = created,
expected = expected,
created_lines_filename = "~/created.xml",
expected_lines_filename = "~/expected.xml"
)
}
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("rln_uclstdev_beta_2_4.xml", {
created <- create_beast2_input_from_model(
input_filename = get_beautier_path("test_output_0.fas"),
inference_model = create_inference_model(
clock_model = create_rln_clock_model(
ucldstdev_distr = create_beta_distr(
id = 0,
alpha = create_alpha_param(id = 4, value = "2.0"),
beta = create_beta_param(id = 5, value = "2.0")
),
mparam_id = 1
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
)
expected <- readLines(get_beautier_path("rln_uclstdev_beta_2_4.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected,
created_lines_filename = "~/created.xml",
expected_lines_filename = "~/expected.xml"
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
################################################################################
# Clock model: strict
################################################################################
test_that("strict_clock_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("strict_clock_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("strict_clock_rate_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
clock_model = create_strict_clock_model(
clock_rate_param = create_clock_rate_param(
id = "test_output_0.fas",
value = "0.5"
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("strict_clock_rate_0_5_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
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