context("clock_models_to_xml_prior_distr")
################################################################################
# Two alignments, unlinked clock models
################################################################################
test_that("RLN RLN", {
expected <- c(
"<prior id=\"ucldStdevPrior.c:anthus_aco\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco\">", # nolint XML
" <Gamma id=\"Gamma.6\" name=\"distr\">",
" <parameter id=\"RealParameter.21\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.22\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd2\">", # nolint XML
" <Gamma id=\"Gamma.14\" name=\"distr\">",
" <parameter id=\"RealParameter.64\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.65\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.14\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_rln_clock_model(
id = "anthus_aco",
ucldstdev_distr = create_gamma_distr(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = "irrelevant")
),
create_rln_clock_model(
id = "anthus_nd2",
ucldstdev_distr = create_gamma_distr(
id = 14,
alpha = create_alpha_param(id = 64, value = "0.5396"),
beta = create_beta_param(id = 65, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 14)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("RLN strict", {
expected <- c(
"<prior id=\"ClockPrior.c:anthus_nd2\" name=\"distribution\" x=\"@clockRate.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_aco\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco\">", # nolint XML
" <Gamma id=\"Gamma.6\" name=\"distr\">",
" <parameter id=\"RealParameter.21\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.22\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_rln_clock_model(
id = "anthus_aco",
ucldstdev_distr = create_gamma_distr(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = "irrelevant")
),
create_strict_clock_model(
id = "anthus_nd2",
clock_rate_distr = create_uniform_distr(id = 3)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict RLN", {
expected <- c(
"<prior id=\"ucldStdevPrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd2\">", # nolint XML
" <Gamma id=\"Gamma.0\" name=\"distr\">",
" <parameter id=\"RealParameter.3\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.4\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.6\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_strict_clock_model(
id = "anthus_aco",
clock_rate_distr = create_uniform_distr(id = 6)
),
create_rln_clock_model(
id = "anthus_nd2",
ucldstdev_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 3, value = "0.5396"),
beta = create_beta_param(id = 4, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 6)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict strict", {
expected <- c(
"<prior id=\"ClockPrior.c:anthus_nd2\" name=\"distribution\" x=\"@clockRate.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_strict_clock_model(
id = "anthus_aco",
clock_rate_distr = create_uniform_distr(id = "irrelevant")
),
create_strict_clock_model(
id = "anthus_nd2",
clock_rate_distr = create_uniform_distr(id = 3)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
################################################################################
# Two alignments, linked clock models
################################################################################
test_that("RLN shared", {
expected <- c(
"<prior id=\"ucldStdevPrior.c:anthus_aco\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco\">", # nolint XML
" <Gamma id=\"Gamma.6\" name=\"distr\">", # nolint XML
" <parameter id=\"RealParameter.21\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.22\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>", # nolint XML
"</prior>" # nolint XML
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_rln_clock_model(
id = "anthus_aco",
ucldstdev_distr = create_gamma_distr(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
)
),
create_rln_clock_model(
id = "anthus_aco"
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict shared", {
testthat::expect_true(
is.null(
beautier:::clock_models_to_xml_prior_distr(
list(
create_strict_clock_model(id = "anthus_aco"),
create_strict_clock_model(id = "anthus_aco")
)
)
)
)
})
################################################################################
# Four alignments
################################################################################
test_that("RLN RLN RLN RLN", {
expected <- c(
"<prior id=\"ucldStdevPrior.c:anthus_aco\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco\">", # nolint XML
" <Gamma id=\"Gamma.6\" name=\"distr\">",
" <parameter id=\"RealParameter.21\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.22\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
# Note there is no 'MeanRatePrior.c' for the first element
"<prior id=\"ucldStdevPrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd2\">", # nolint XML
" <Gamma id=\"Gamma.14\" name=\"distr\">",
" <parameter id=\"RealParameter.64\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.65\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.14\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd3\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd3\">", # nolint XML
" <Gamma id=\"Gamma.16\" name=\"distr\">",
" <parameter id=\"RealParameter.87\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.88\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd3\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd3\">", # nolint XML
" <Uniform id=\"Uniform.23\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd4\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd4\">", # nolint XML
" <Gamma id=\"Gamma.17\" name=\"distr\">",
" <parameter id=\"RealParameter.91\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.92\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd4\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd4\">", # nolint XML
" <Uniform id=\"Uniform.27\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_rln_clock_model(
id = "anthus_aco",
ucldstdev_distr = create_gamma_distr(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 1),
mparam_id = 1
),
create_rln_clock_model(
id = "anthus_nd2",
ucldstdev_distr = create_gamma_distr(
id = 14,
alpha = create_alpha_param(id = 64, value = "0.5396"),
beta = create_beta_param(id = 65, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 14),
mparam_id = 1
),
create_rln_clock_model(
id = "anthus_nd3",
ucldstdev_distr = create_gamma_distr(
id = 16,
alpha = create_alpha_param(id = 87, value = "0.5396"),
beta = create_beta_param(id = 88, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 14),
mparam_id = 1
),
create_rln_clock_model(
id = "anthus_nd4",
ucldstdev_distr = create_gamma_distr(
id = 17,
alpha = create_alpha_param(id = 91, value = "0.5396"),
beta = create_beta_param(id = 92, value = "0.3819")
),
mean_rate_prior_distr = create_uniform_distr(id = 27),
mparam_id = 1
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict strict strict strict", {
expected <- c(
"<prior id=\"ClockPrior.c:anthus_nd4\" name=\"distribution\" x=\"@clockRate.c:anthus_nd4\">", # nolint XML
" <Uniform id=\"Uniform.24\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ClockPrior.c:anthus_nd3\" name=\"distribution\" x=\"@clockRate.c:anthus_nd3\">", # nolint XML
" <Uniform id=\"Uniform.20\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ClockPrior.c:anthus_nd2\" name=\"distribution\" x=\"@clockRate.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_strict_clock_model(
id = "anthus_aco",
clock_rate_distr = create_uniform_distr(id = "irrelevant")
),
create_strict_clock_model(
id = "anthus_nd2",
clock_rate_distr = create_uniform_distr(id = 3)
),
create_strict_clock_model(
id = "anthus_nd3",
clock_rate_distr = create_uniform_distr(id = 20)
),
create_strict_clock_model(
id = "anthus_nd4",
clock_rate_distr = create_uniform_distr(id = 24)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("RLN RLN strict strict", {
expected <- c(
"<prior id=\"ClockPrior.c:anthus_nd4\" name=\"distribution\" x=\"@clockRate.c:anthus_nd4\">", # nolint XML
" <Uniform id=\"Uniform.24\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ClockPrior.c:anthus_nd3\" name=\"distribution\" x=\"@clockRate.c:anthus_nd3\">", # nolint XML
" <Uniform id=\"Uniform.20\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_aco\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco\">", # nolint XML
" <Gamma id=\"Gamma.6\" name=\"distr\">",
" <parameter id=\"RealParameter.21\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.22\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd2\">", # nolint XML
" <Gamma id=\"Gamma.14\" name=\"distr\">",
" <parameter id=\"RealParameter.64\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.65\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.14\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_rln_clock_model(
id = "anthus_aco",
mean_rate_prior_distr = create_uniform_distr(id = "irrelevant"),
ucldstdev_distr = create_gamma_distr(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
)
),
create_rln_clock_model(
id = "anthus_nd2",
mean_rate_prior_distr = create_uniform_distr(id = 14),
ucldstdev_distr = create_gamma_distr(
id = 14,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
)
),
create_strict_clock_model(
id = "anthus_nd3",
clock_rate_distr = create_uniform_distr(id = 20)
),
create_strict_clock_model(
id = "anthus_nd4",
clock_rate_distr = create_uniform_distr(id = 24)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict RLN RLN strict", {
expected <- c(
"<prior id=\"ClockPrior.c:anthus_nd4\" name=\"distribution\" x=\"@clockRate.c:anthus_nd4\">", # nolint XML
" <Uniform id=\"Uniform.24\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd2\">", # nolint XML
" <Gamma id=\"Gamma.14\" name=\"distr\">",
" <parameter id=\"RealParameter.64\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.65\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd2\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.14\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd3\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd3\">", # nolint XML
" <Gamma id=\"Gamma.22\" name=\"distr\">",
" <parameter id=\"RealParameter.106\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.107\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd3\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd3\">", # nolint XML
" <Uniform id=\"Uniform.26\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_strict_clock_model(
id = "anthus_aco",
clock_rate_distr = create_uniform_distr(id = "irrelevant")
),
create_rln_clock_model(
id = "anthus_nd2",
mean_rate_prior_distr = create_uniform_distr(id = 14),
ucldstdev_distr = create_gamma_distr(
id = 14,
alpha = create_alpha_param(id = 64, value = "0.5396"),
beta = create_beta_param(id = 65, value = "0.3819")
)
),
create_rln_clock_model(
id = "anthus_nd3",
mean_rate_prior_distr = create_uniform_distr(id = 26),
ucldstdev_distr = create_gamma_distr(
id = 22,
alpha = create_alpha_param(id = 106, value = "0.5396"),
beta = create_beta_param(id = 107, value = "0.3819")
)
),
create_strict_clock_model(
id = "anthus_nd4",
clock_rate_distr = create_uniform_distr(id = 24)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict strict RLN RLN", {
expected <- c(
"<prior id=\"ucldStdevPrior.c:anthus_nd3\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd3\">", # nolint XML
" <Gamma id=\"Gamma.22\" name=\"distr\">",
" <parameter id=\"RealParameter.106\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.107\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd3\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd3\">", # nolint XML
" <Uniform id=\"Uniform.26\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ClockPrior.c:anthus_nd2\" name=\"distribution\" x=\"@clockRate.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd4\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd4\">", # nolint XML
" <Gamma id=\"Gamma.30\" name=\"distr\">",
" <parameter id=\"RealParameter.148\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.149\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd4\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd4\">", # nolint XML
" <Uniform id=\"Uniform.34\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_strict_clock_model(
id = "anthus_aco",
clock_rate_distr = create_uniform_distr(id = "irrelevant")
),
create_strict_clock_model(
id = "anthus_nd2",
clock_rate_distr = create_uniform_distr(id = 3)
),
create_rln_clock_model(
id = "anthus_nd3",
mean_rate_prior_distr = create_uniform_distr(id = 26),
ucldstdev_distr = create_gamma_distr(
id = 22,
alpha = create_alpha_param(id = 106, value = "0.5396"),
beta = create_beta_param(id = 107, value = "0.3819")
)
),
create_rln_clock_model(
id = "anthus_nd4",
mean_rate_prior_distr = create_uniform_distr(id = 34),
ucldstdev_distr = create_gamma_distr(
id = 30,
alpha = create_alpha_param(id = 148, value = "0.5396"),
beta = create_beta_param(id = 149, value = "0.3819")
)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("RLN strict strict RLN", {
expected <- c(
"<prior id=\"ClockPrior.c:anthus_nd2\" name=\"distribution\" x=\"@clockRate.c:anthus_nd2\">", # nolint XML
" <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_nd4\" name=\"distribution\" x=\"@ucldStdev.c:anthus_nd4\">", # nolint XML
" <Gamma id=\"Gamma.30\" name=\"distr\">",
" <parameter id=\"RealParameter.148\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.149\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>",
"<prior id=\"MeanRatePrior.c:anthus_nd4\" name=\"distribution\" x=\"@ucldMean.c:anthus_nd4\">", # nolint XML
" <Uniform id=\"Uniform.34\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ClockPrior.c:anthus_nd3\" name=\"distribution\" x=\"@clockRate.c:anthus_nd3\">", # nolint XML
" <Uniform id=\"Uniform.20\" name=\"distr\" upper=\"Infinity\"/>",
"</prior>",
"<prior id=\"ucldStdevPrior.c:anthus_aco\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco\">", # nolint XML
" <Gamma id=\"Gamma.6\" name=\"distr\">",
" <parameter id=\"RealParameter.21\" estimate=\"false\" name=\"alpha\">0.5396</parameter>", # nolint XML
" <parameter id=\"RealParameter.22\" estimate=\"false\" name=\"beta\">0.3819</parameter>", # nolint XML
" </Gamma>",
"</prior>"
)
created <- beautier:::clock_models_to_xml_prior_distr(
list(
create_rln_clock_model(
id = "anthus_aco",
mean_rate_prior_distr = create_uniform_distr(id = "irrelevant"),
ucldstdev_distr = create_gamma_distr(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
)
),
create_strict_clock_model(
id = "anthus_nd2",
clock_rate_distr = create_uniform_distr(id = 3)
),
create_strict_clock_model(
id = "anthus_nd3",
clock_rate_distr = create_uniform_distr(id = 20)
),
create_rln_clock_model(
id = "anthus_nd4",
mean_rate_prior_distr = create_uniform_distr(id = 34),
ucldstdev_distr = create_gamma_distr(
id = 30,
alpha = create_alpha_param(id = 148, value = "0.5396"),
beta = create_beta_param(id = 149, value = "0.3819")
)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
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