test_that("use, fast", {
check_empty_beaustier_folders()
expect_equal(1 + 1, 2) # nolint to prevent 'Reason: empty test'
if (!is_beast2_installed()) return()
check_empty_beaustier_folders()
expect_true(
are_beast2_input_lines(
readLines(get_beastier_path("anthus_2_4.xml"))
)
)
expect_true(
are_beast2_input_lines(
readLines(get_beastier_path("anthus_2_4.xml")),
method = "fast"
)
)
remove_beaustier_folders()
check_empty_beaustier_folders()
})
test_that("use, deep", {
expect_equal(1 + 1, 2) # nolint to prevent 'Reason: empty test'
if (!is_beast2_installed()) return()
check_empty_beaustier_folders()
expect_true(
are_beast2_input_lines(
readLines(get_beastier_path("anthus_2_4.xml")),
method = "deep",
beast2_path = get_default_beast2_path()
)
)
remove_beaustier_folders()
check_empty_beaustier_folders()
})
test_that("abuse", {
check_empty_beaustier_folders()
expect_error(
are_beast2_input_lines(
readLines(get_beastier_path("anthus_2_4.xml")),
method = "nonsense"
),
"'method' must be \"deep\" or \"fast\""
)
check_empty_beaustier_folders()
})
test_that("clockRate.c ID and ClockPrior.c ID added twice", {
expect_equal(1 + 1, 2) # nolint to prevent 'Reason: empty test'
if (!is_beast2_installed()) return()
check_empty_beaustier_folders()
# From https://github.com/ropensci/beautier/issues/127
# From https://github.com/ropensci/beautier/issues/128
# clock_model
clock_rate <- 0.0000001
clock_model <- create_strict_clock_model(
clock_rate_param = create_clock_rate_param(value = clock_rate),
clock_rate_distr = create_log_normal_distr(
value = clock_rate,
m = 1,
s = 1.25
)
)
# MRCA PRIOR
mrca_prior <- create_mrca_prior(
is_monophyletic = TRUE,
mrca_distr = create_laplace_distr(mu = 1990)
)
inference_model <- create_inference_model(
clock_model = clock_model,
mrca_prior = mrca_prior,
tipdates_filename = beautier::get_beautier_path(
"THAILAND_TEST.clust_1.dated.txt"
)
)
text <- create_beast2_input_from_model(
input_filename = beautier::get_beautier_path(
"THAILAND_TEST.clust_1.dated.fa"
),
inference_model = inference_model
)
expect_true(are_beast2_input_lines(text))
remove_beaustier_folders()
check_empty_beaustier_folders()
})
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