context("test-create_beast2_input_beast")
test_that("use, two alignments", {
fasta_filenames <- beautier::get_beautier_paths(
c("anthus_aco.fas", "anthus_nd2.fas")
)
ids <- beautier:::get_alignment_id(fasta_filenames)
testthat::expect_silent(
beautier:::create_beast2_input_beast(
input_filenames = fasta_filenames,
tree_priors = list(
create_yule_tree_prior(
id = ids[1],
birth_rate_distr = create_uniform_distr(id = 1)
),
create_yule_tree_prior(
id = ids[2],
birth_rate_distr = create_uniform_distr(id = 2)
)
),
clock_models = list(
create_strict_clock_model(
id = ids[1],
clock_rate_distr = create_uniform_distr(id = 3),
clock_rate_param = create_clock_rate_param(id = 4)
),
create_strict_clock_model(
id = ids[2],
clock_rate_distr = create_uniform_distr(id = 5),
clock_rate_param = create_clock_rate_param(id = 6)
)
)
)
)
})
test_that("use, two alignments, fixed crown ages", {
fasta_filenames <- beautier::get_beautier_paths(
c("anthus_aco.fas", "anthus_nd2.fas")
)
ids <- beautier:::get_alignment_id(fasta_filenames)
testthat::expect_silent(
beautier:::create_beast2_input_beast(
input_filenames = fasta_filenames,
tree_priors = list(
create_yule_tree_prior(
id = ids[1],
birth_rate_distr = create_uniform_distr(id = 1)
),
create_yule_tree_prior(
id = ids[2],
birth_rate_distr = create_uniform_distr(id = 2)
)
),
clock_models = list(
create_strict_clock_model(
id = ids[1],
clock_rate_distr = create_uniform_distr(id = 3),
clock_rate_param = create_clock_rate_param(id = 4)
),
create_strict_clock_model(
id = ids[2],
clock_rate_distr = create_uniform_distr(id = 5),
clock_rate_param = create_clock_rate_param(id = 6)
)
),
fixed_crown_ages = c(TRUE, TRUE)
)
)
})
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