context(
paste(
"create_beast2_input by reproducing files,",
"simple and single alignments"
)
)
test_that("anthus_aco_sub_two_mrca_priors.xml", {
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filenames = fasta_filename,
tree_priors = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
mrca_priors = list(
create_mrca_prior(
name = "first_two",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename)[1:2],
clock_prior_distr_id = 0
),
create_mrca_prior(
name = "last_three",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename)[3:5],
clock_prior_distr_id = 0
)
),
misc_options = create_misc_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(get_beautier_path(
"anthus_aco_sub_two_mrca_priors.xml")
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("test_0_two_mrca_priors.xml, #30", {
fasta_filename <- get_beautier_path("test_output_0.fas")
created <- create_beast2_input(
input_filenames = fasta_filename,
clock_models = create_rln_clock_model(
ucldstdev_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 2, value = "0.5396"),
beta = create_beta_param(id = 3, value = "0.3819")
),
mparam_id = 1
),
tree_priors = create_cep_tree_prior(
pop_size_distr = create_one_div_x_distr(id = 1),
growth_rate_distr = create_laplace_distr(
id = 0,
mu = create_mu_param(id = 4, value = "0.001"),
scale = create_scale_param(id = 5, value = "30.701135")
)
),
mrca_priors = list(
create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
is_monophyletic = TRUE,
clock_prior_distr_id = 0
),
create_mrca_prior(
name = "one_and_three",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename)[c(2, 5)],
is_monophyletic = TRUE,
clock_prior_distr_id = 0
)
),
misc_options = create_misc_options(nucleotides_uppercase = FALSE)
)
expected <- readLines(get_beautier_path(
"test_output_0_two_mrca_priors.xml")
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("issue_30.xml, #30", {
fasta_filename <- get_beautier_path("test_output_0.fas")
created <- create_beast2_input(
input_filenames = fasta_filename,
tree_priors = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_priors = list(
create_mrca_prior(
name = "most",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = c(paste0("t", seq(1, 4))),
is_monophyletic = FALSE,
clock_prior_distr_id = 0
),
create_mrca_prior(
name = "some_mono",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = c(paste0("t", seq(2, 3))),
is_monophyletic = TRUE,
clock_prior_distr_id = 0
)
),
misc_options = create_misc_options(nucleotides_uppercase = FALSE)
)
expected <- readLines(get_beautier_path(
"issue_30.xml")
)
expect_true(are_equivalent_xml_lines(created, expected))
})
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