tests/testthat/test-create_beast2_input_by_reproducing_files_simple.R
In richelbilderbeek/beautier: 'BEAUti' from R
################################################################################
# Defaults for different versions
################################################################################
test_that("2.4", {
created <- create_beast2_input(
input_filename = get_fasta_filename(),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options_v2_4()
)
expected <- readLines(get_beautier_path("2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("v2.5", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.0",
nucleotides_uppercase = TRUE
)
)
expected <- readLines(get_beautier_path("anthus_aco_sub_20181016.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("v2.5.1", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.1",
nucleotides_uppercase = TRUE
)
)
expected <- readLines(get_beautier_path("anthus_aco_sub_2_5_1.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_2_6.xml", {
created <- create_beast2_input_from_model(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
inference_model = create_inference_model(
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options_v2_6(
nucleotides_uppercase = TRUE,
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" # nolint indeed a long line
)
)
)
expected <- readLines(get_beautier_path("anthus_aco_sub_2_6.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site models
################################################################################
################################################################################
# Site model: GTR
################################################################################
test_that("gtr_2_4.xml", {
created <- create_beast2_input(
input_filename = get_fasta_filename(),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 9, value = "0.05"),
beta = create_beta_param(id = 10, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 13, value = "0.05"),
beta = create_beta_param(id = 14, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 17, value = "0.05"),
beta = create_beta_param(id = 18, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("gtr_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_1_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 1
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("gtr_gcc_1_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_2_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("gtr_gcc_2_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_2_shape_1_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"gtr_gcc_2_shape_1_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5,
prop_invariant = 0.5
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"gtr_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_no_rate_estimation_2_4.xml", {
created <- create_beast2_input(
input_filename = get_fasta_filename(),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
rate_ac_param = create_rate_ac_param(value = "1.0", estimate = FALSE),
rate_ag_param = create_rate_ag_param(value = "1.0", estimate = FALSE),
rate_at_param = create_rate_at_param(value = "1.0", estimate = FALSE),
rate_cg_param = create_rate_cg_param(value = "1.0", estimate = FALSE),
rate_ct_param = create_rate_ct_param(value = "1.0"),
rate_gt_param = create_rate_gt_param(value = "1.0", estimate = FALSE)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"gtr_no_rate_estimation_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site model: HKY
################################################################################
test_that("hky_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_2_4.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("hky_2_6.xml", {
check_empty_beautier_folder()
inference_model <- create_inference_model(
site_model = create_hky_site_model(),
beauti_options = beautier::create_beauti_options_v2_6(
nucleotides_uppercase = TRUE,
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" # nolint indeed a long line
)
)
inference_model$tree_prior$birth_rate_distr$id <- "1"
inference_model$site_model$kappa_prior_distr$m$id <- "1"
inference_model$site_model$kappa_prior_distr$s$id <- "2"
inference_model$site_model$gamma_site_model$freq_prior_uniform_distr_id <- "3"
beautier_file <- get_beautier_tempfilename(pattern = "anthus_aco_sub_2_6")
create_beast2_input_file_from_model(
input_filename = beautier::get_beautier_path("anthus_aco_sub.fas"),
output_filename = beautier_file,
inference_model = inference_model
)
# If this passes, this is done!
beauti_filename <- beautier::get_beautier_path("hky_2_6.xml")
expect_true(
beautier::are_equivalent_xml_files(
beautier_file,
beauti_filename
)
)
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("hky_kappa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_param = create_kappa_param(value = "3.4"),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"hky_kappa_2_4.xml"
)
)
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("hky_prop_invariant_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
prop_invariant = 0.5
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_prop_invariant_0_5_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("hky_gcc_1_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 1
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_gcc_1_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("hky_gcc_2_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_gcc_2_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("hky_gcc_4_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 4
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"hky_gcc_4_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site model: JC69
################################################################################
test_that("jc69_2_4.xml", {
input_fasta_filename <- get_beautier_path("test_output_0.fas")
id <- get_alignment_id(input_fasta_filename)
created <- create_beast2_input(
input_filename = input_fasta_filename,
site_model = create_jc69_site_model(
id = id
),
tree_prior = create_yule_tree_prior(
id = id,
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("jc69_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("jc69_gcc_2_2_4.xml", {
input_fasta_filename <- get_beautier_path("test_output_0.fas")
id <- get_alignment_id(input_fasta_filename)
created <- create_beast2_input(
input_filename = input_fasta_filename,
site_model = create_jc69_site_model(
id = id,
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"jc69_gcc_2_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("jc69_gcc_2_shape_1_5_2_4.xml", {
input_fasta_filename <- get_beautier_path("test_output_0.fas")
id <- get_alignment_id(input_fasta_filename)
created <- create_beast2_input(
input_filename = input_fasta_filename,
site_model = create_jc69_site_model(
id = id,
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"jc69_gcc_2_shape_1_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("jc69_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_jc69_site_model(
id = "test_output_0",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5,
prop_invariant = 0.5
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"jc69_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site model: TN93
################################################################################
test_that("tn93_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_1_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA),
),
kappa_2_prior_distr = create_log_normal_distr(
id = 2,
m = create_m_param(id = 5, value = "1.0"),
s = create_s_param(id = 6, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"tn93_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("tn93_gcc_1_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1),
kappa_1_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
),
kappa_2_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"tn93_gcc_1_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("tn93_gcc_2_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2),
kappa_1_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
),
kappa_2_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"tn93_gcc_2_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("tn93_kappas_not_estimated.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_1_param = create_kappa_1_param(value = "2.0", estimate = FALSE),
kappa_2_param = create_kappa_2_param(value = "2.0", estimate = FALSE),
kappa_1_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA)
),
kappa_2_prior_distr = create_log_normal_distr(
id = 2,
m = create_m_param(id = 5, value = "1.0"),
s = create_s_param(id = 6, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"tn93_kappas_not_estimated.xml"
)
)
expect_true(
are_equivalent_xml_lines(
remove_empty_lines(created, trim = TRUE),
remove_empty_lines(expected, trim = TRUE),
verbose = TRUE
)
)
})
################################################################################
# Tree priors
################################################################################
################################################################################
# Tree prior: BD
################################################################################
test_that("bd_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_bd_tree_prior(
birth_rate_distr = create_uniform_distr(
id = 3, upper = "1000.0"
),
death_rate_distr = create_uniform_distr(
id = 4, upper = NA
)
)
)
expected <- readLines(
get_beautier_path(
"bd_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("bd_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_bd_tree_prior(
birth_rate_distr = create_uniform_distr(
id = 3, upper = "1000.0"
),
death_rate_distr = create_uniform_distr(
id = 4, upper = NA
)
)
)
expected <- readLines(
get_beautier_path(
"bd_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("cbs_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_cbs_tree_prior(pop_sizes_scaler_scale_factor = 0.75)
)
expected <- readLines(
get_beautier_path(
"cbs_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("ccp_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_ccp_tree_prior(
pop_size_distr = create_one_div_x_distr(
id = 1,
value = 0.3
)
)
)
expected <- readLines(
get_beautier_path(
"ccp_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("cep_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_cep_tree_prior(
pop_size_distr = create_one_div_x_distr(id = 2),
growth_rate_distr = create_laplace_distr(
id = 0,
mu = create_mu_param(id = 1, value = "0.001"),
scale = create_scale_param(id = 2, value = "30.701135")
)
)
)
expected <- readLines(
get_beautier_path(
"cep_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: CBS
################################################################################
test_that("cbs_2_4.xml", {
# Tested in detail by 'check_file_and_model_agree'
expect_error(
create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_cbs_tree_prior()
),
"'group_sizes_dimension' \\(5\\) must be less than the number of taxa \\(5\\)" # nolint
)
})
test_that("cbs_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_cbs_tree_prior(
pop_sizes_scaler_scale_factor = 0.75
)
)
expected <- readLines(
get_beautier_path(
"cbs_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_cbs_groupsize_4_dim.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_cbs_tree_prior(
group_sizes_dimension = 4,
pop_sizes_scaler_scale_factor = 0.75
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_cbs_groupsize_4_dim.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: CCP
################################################################################
test_that("ccp_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_ccp_tree_prior(
pop_size_distr = create_one_div_x_distr(
id = 1,
value = 0.3
)
)
)
expected <- readLines(
get_beautier_path(
"ccp_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("ccp_pop_size_gamma_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_ccp_tree_prior(
pop_size_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 9, value = "2.0"),
beta = create_beta_param(id = 10, value = "2.0"),
value = 0.3
)
)
)
expected <- readLines(
get_beautier_path(
"ccp_pop_size_gamma_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: CEP
################################################################################
test_that("cep_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = 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 = 1, value = "0.001"),
scale = create_scale_param(id = 2, value = "30.701135")
)
)
)
expected <- readLines(get_beautier_path("cep_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: Yule
################################################################################
test_that("yule_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("yule_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Prior distributions
################################################################################
test_that("birth_rate_uniform_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(
"birth_rate_uniform_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_normal_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_normal_distr(
id = 0,
mean = create_mean_param(id = 1, value = "0.0"),
sigma = create_sigma_param(id = 2, value = "1.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_normal_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_one_div_x_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_one_div_x_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_one_div_x_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_log_normal_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_log_normal_distr(
id = 0,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(
id = 4,
value = "1.25",
lower = "0.0",
upper = "5.0"
)
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_log_normal_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_exp_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_exp_distr(
id = 1,
mean = create_mean_param(id = 5, value = "1.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_exp_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_gamma_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_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 6, value = "2.0"),
beta = create_beta_param(id = 7, value = "2.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_gamma_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_beta_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_beta_distr(
id = 0,
alpha = create_alpha_param(id = 8, value = "2.0"),
beta = create_beta_param(id = 9, value = "2.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_beta_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_laplace_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_laplace_distr(
id = 0,
mu = create_mu_param(id = 10, value = "0.0"),
scale = create_scale_param(id = 11, value = "1.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_laplace_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_inv_gamma_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_inv_gamma_distr(
id = 0,
alpha = create_alpha_param(
id = 12,
value = "2.0"
),
beta = create_beta_param(
id = 13,
value = "2.0"
)
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_inv_gamma_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_poisson_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_poisson_distr(
id = 0,
lambda = create_lambda_param(id = 14, value = "0.693")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_poisson_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# MCMC options
################################################################################
################################################################################
# MRCA priors
################################################################################
# No calibration yet
test_that("anthus_aco_sub.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibration.xml", {
# This XML file has a normal distribution for the MRCA prior
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
mrca_distr = create_normal_distr(
id = 0,
mean = create_mean_param(id = 1, value = "0.02"),
sigma = create_sigma_param(id = 2, value = "0.001")
),
is_monophyletic = TRUE,
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibrated_no_prior.xml", {
# This XML file has no prior distribution
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "every",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated_no_prior.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibrated_rln.xml", {
# This XML file has
# - an MRCA prior distribution prior,
# - an RLN clock model
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
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(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mparam_id = 20
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "every",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated_rln.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibrated_rln_monophyletic.xml", {
# This XML file has
# - an MRCA prior distribution prior,
# - an RLN clock model, that is monophyletic
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
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(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mparam_id = 20
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "every",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
clock_prior_distr_id = 0,
is_monophyletic = TRUE
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated_rln_monophyletic.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# MRCA priors again 2018-10-26
################################################################################
test_that("Base point: anthus_aco_sub.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = FALSE
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + monophyletic", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = TRUE
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_monophyletic.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + monophyletic + one_div_x", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = TRUE,
mrca_distr = create_one_div_x_distr(id = 1),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_one_div_x_monophyletic.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + one_div_x", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr(id = 1),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_one_div_x.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + one_div_x + RLN", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
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(id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mparam_id = 20,
mean_rate_prior_distr = create_uniform_distr(id = 4)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr(id = 1),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_one_div_x_rln.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tip dating
################################################################################
test_that("No tip dating yet", {
created <- create_beast2_input(
input_filename = get_beautier_path("G_VII_pre2003_msa.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.0",
nucleotides_uppercase = TRUE
)
)
expected <- readLines(get_beautier_path("G_VII_pre2003_no_tip.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Tip dating, v2.5", {
created <- create_beast2_input(
input_filename = get_beautier_path("G_VII_pre2003_msa.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
tipdates_filename = get_beautier_path("G_VII_pre2003_dates_4.txt"),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.1",
nucleotides_uppercase = TRUE,
sequence_indent = 24
)
)
expected <- readLines(get_beautier_path("G_VII_pre2003.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Tip dating, v2.6", {
inference_model <- create_inference_model(
clock_model = create_strict_clock_model(rate_scaler_factor = ""),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
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" # nolint indeed a long line
)
)
inference_model <- init_inference_model(
input_filename = get_beautier_path("test_output_0.fas"),
inference_model = inference_model
)
created <- create_beast2_input_from_model(
input_filename = get_beautier_path("test_output_0.fas"),
inference_model = inference_model
)
expected <- readLines(get_beautier_path("tipdates_2_6.xml"))
# Creates temporary files in beautier folder
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("Tip dating with RLN 1/3", {
skip("Issue #116. RLN + tipdating")
# Probably needs to get proper IDs and such ...
# Prerequisite for https://github.com/ropensci/babette/issues/90
created <- create_beast2_input(
input_filename = get_beautier_path("Felinecoronavirus_Envelope_1.fas"),
tipdates_filename = get_beautier_path(
"Felinecoronavirus_Envelope_1_no_quotes.txt"
),
beauti_options = create_beauti_options(
beast2_version = "2.6",
nucleotides_uppercase = TRUE,
sequence_indent = 8
)
)
expected <- readLines(get_beautier_path("Felinecoronavirus_Envelope_1.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected, verbose = TRUE))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("RLN and non-monophyletic MRCA with distribution, beastier", {
# babette issue 106. babette Issue #106
# https://github.com/ropensci/babette/issues/106
# Thanks to Raphael Scherrer for sharing this bug
fasta_filename <- get_fasta_filename()
lines <- beautier::create_beast2_input(
input_filename = fasta_filename,
clock_model = create_rln_clock_model(),
mrca_prior = create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr() # Use simpler distribution
),
beauti_options = create_beauti_options_v2_6()
)
# The next testing function does compare line-by-line
if ("beastier" %in% installed.packages()[,1]) {
expect_true(
beastier::are_beast2_input_lines(
lines, method = "deep"
)
)
}
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("RLN and non-monophyletic MRCA with distribution, beastier", {
# This is the same test as above, yet made to function with beautier
# functionality only. It does mess up the cleanliness of
# the creation of the inference model
# babette issue 106. babette Issue #106
# https://github.com/ropensci/babette/issues/106
# Thanks to Raphael Scherrer for sharing this bug
fasta_filename <- get_fasta_filename()
lines <- beautier::create_beast2_input(
input_filename = fasta_filename,
tree_prior = create_tree_prior_yule(birth_rate_distr = create_uniform_distr(id = "1")),
clock_model = create_rln_clock_model(
mparam_id = "1",
mean_rate_prior_distr = create_uniform_distr(id = "3"),
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")
)
),
mrca_prior = create_mrca_prior(
name = "all_taxa",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr(id = "1") # Use simpler distribution
),
beauti_options = create_beauti_options_v2_6()
)
if ("beastier" %in% installed.packages()[,1]) {
expect_true(
beastier::are_beast2_input_lines(
lines, method = "deep"
)
)
}
expected <- readLines(get_beautier_path("babette_issue_26.xml"))
# Creates temporary files in beautier folder
created <- lines
compare_lines(
lines = lines,
expected = expected,
created_lines_filename = "~/created.txt",
expected_lines_filename = "~/expected.txt"
)
expect_true(are_equivalent_xml_lines(created, expected, verbose = TRUE))
remove_beautier_folder()
check_empty_beautier_folder()
})
richelbilderbeek/beautier documentation built on April 4, 2024, 12:33 p.m.
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################################################################################
# Defaults for different versions
################################################################################
test_that("2.4", {
created <- create_beast2_input(
input_filename = get_fasta_filename(),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options_v2_4()
)
expected <- readLines(get_beautier_path("2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("v2.5", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.0",
nucleotides_uppercase = TRUE
)
)
expected <- readLines(get_beautier_path("anthus_aco_sub_20181016.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("v2.5.1", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.1",
nucleotides_uppercase = TRUE
)
)
expected <- readLines(get_beautier_path("anthus_aco_sub_2_5_1.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_2_6.xml", {
created <- create_beast2_input_from_model(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
inference_model = create_inference_model(
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options_v2_6(
nucleotides_uppercase = TRUE,
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" # nolint indeed a long line
)
)
)
expected <- readLines(get_beautier_path("anthus_aco_sub_2_6.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site models
################################################################################
################################################################################
# Site model: GTR
################################################################################
test_that("gtr_2_4.xml", {
created <- create_beast2_input(
input_filename = get_fasta_filename(),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 9, value = "0.05"),
beta = create_beta_param(id = 10, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 13, value = "0.05"),
beta = create_beta_param(id = 14, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 17, value = "0.05"),
beta = create_beta_param(id = 18, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("gtr_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_1_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 1
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("gtr_gcc_1_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_2_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("gtr_gcc_2_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_2_shape_1_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"gtr_gcc_2_shape_1_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5,
prop_invariant = 0.5
),
rate_ac_prior_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 1, value = "0.05"),
beta = create_beta_param(id = 2, value = "10.0")
),
rate_ag_prior_distr = create_gamma_distr(
id = 1,
alpha = create_alpha_param(id = 3, value = "0.05"),
beta = create_beta_param(id = 4, value = "20.0")
),
rate_at_prior_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 5, value = "0.05"),
beta = create_beta_param(id = 6, value = "10.0")
),
rate_cg_prior_distr = create_gamma_distr(
id = 3,
alpha = create_alpha_param(id = 7, value = "0.05"),
beta = create_beta_param(id = 8, value = "10.0")
),
rate_gt_prior_distr = create_gamma_distr(
id = 5,
alpha = create_alpha_param(id = 11, value = "0.05"),
beta = create_beta_param(id = 12, value = "10.0")
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"gtr_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("gtr_no_rate_estimation_2_4.xml", {
created <- create_beast2_input(
input_filename = get_fasta_filename(),
site_model = create_gtr_site_model(
id = get_alignment_id(get_fasta_filename()),
rate_ac_param = create_rate_ac_param(value = "1.0", estimate = FALSE),
rate_ag_param = create_rate_ag_param(value = "1.0", estimate = FALSE),
rate_at_param = create_rate_at_param(value = "1.0", estimate = FALSE),
rate_cg_param = create_rate_cg_param(value = "1.0", estimate = FALSE),
rate_ct_param = create_rate_ct_param(value = "1.0"),
rate_gt_param = create_rate_gt_param(value = "1.0", estimate = FALSE)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"gtr_no_rate_estimation_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site model: HKY
################################################################################
test_that("hky_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_2_4.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("hky_2_6.xml", {
check_empty_beautier_folder()
inference_model <- create_inference_model(
site_model = create_hky_site_model(),
beauti_options = beautier::create_beauti_options_v2_6(
nucleotides_uppercase = TRUE,
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" # nolint indeed a long line
)
)
inference_model$tree_prior$birth_rate_distr$id <- "1"
inference_model$site_model$kappa_prior_distr$m$id <- "1"
inference_model$site_model$kappa_prior_distr$s$id <- "2"
inference_model$site_model$gamma_site_model$freq_prior_uniform_distr_id <- "3"
beautier_file <- get_beautier_tempfilename(pattern = "anthus_aco_sub_2_6")
create_beast2_input_file_from_model(
input_filename = beautier::get_beautier_path("anthus_aco_sub.fas"),
output_filename = beautier_file,
inference_model = inference_model
)
# If this passes, this is done!
beauti_filename <- beautier::get_beautier_path("hky_2_6.xml")
expect_true(
beautier::are_equivalent_xml_files(
beautier_file,
beauti_filename
)
)
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("hky_kappa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_param = create_kappa_param(value = "3.4"),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"hky_kappa_2_4.xml"
)
)
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("hky_prop_invariant_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
prop_invariant = 0.5
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_prop_invariant_0_5_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("hky_gcc_1_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 1
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_gcc_1_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("hky_gcc_2_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("hky_gcc_2_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("hky_gcc_4_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_hky_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 4
),
kappa_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"hky_gcc_4_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site model: JC69
################################################################################
test_that("jc69_2_4.xml", {
input_fasta_filename <- get_beautier_path("test_output_0.fas")
id <- get_alignment_id(input_fasta_filename)
created <- create_beast2_input(
input_filename = input_fasta_filename,
site_model = create_jc69_site_model(
id = id
),
tree_prior = create_yule_tree_prior(
id = id,
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(get_beautier_path("jc69_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("jc69_gcc_2_2_4.xml", {
input_fasta_filename <- get_beautier_path("test_output_0.fas")
id <- get_alignment_id(input_fasta_filename)
created <- create_beast2_input(
input_filename = input_fasta_filename,
site_model = create_jc69_site_model(
id = id,
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"jc69_gcc_2_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("jc69_gcc_2_shape_1_5_2_4.xml", {
input_fasta_filename <- get_beautier_path("test_output_0.fas")
id <- get_alignment_id(input_fasta_filename)
created <- create_beast2_input(
input_filename = input_fasta_filename,
site_model = create_jc69_site_model(
id = id,
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"jc69_gcc_2_shape_1_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("jc69_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_jc69_site_model(
id = "test_output_0",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 1.5,
prop_invariant = 0.5
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"jc69_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Site model: TN93
################################################################################
test_that("tn93_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_1_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA),
),
kappa_2_prior_distr = create_log_normal_distr(
id = 2,
m = create_m_param(id = 5, value = "1.0"),
s = create_s_param(id = 6, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"tn93_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("tn93_gcc_1_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1),
kappa_1_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
),
kappa_2_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"tn93_gcc_1_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("tn93_gcc_2_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2),
kappa_1_prior_distr = create_log_normal_distr(
id = 0,
m = create_m_param(id = 1, value = "1.0"),
s = create_s_param(id = 2, value = "1.25", lower = NA, upper = NA)
),
kappa_2_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"tn93_gcc_2_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("tn93_kappas_not_estimated.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
site_model = create_tn93_site_model(
id = get_alignment_id(get_fasta_filename()),
kappa_1_param = create_kappa_1_param(value = "2.0", estimate = FALSE),
kappa_2_param = create_kappa_2_param(value = "2.0", estimate = FALSE),
kappa_1_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(id = 4, value = "1.25", lower = NA, upper = NA)
),
kappa_2_prior_distr = create_log_normal_distr(
id = 2,
m = create_m_param(id = 5, value = "1.0"),
s = create_s_param(id = 6, value = "1.25", lower = NA, upper = NA)
)
),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"tn93_kappas_not_estimated.xml"
)
)
expect_true(
are_equivalent_xml_lines(
remove_empty_lines(created, trim = TRUE),
remove_empty_lines(expected, trim = TRUE),
verbose = TRUE
)
)
})
################################################################################
# Tree priors
################################################################################
################################################################################
# Tree prior: BD
################################################################################
test_that("bd_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_bd_tree_prior(
birth_rate_distr = create_uniform_distr(
id = 3, upper = "1000.0"
),
death_rate_distr = create_uniform_distr(
id = 4, upper = NA
)
)
)
expected <- readLines(
get_beautier_path(
"bd_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("bd_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_bd_tree_prior(
birth_rate_distr = create_uniform_distr(
id = 3, upper = "1000.0"
),
death_rate_distr = create_uniform_distr(
id = 4, upper = NA
)
)
)
expected <- readLines(
get_beautier_path(
"bd_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("cbs_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_cbs_tree_prior(pop_sizes_scaler_scale_factor = 0.75)
)
expected <- readLines(
get_beautier_path(
"cbs_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("ccp_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_ccp_tree_prior(
pop_size_distr = create_one_div_x_distr(
id = 1,
value = 0.3
)
)
)
expected <- readLines(
get_beautier_path(
"ccp_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("cep_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_cep_tree_prior(
pop_size_distr = create_one_div_x_distr(id = 2),
growth_rate_distr = create_laplace_distr(
id = 0,
mu = create_mu_param(id = 1, value = "0.001"),
scale = create_scale_param(id = 2, value = "30.701135")
)
)
)
expected <- readLines(
get_beautier_path(
"cep_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: CBS
################################################################################
test_that("cbs_2_4.xml", {
# Tested in detail by 'check_file_and_model_agree'
expect_error(
create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_cbs_tree_prior()
),
"'group_sizes_dimension' \\(5\\) must be less than the number of taxa \\(5\\)" # nolint
)
})
test_that("cbs_6_taxa_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_6.fas"),
tree_prior = create_cbs_tree_prior(
pop_sizes_scaler_scale_factor = 0.75
)
)
expected <- readLines(
get_beautier_path(
"cbs_6_taxa_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_cbs_groupsize_4_dim.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_cbs_tree_prior(
group_sizes_dimension = 4,
pop_sizes_scaler_scale_factor = 0.75
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_cbs_groupsize_4_dim.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: CCP
################################################################################
test_that("ccp_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_ccp_tree_prior(
pop_size_distr = create_one_div_x_distr(
id = 1,
value = 0.3
)
)
)
expected <- readLines(
get_beautier_path(
"ccp_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("ccp_pop_size_gamma_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = create_ccp_tree_prior(
pop_size_distr = create_gamma_distr(
id = 2,
alpha = create_alpha_param(id = 9, value = "2.0"),
beta = create_beta_param(id = 10, value = "2.0"),
value = 0.3
)
)
)
expected <- readLines(
get_beautier_path(
"ccp_pop_size_gamma_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: CEP
################################################################################
test_that("cep_2_4.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("test_output_0.fas"),
tree_prior = 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 = 1, value = "0.001"),
scale = create_scale_param(id = 2, value = "30.701135")
)
)
)
expected <- readLines(get_beautier_path("cep_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tree prior: Yule
################################################################################
test_that("yule_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("yule_2_4.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Prior distributions
################################################################################
test_that("birth_rate_uniform_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(
"birth_rate_uniform_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_normal_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_normal_distr(
id = 0,
mean = create_mean_param(id = 1, value = "0.0"),
sigma = create_sigma_param(id = 2, value = "1.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_normal_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_one_div_x_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_one_div_x_distr(id = 1)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_one_div_x_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_log_normal_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_log_normal_distr(
id = 0,
m = create_m_param(id = 3, value = "1.0"),
s = create_s_param(
id = 4,
value = "1.25",
lower = "0.0",
upper = "5.0"
)
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_log_normal_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_exp_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_exp_distr(
id = 1,
mean = create_mean_param(id = 5, value = "1.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_exp_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_gamma_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_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 6, value = "2.0"),
beta = create_beta_param(id = 7, value = "2.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_gamma_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_beta_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_beta_distr(
id = 0,
alpha = create_alpha_param(id = 8, value = "2.0"),
beta = create_beta_param(id = 9, value = "2.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_beta_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_laplace_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_laplace_distr(
id = 0,
mu = create_mu_param(id = 10, value = "0.0"),
scale = create_scale_param(id = 11, value = "1.0")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_laplace_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_inv_gamma_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_inv_gamma_distr(
id = 0,
alpha = create_alpha_param(
id = 12,
value = "2.0"
),
beta = create_beta_param(
id = 13,
value = "2.0"
)
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_inv_gamma_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("birth_rate_poisson_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_poisson_distr(
id = 0,
lambda = create_lambda_param(id = 14, value = "0.693")
)
)
)
expected <- readLines(
get_beautier_path(
"birth_rate_poisson_2_4.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# MCMC options
################################################################################
################################################################################
# MRCA priors
################################################################################
# No calibration yet
test_that("anthus_aco_sub.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibration.xml", {
# This XML file has a normal distribution for the MRCA prior
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
mrca_distr = create_normal_distr(
id = 0,
mean = create_mean_param(id = 1, value = "0.02"),
sigma = create_sigma_param(id = 2, value = "0.001")
),
is_monophyletic = TRUE,
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibrated_no_prior.xml", {
# This XML file has no prior distribution
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "every",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated_no_prior.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibrated_rln.xml", {
# This XML file has
# - an MRCA prior distribution prior,
# - an RLN clock model
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
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(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mparam_id = 20
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "every",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated_rln.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("anthus_aco_sub_calibrated_rln_monophyletic.xml", {
# This XML file has
# - an MRCA prior distribution prior,
# - an RLN clock model, that is monophyletic
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
created <- create_beast2_input(
input_filename = fasta_filename,
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(
id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mparam_id = 20
),
mcmc = create_mcmc(chain_length = 10000),
mrca_prior = create_mrca_prior(
name = "every",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
clock_prior_distr_id = 0,
is_monophyletic = TRUE
),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_calibrated_rln_monophyletic.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# MRCA priors again 2018-10-26
################################################################################
test_that("Base point: anthus_aco_sub.xml", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = FALSE
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + monophyletic", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = TRUE
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_monophyletic.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + monophyletic + one_div_x", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = TRUE,
mrca_distr = create_one_div_x_distr(id = 1),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_one_div_x_monophyletic.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + one_div_x", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr(id = 1),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_one_div_x.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Base point + all taxa + one_div_x + RLN", {
created <- create_beast2_input(
input_filename = get_beautier_path("anthus_aco_sub.fas"),
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(id = 6,
alpha = create_alpha_param(id = 21, value = "0.5396"),
beta = create_beta_param(id = 22, value = "0.3819")
),
mparam_id = 20,
mean_rate_prior_distr = create_uniform_distr(id = 4)
),
mrca_prior = create_mrca_prior(
name = "all",
alignment_id = get_alignment_id(get_beautier_path("anthus_aco_sub.fas")),
taxa_names = get_taxa_names(get_beautier_path("anthus_aco_sub.fas")),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr(id = 1),
clock_prior_distr_id = 0
),
beauti_options = create_beauti_options(
nucleotides_uppercase = TRUE,
beast2_version = "2.5",
required = "BEAST v2.5.0"
)
)
expected <- readLines(
get_beautier_path(
"anthus_aco_sub_20181016_all_one_div_x_rln.xml"
)
)
expect_true(are_equivalent_xml_lines(created, expected))
})
################################################################################
# Tip dating
################################################################################
test_that("No tip dating yet", {
created <- create_beast2_input(
input_filename = get_beautier_path("G_VII_pre2003_msa.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.0",
nucleotides_uppercase = TRUE
)
)
expected <- readLines(get_beautier_path("G_VII_pre2003_no_tip.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Tip dating, v2.5", {
created <- create_beast2_input(
input_filename = get_beautier_path("G_VII_pre2003_msa.fas"),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
tipdates_filename = get_beautier_path("G_VII_pre2003_dates_4.txt"),
beauti_options = create_beauti_options(
beast2_version = "2.5",
required = "BEAST v2.5.1",
nucleotides_uppercase = TRUE,
sequence_indent = 24
)
)
expected <- readLines(get_beautier_path("G_VII_pre2003.xml"))
expect_true(are_equivalent_xml_lines(created, expected))
})
test_that("Tip dating, v2.6", {
inference_model <- create_inference_model(
clock_model = create_strict_clock_model(rate_scaler_factor = ""),
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_uniform_distr(id = 1)
),
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" # nolint indeed a long line
)
)
inference_model <- init_inference_model(
input_filename = get_beautier_path("test_output_0.fas"),
inference_model = inference_model
)
created <- create_beast2_input_from_model(
input_filename = get_beautier_path("test_output_0.fas"),
inference_model = inference_model
)
expected <- readLines(get_beautier_path("tipdates_2_6.xml"))
# Creates temporary files in beautier folder
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("Tip dating with RLN 1/3", {
skip("Issue #116. RLN + tipdating")
# Probably needs to get proper IDs and such ...
# Prerequisite for https://github.com/ropensci/babette/issues/90
created <- create_beast2_input(
input_filename = get_beautier_path("Felinecoronavirus_Envelope_1.fas"),
tipdates_filename = get_beautier_path(
"Felinecoronavirus_Envelope_1_no_quotes.txt"
),
beauti_options = create_beauti_options(
beast2_version = "2.6",
nucleotides_uppercase = TRUE,
sequence_indent = 8
)
)
expected <- readLines(get_beautier_path("Felinecoronavirus_Envelope_1.xml"))
# Creates temporary files in beautier folder
compare_lines(
lines = created,
expected = expected
)
expect_true(are_equivalent_xml_lines(created, expected, verbose = TRUE))
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("RLN and non-monophyletic MRCA with distribution, beastier", {
# babette issue 106. babette Issue #106
# https://github.com/ropensci/babette/issues/106
# Thanks to Raphael Scherrer for sharing this bug
fasta_filename <- get_fasta_filename()
lines <- beautier::create_beast2_input(
input_filename = fasta_filename,
clock_model = create_rln_clock_model(),
mrca_prior = create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr() # Use simpler distribution
),
beauti_options = create_beauti_options_v2_6()
)
# The next testing function does compare line-by-line
if ("beastier" %in% installed.packages()[,1]) {
expect_true(
beastier::are_beast2_input_lines(
lines, method = "deep"
)
)
}
remove_beautier_folder()
check_empty_beautier_folder()
})
test_that("RLN and non-monophyletic MRCA with distribution, beastier", {
# This is the same test as above, yet made to function with beautier
# functionality only. It does mess up the cleanliness of
# the creation of the inference model
# babette issue 106. babette Issue #106
# https://github.com/ropensci/babette/issues/106
# Thanks to Raphael Scherrer for sharing this bug
fasta_filename <- get_fasta_filename()
lines <- beautier::create_beast2_input(
input_filename = fasta_filename,
tree_prior = create_tree_prior_yule(birth_rate_distr = create_uniform_distr(id = "1")),
clock_model = create_rln_clock_model(
mparam_id = "1",
mean_rate_prior_distr = create_uniform_distr(id = "3"),
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")
)
),
mrca_prior = create_mrca_prior(
name = "all_taxa",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
is_monophyletic = FALSE,
mrca_distr = create_one_div_x_distr(id = "1") # Use simpler distribution
),
beauti_options = create_beauti_options_v2_6()
)
if ("beastier" %in% installed.packages()[,1]) {
expect_true(
beastier::are_beast2_input_lines(
lines, method = "deep"
)
)
}
expected <- readLines(get_beautier_path("babette_issue_26.xml"))
# Creates temporary files in beautier folder
created <- lines
compare_lines(
lines = lines,
expected = expected,
created_lines_filename = "~/created.txt",
expected_lines_filename = "~/expected.txt"
)
expect_true(are_equivalent_xml_lines(created, expected, verbose = TRUE))
remove_beautier_folder()
check_empty_beautier_folder()
})
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