context("init_clock_models")
test_that("initialize RLN clock model", {
fasta_filenames <- beautier::get_beautier_path("test_output_0.fas")
before <- list(create_rln_clock_model())
expect_true(is_rln_clock_model(before[[1]]))
expect_true(!are_init_clock_models(before))
after <- init_clock_models(
before,
fasta_filenames = fasta_filenames
)
testthat::expect_true(is_rln_clock_model(after[[1]]))
testthat::expect_true(are_init_clock_models(after))
})
test_that("initialize strict clock model", {
fasta_filenames <- beautier::get_beautier_path("test_output_0.fas")
before <- list(create_strict_clock_model())
expect_true(is_strict_clock_model(before[[1]]))
expect_true(!are_init_clock_models(before))
after <- init_clock_models(
before,
fasta_filenames = fasta_filenames
)
testthat::expect_true(is_strict_clock_model(after[[1]]))
testthat::expect_true(are_init_clock_models(after))
})
test_that("initialize RLN clock model", {
fasta_filenames <- beautier::get_beautier_path("test_output_0.fas")
clock_model <- create_rln_clock_model(
ucldstdev_distr = create_gamma_distr(
id = 0,
alpha = create_alpha_param(id = 2, value = "0.5396"),
beta = create_beta_param(id = 3, value = "0.3819")
),
mparam_id = 1
)
before <- list(clock_model)
expect_true(is_rln_clock_model(before[[1]]))
expect_true(!are_init_clock_models(before))
after <- init_clock_models(
before,
fasta_filenames = fasta_filenames
)
testthat::expect_true(is_rln_clock_model(after[[1]]))
testthat::expect_true(are_init_clock_models(after))
})
test_that("initialize RLN clock model with correct dimensions", {
fasta_filenames <- beautier::get_beautier_path("test_output_5.fas")
after <- init_clock_models(
list(create_rln_clock_model()), fasta_filenames = fasta_filenames
)
testthat::expect_equal(after[[1]]$dimension, 8)
fasta_filenames <- beautier::get_beautier_path("test_output_6.fas")
after <- init_clock_models(
list(create_rln_clock_model()), fasta_filenames = fasta_filenames
)
testthat::expect_equal(after[[1]]$dimension, 10)
})
test_that("initialize RLN clock model with correct mparam_id", {
fasta_filenames <- beautier::get_beautier_path("test_output_5.fas")
after <- init_clock_models(
list(create_rln_clock_model(mparam_id = 42)),
fasta_filenames = fasta_filenames
)
testthat::expect_equal(after[[1]]$mparam_id, 42)
})
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