context("test-check_mrca_prior")
test_that("use, default", {
mrca_prior <- create_mrca_prior()
expect_silent(check_mrca_prior(mrca_prior))
})
test_that("use, alignment ID and taxon names", {
fasta_filename <- get_beautier_path("anthus_aco.fas")
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = fasta_filename),
taxa_names = get_taxa_names(filename = fasta_filename)
)
expect_silent(check_mrca_prior(mrca_prior))
})
test_that("negatives", {
# NA is a valid null-MRCA-prior
expect_silent(check_mrca_prior(NA))
expect_error(check_mrca_prior("nonsense"))
expect_error(check_mrca_prior(NULL))
expect_error(check_mrca_prior(314))
})
context("test-check_mrca_prior")
test_that("use", {
expect_silent(check_mrca_prior(create_mrca_prior()))
expect_error(
check_mrca_prior(
create_mrca_prior(alignment_id = c(1, 2))
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(alignment_id = NULL)
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(taxa_names = c(1, 2))
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(taxa_names = NULL)
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(is_monophyletic = "nonsense")
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(is_monophyletic = NULL)
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(mrca_distr = "nonsense")
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(name = c(1, 2))
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(name = NULL)
)
)
expect_error(
check_mrca_prior(
create_mrca_prior(clock_prior_distr_id = "nonsense")
),
"'clock_prior_distr_id' must be one NA or one number"
)
expect_error(
check_mrca_prior(
create_mrca_prior(clock_prior_distr_id = c(1, 2))
),
"'clock_prior_distr_id' must be one NA or one number"
)
expect_error(
check_mrca_prior(
create_mrca_prior(clock_prior_distr_id = NULL)
),
"'clock_prior_distr_id' must be one NA or one number"
)
})
test_that("in-depth use", {
good_mrca_prior <- create_mrca_prior()
# OK
expect_silent(
check_mrca_prior(
good_mrca_prior
)
)
# Wrong parameter names
mrca_prior <- good_mrca_prior
mrca_prior$name <- NULL
expect_error(
check_mrca_prior(
mrca_prior
),
"'name' must be an element of an 'mrca_prior'"
)
mrca_prior <- good_mrca_prior
mrca_prior$alignment_id <- NULL
expect_error(
check_mrca_prior(
mrca_prior
),
"'alignment_id' must be an element of an 'mrca_prior'"
)
mrca_prior <- good_mrca_prior
mrca_prior$taxa_names <- NULL
expect_error(
check_mrca_prior(mrca_prior),
"'taxa_names' must be an element of an 'mrca_prior'"
)
mrca_prior <- good_mrca_prior
mrca_prior$is_monophyletic <- NULL
expect_error(
check_mrca_prior(mrca_prior),
"'is_monophyletic' must be an element of an 'mrca_prior'"
)
mrca_prior <- good_mrca_prior
mrca_prior$mrca_distr <- NULL
expect_error(
check_mrca_prior(mrca_prior),
"'mrca_distr' must be an element of an 'mrca_prior'"
)
mrca_prior <- good_mrca_prior
mrca_prior$clock_prior_distr_id <- NULL
expect_error(
check_mrca_prior(mrca_prior),
"'clock_prior_distr_id' must be an element of an 'mrca_prior'"
)
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.