test_that("use", {
check_empty_beautier_folder()
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
mrca_prior <- create_mrca_prior(
name = "my_mrca_prior_name",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
mrca_distr = create_normal_distr()
)
expect_true(is_mrca_prior(mrca_prior))
expect_true(is_mrca_prior(NA))
expect_false(is_mrca_prior("nonsense"))
expect_false(is_mrca_prior(42))
expect_false(is_mrca_prior(NULL))
check_empty_beautier_folder()
})
test_that("use, two", {
mrca_prior <- create_mrca_prior(
name = "my_mrca_prior_name",
alignment_id = "anthus_aco",
taxa_names = c("a", "b"),
mrca_distr = create_one_div_x_distr()
)
mrca_priors <- list(mrca_prior, mrca_prior)
expect_false(is_mrca_prior(mrca_priors))
expect_true(is_mrca_prior(mrca_priors[[1]]))
expect_true(is_mrca_prior(mrca_priors[[2]]))
})
test_that("devious", {
fasta_filename <- get_beautier_path("anthus_aco_sub.fas")
g <- create_mrca_prior(
name = "my_mrca_prior_name",
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
mrca_distr = create_normal_distr()
)
expect_true(is_mrca_prior(g))
# No 'name'
h <- g[names(g) != "name"]
expect_false(is_mrca_prior(h))
# No 'alignment_id'
h <- g[names(g) != "alignment_id"]
expect_false(is_mrca_prior(h))
# No 'taxa_names'
h <- g[names(g) != "taxa_names"]
expect_false(is_mrca_prior(h))
# No 'is_monophyletic'
h <- g[names(g) != "is_monophyletic"]
expect_false(is_mrca_prior(h))
# No 'mrca_distr'
h <- g[names(g) != "mrca_distr"]
expect_false(is_mrca_prior(h))
# No 'clock_prior_distr_id'
h <- g[names(g) != "clock_prior_distr_id"]
expect_false(is_mrca_prior(h))
# mrca_distr is not a distribution
h <- g
h$mrca_distr <- "nonsense"
expect_false(is_mrca_prior(h))
check_empty_beautier_folder()
})
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