test_that("use", {
if (!beastier::is_beast2_installed()) return()
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
fasta_filename <- get_babette_path("anthus_aco.fas")
inference_model <- beautier::create_inference_model(
mcmc = create_test_mcmc(chain_length = 10000),
mrca_prior = beautier::create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename),
taxa_names = get_taxa_names(fasta_filename),
is_monophyletic = TRUE,
mrca_distr = create_normal_distr(mean = 1.0, sigma = 0.01)
)
)
beast2_options <- create_beast2_options()
bbt_out <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
expect_silent(
plot_densitree(bbt_out$anthus_aco_trees[5:10])
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
})
test_that("minimal use", {
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
# Submitted at https://github.com/KlausVigo/phangorn/commit/8440b88fb09249a2653562f0eaee04a51789bcba # nolint indeed URLs can be long
phylogeny_1 <- ape::read.tree(text = "((A:2, B:2):1, C:3);")
phylogeny_2 <- ape::read.tree(text = "((A:1, B:1):2, C:3);")
trees <- c(phylogeny_1, phylogeny_2)
expect_silent(phangorn::densiTree(trees))
expect_silent(plot_densitree(trees))
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
})
test_that("abuse", {
expect_error(
plot_densitree("nonsense"),
"'phylos' must be of class 'multiPhylo'"
)
})
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