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More tests on Travis, setup of ropensci/beautier#46
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richelbilderbeek committed Sep 22, 2018
1 parent 8256c8a commit 8de8b1d
Showing 1 changed file with 124 additions and 61 deletions.
185 changes: 124 additions & 61 deletions tests/testthat/test-bbt_run.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
context("bbt_run")

test_that("use, one alignment", {
testit::assert(beastier::is_beast2_installed())

out <- NA

Expand Down Expand Up @@ -40,6 +41,7 @@ test_that("use, one alignment", {
})

test_that("use, one alignment, verbose, cleanup", {
testit::assert(beastier::is_beast2_installed())

testthat::expect_output(
bbt_run(
Expand All @@ -51,6 +53,7 @@ test_that("use, one alignment, verbose, cleanup", {
})

test_that("use, one alignment, verbose, no cleanup", {
testit::assert(beastier::is_beast2_installed())

fasta_filenames <- get_babette_path("anthus_aco.fas")
beast2_input_filename <- tempfile(fileext = ".xml")
Expand Down Expand Up @@ -84,6 +87,7 @@ test_that("use, one alignment, verbose, no cleanup", {
})

test_that("use, one alignment, same RNG should give same results", {
testit::assert(beastier::is_beast2_installed())

rng_seed <- 42
out_1 <- bbt_run(
Expand All @@ -107,6 +111,7 @@ test_that("use, one alignment, same RNG should give same results", {
})

test_that("use, two alignments, estimated crown ages", {
testit::assert(beastier::is_beast2_installed())

out <- NA

Expand Down Expand Up @@ -148,12 +153,8 @@ test_that("use, two alignments, estimated crown ages", {
testthat::expect_true("rejectFC" %in% names(out$operators))
testthat::expect_true("rejectIv" %in% names(out$operators))
testthat::expect_true("rejectOp" %in% names(out$operators))

})




test_that("abuse", {

testthat::expect_error(
Expand All @@ -171,12 +172,13 @@ test_that("abuse", {
################################################################################

test_that("Run all defaults", {

created <- beautier::create_beast2_input(
input_filenames = beautier::get_fasta_filename()
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)

testthat::expect_true(are_beast2_input_lines(created))
})

################################################################################
Expand All @@ -188,28 +190,60 @@ test_that("Run all defaults", {
################################################################################

test_that("Run GTR", {

created <- beautier::create_beast2_input(
input_filenames = beautier::get_fasta_filename(),
site_models = create_gtr_site_model()
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
site_models = create_gtr_site_model(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)

testthat::expect_true(are_beast2_input_lines(created))
})

################################################################################
# Site model: HKY
################################################################################

test_that("Run HKY", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
site_models = create_hky_site_model(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
})

################################################################################
# Site model: JC69
################################################################################

test_that("Run JC69", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
site_models = create_jc69_site_model(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
})

################################################################################
# Site model: TN93
################################################################################

test_that("Run TN93", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
site_models = create_tn93_site_model(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
})

################################################################################
# Clock models
Expand All @@ -218,35 +252,30 @@ test_that("Run GTR", {
################################################################################
# Clock model: RLN
################################################################################

test_that("Use of a strict clock", {

input_fasta_filename <- beautier::get_fasta_filename()
id <- get_alignment_id(input_fasta_filename)
lines <- beautier::create_beast2_input(
input_filenames = input_fasta_filename,
clock_models = create_strict_clock_model(
clock_rate_param = create_clock_rate_param(id = id)
test_that("Run RLN clock", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
clock_models = create_rln_clock_model(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
testthat::expect_true(are_beast2_input_lines(lines))
})

test_that("Use of a RLN clock", {

lines <- beautier::create_beast2_input(
input_filenames = beautier::get_fasta_filename(),
clock_models = create_rln_clock_model()
)
testthat::expect_true(are_beast2_input_lines(lines))

})

################################################################################
# Clock model: strict
################################################################################


test_that("Run strict clock", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
clock_models = create_strict_clock_model(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
})

################################################################################
# Tree priors
Expand All @@ -255,58 +284,79 @@ test_that("Use of a RLN clock", {
################################################################################
# Tree prior: BD
################################################################################

test_that("Run BD tree prior", {

created <- beautier::create_beast2_input(
input_filenames = beautier::get_fasta_filename(),
tree_priors = create_bd_tree_prior()
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
tree_priors = create_bd_tree_prior(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)

testthat::expect_true(are_beast2_input_lines(created))
})


################################################################################
# Tree prior: CBS
################################################################################

test_that("Run CBP", {

lines <- create_beast2_input(
input_filenames = get_beautier_path("anthus_aco_sub.fas"),
tree_priors = create_cbs_tree_prior(group_sizes_dimension = 4)
test_that("Run CBS tree prior", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
tree_priors = create_cbs_tree_prior(
group_sizes_dimension = 4
),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
testthat::expect_true(are_beast2_input_lines(lines))
})

################################################################################
# Tree prior: CCP
################################################################################
test_that("Run CCP tree prior", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
tree_priors = create_ccp_tree_prior(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
})

################################################################################
# Tree prior: CEP
################################################################################

test_that("Run CEP", {

lines <- beautier::create_beast2_input(
input_filenames = beautier::get_fasta_filename(),
tree_priors = beautier::create_cep_tree_prior()
test_that("Run CEP tree prior", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
tree_priors = create_cep_tree_prior(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
testthat::expect_true(are_beast2_input_lines(lines))

})

################################################################################
# Tree prior: Yule
################################################################################
test_that("Run Yule tree prior", {
if (!beastier:::is_on_travis()) return()
expect_silent(
bbt_run(
fasta_filenames = get_beautier_path("anthus_aco_sub.fas"),
tree_priors = create_yule_tree_prior(),
mcmc = beautier::create_mcmc(chain_length = 2000)
)
)
})


################################################################################
# MRCA priors
################################################################################

test_that("Run MRCA, no distr", {

fasta_filename <- get_fasta_filename()
Expand Down Expand Up @@ -496,3 +546,16 @@ test_that("abuse", {
"'rng_seed' should be NA or non-zero positive"
)
})

test_that("Interaction kappa1, kappa2 and S in TN93", {
# https://github.com/richelbilderbeek/beautier/issues/46
# creating a TN93 model with the default settings
# creates two log-normal distributions
# as priors for kappa1 and kappa2,
# where the S parameter has lower=0, upper=0 and value=1.25.
# This works if S is not estimated,
# because BEAST2 only checks upper and lower
# when modifying the value (not when initialising it)
# but it will break if S is estimated.

})

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