context("extract_parameters")
test_that("extract_erg: use", {
file <- read_file(find_path("toy_example_1.RDa"))
erg <- extract_erg(file)
expect_true(erg >= 0.0)
})
test_that("extract_erg: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_erg(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$erg <- NULL
expect_error(
extract_erg(file),
"parameter 'erg' absent"
)
})
test_that("extract_eri", {
file <- read_file(find_path("toy_example_1.RDa"))
eri <- extract_eri(file)
expect_true(eri >= 0.0)
})
test_that("extract_eri: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_eri(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$eri <- NULL
expect_error(
extract_eri(file),
"parameter 'eri' absent"
)
})
test_that("extract_scr", {
file <- read_file(find_path("toy_example_1.RDa"))
scr <- extract_scr(file)
expect_true(scr >= 0.0)
})
test_that("extract_scr: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_scr(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$scr <- NULL
expect_error(
extract_scr(file),
"parameter 'scr' absent"
)
})
test_that("extract_sirg", {
file <- read_file(find_path("toy_example_1.RDa"))
expect_true("sirg" %in% names(file$parameters))
expect_false(
"species_initiation_rate_good_species" %in% names(file$parameters)
)
sirg <- extract_sirg(file)
expect_true(sirg >= 0.0)
})
test_that("extract_sirg: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_sirg(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$sirg <- NULL
expect_error(
extract_sirg(file),
"parameter 'sirg' absent"
)
})
test_that("extract_siri", {
file <- read_file(find_path("toy_example_1.RDa"))
siri <- extract_siri(file)
expect_true(siri >= 0.0)
})
test_that("extract_siri: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_siri(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$siri <- NULL
expect_error(
extract_siri(file),
"parameter 'siri' absent"
)
})
test_that("extract_napst", {
file <- read_file(find_path("toy_example_1.RDa"))
napst <- extract_napst(file)
expect_equal(napst, 1)
})
test_that("extract_napst: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_napst(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$n_alignments <- NULL
expect_error(
extract_napst(file),
"parameter 'n_alignments' absent"
)
})
test_that("extract_nppa: use", {
file <- read_file(find_path("toy_example_1.RDa"))
nppa <- extract_nppa(file)
expect_equal(nppa, 1)
})
test_that("extract_nppa: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_nppa(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$n_beast_runs <- NULL
expect_error(
extract_nppa(file),
"parameter 'n_beast_runs' absent"
)
})
test_that("extract_nspp: use", {
file <- read_file(find_path("toy_example_1.RDa"))
nspp <- extract_nspp(file)
expect_equal(nspp, 10)
})
test_that("extract_nspp: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_nspp(file),
"file\\$parameters not found"
)
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters$mcmc_chainlength <- NULL
file$parameters$nspp <- NULL
expect_error(
extract_nspp(file),
"parameter 'nspp' absent"
)
})
test_that("extract_fixed_crown_age returns FALSE per default", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
fixed_crown_age <- wiritttes::extract_fixed_crown_age(file)
testthat::expect_false(fixed_crown_age)
})
test_that("extract_fixed_crown_age returns TRUE when set", {
filename <- tempfile("extract_fixed_crown_age_true")
wiritttes::save_parameters_to_file(
rng_seed = 42,
sirg = 0.2,
siri = 0.2,
scr = 0.2,
erg = 0.1,
eri = 0.1,
age = 10,
mutation_rate = 0.01,
n_alignments = 1,
sequence_length = 5,
nspp = 10,
n_beast_runs = 1,
filename = filename,
fixed_crown_age = TRUE
)
fixed_crown_age <- wiritttes::extract_fixed_crown_age(
wiritttes::read_file(filename = filename))
testthat::expect_true(fixed_crown_age)
file.remove(filename)
})
test_that("extract_fixed_crown_age: abuse", {
file <- read_file(find_path("toy_example_1.RDa"))
file$parameters <- NULL
expect_error(
extract_fixed_crown_age(file),
"file\\$parameters not found"
)
})
test_that("extract_age: use", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
age <- wiritttes::extract_age(file)
testthat::expect_equal(age, 5)
})
test_that("extract_age abuse", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters <- NULL
testthat::expect_error(
wiritttes::extract_age(file),
"file\\$parameters not found"
)
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters$age <- NULL
testthat::expect_error(
wiritttes::extract_age(file),
"parameter 'age' absent"
)
})
test_that("extract_mutation_rate: use", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
mutation_rate <- wiritttes::extract_mutation_rate(file)
testthat::expect_equal(mutation_rate, 0.01, tolerance = 0.0001)
})
test_that("extract_mutation_rate abuse", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters <- NULL
testthat::expect_error(
wiritttes::extract_mutation_rate(file),
"file\\$parameters not found"
)
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters$mutation_rate <- NULL
testthat::expect_error(
wiritttes::extract_mutation_rate(file),
"parameter 'mutation_rate' absent"
)
})
test_that("extract_seed: use", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
seed <- wiritttes::extract_seed(file)
testthat::expect_equal(seed, 1)
})
test_that("extract_seed abuse", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters <- NULL
testthat::expect_error(
wiritttes::extract_seed(file),
"file\\$parameters not found"
)
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters$rng_seed <- NULL
testthat::expect_error(
wiritttes::extract_seed(file),
"parameter 'rng_seed' absent"
)
})
test_that("extract_sequence_length: use", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
sequence_length <- wiritttes::extract_sequence_length(file)
testthat::expect_equal(sequence_length, 1000)
})
test_that("extract_sequence_length abuse", {
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters <- NULL
testthat::expect_error(
wiritttes::extract_sequence_length(file),
"file\\$parameters not found"
)
file <- wiritttes::read_file(wiritttes::find_path("toy_example_1.RDa"))
file$parameters$sequence_length <- NULL
testthat::expect_error(
wiritttes::extract_sequence_length(file),
"parameter 'sequence_length' absent"
)
})
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