test_that("matches article", {
if (rappdirs::app_dir()$os == "win") {
skip("This can only run on Linux.")
}
folder_name <- peregrine::get_pff_tempfile()
gen_exp <- create_razzo_gen_experiment(
folder_name = folder_name
)
# --------------------
# Inference conditions
# --------------------
expect_equal(gen_exp$inference_conditions$model_type, "generative")
expect_equal(gen_exp$inference_conditions$run_if, "always")
expect_equal(gen_exp$inference_conditions$do_measure_evidence, TRUE)
# --------------------
# Inference model
# --------------------
expect_equal(gen_exp$inference_model$site_model$name, "JC69")
expect_equal(gen_exp$inference_model$clock_model$name, "strict")
expect_equal(gen_exp$inference_model$tree_prior$name, "birth_death")
expect_equal(
gen_exp$inference_model$mrca_prior$mrca_distr$name,
"normal"
)
expect_equal(
gen_exp$inference_model$mrca_prior$mrca_distr$mean$value,
get_razzo_crown_age()
)
expect_equal(
gen_exp$inference_model$mrca_prior$mrca_distr$sigma$value,
0.0001
)
expect_equal(
gen_exp$inference_model$mcmc$chain_length,
get_razzo_mcmc_chain_length()
)
expect_equal(
gen_exp$inference_model$mcmc$store_every,
get_razzo_mcmc_store_every()
)
expect_equal(
gen_exp$est_evidence_mcmc$chain_length,
get_razzo_mcmc_chain_length()
)
# gen_exp$est_evidence_mcmc
ns_mcmc_gen <- razzo::create_razzo_ns_mcmc(
folder_name = folder_name,
model_type = "generative"
)
expect_equal(
gen_exp$est_evidence_mcmc$chain_length,
ns_mcmc_gen$chain_length
)
expect_equal(
gen_exp$est_evidence_mcmc$store_every,
ns_mcmc_gen$store_every
)
expect_equal(
gen_exp$est_evidence_mcmc$epsilon,
ns_mcmc_gen$epsilon
)
expect_equal(
gen_exp$est_evidence_mcmc$particle_count,
ns_mcmc_gen$particle_count
)
expect_equal(
gen_exp$est_evidence_mcmc$sub_chain_length,
ns_mcmc_gen$sub_chain_length
)
expect_equal(
gen_exp$est_evidence_mcmc$tracelog$filename,
ns_mcmc_gen$tracelog$filename
)
expect_equal(
gen_exp$est_evidence_mcmc$tracelog$log_every,
ns_mcmc_gen$tracelog$log_every
)
expect_equal(
gen_exp$est_evidence_mcmc$treelog$filename,
ns_mcmc_gen$treelog$filename
)
expect_equal(
gen_exp$est_evidence_mcmc$treelog$log_every,
ns_mcmc_gen$treelog$log_every
)
skip("TODO")
# gen_exp$beast2_options$rng_seed must match MBD RNG seed
})
test_that("razzo naming scheme", {
if (rappdirs::app_dir()$os == "win") {
skip("This can only run on Linux.")
}
folder_name <- peregrine::get_pff_tempfile()
gen_exp <- create_razzo_gen_experiment(folder_name = folder_name)
# gen_exp$inference_model
expect_equal(
gen_exp$inference_model$mcmc$tracelog$filename,
file.path(folder_name, "mbd_gen.log")
)
expect_equal(
gen_exp$inference_model$mcmc$treelog$filename,
file.path(folder_name, "mbd_gen.trees")
)
# gen_exp$beast2_options
expect_equal(
gen_exp$beast2_options$input_filename,
file.path(folder_name, "mbd_gen.xml")
)
expect_equal(
gen_exp$beast2_options$output_state_filename,
file.path(folder_name, "mbd_gen.xml.state")
)
# gen_exp$errors_filename
expect_equal(
gen_exp$errors_filename,
file.path(folder_name, "mbd_nltts_gen.csv")
)
# est_evidence_mcmc
expect_equal(
gen_exp$est_evidence_mcmc$treelog$filename,
file.path(folder_name, "mbd_gen_evidence.trees")
)
expect_equal(
gen_exp$est_evidence_mcmc$tracelog$filename,
file.path(folder_name, "mbd_gen_evidence.log")
)
})
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