View source: R/create_gen_experiment.R
create_gen_experiment | R Documentation |
Create a valid testing pirouette generative experiment.
create_gen_experiment(
inference_conditions = create_inference_conditions(),
inference_model = beautier::create_inference_model(mcmc =
beautier::create_mcmc(store_every = 1000)),
beast2_options = beastier::create_beast2_options(),
est_evidence_mcmc = beautier::create_ns_mcmc(epsilon = 1e-12),
errors_filename = pirouette::get_temp_errors_filename()
)
inference_conditions |
conditions under which the inference model is used in the inference |
inference_model |
an inference model, which is a combination of site model, clock model, tree prior and BEAST2 input and input filenames. |
beast2_options |
BEAST2 options, as can be created by create_beast2_options |
est_evidence_mcmc |
MCMC used in the estimation of the evidence (aka marginal likelihood). The MCMC must be a Nested Sampling MCMC, as can be created by create_ns_mcmc. |
errors_filename |
baseline name for errors filenames, as created by get_temp_errors_filename |
a pirouette experiment.
Richèl J.C. Bilderbeek
if (beautier::is_on_ci()) {
# Create a candidate experiment
if (rappdirs::app_dir()$os != "win") {
# it does not work on Windows
experiment <- create_cand_experiment()
check_experiment(experiment)
}
# Create a generative experiment
experiment <- create_gen_experiment()
check_experiment(experiment)
# Use the experiment to create the full pirouette parameter set
pir_params <- create_pir_params(
alignment_params = create_alignment_params(),
experiments = list(experiment)
)
if (rappdirs::app_dir()$os != "win" &&
beautier::is_on_ci() && beastier::is_beast2_installed()
) {
pir_out <- pir_run(
phylogeny = ape::read.tree(text = "((A:2, B:2):1, C:3);"),
pir_params = pir_params
)
pir_plot(pir_out)
}
}
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