create_experiment: Create a valid pirouette experiment.

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

Create a valid pirouette experiment.

Description

The arguments are checked by check_experiment.

Usage

create_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(input_filename =
    beastier::create_temp_input_filename(), output_state_filename =
    beastier::create_temp_state_filename()),
  est_evidence_mcmc = beautier::create_ns_mcmc(epsilon = 1e-12),
  beast2_bin_path = beastier::get_default_beast2_bin_path(),
  errors_filename = pirouette::get_temp_errors_filename()
)

Arguments

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.
beast2_bin_path	path to BEAST2 binary file. The use of the binary BEAST2 file is required for estimation of the evidence (aka marginal likelihood). The default BEAST2 binary path can be obtained using get_default_beast2_bin_path
errors_filename	baseline name for errors filenames, as created by get_temp_errors_filename

Value

a pirouette experiment.

Author(s)

Richèl J.C. Bilderbeek, Giovanni Laudanno

Examples

if (beautier::is_on_ci()) {
  create_experiment()
}

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.