create_cand_experiment: Create a valid testing pirouette candidate experiment.

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

Create a valid testing pirouette candidate experiment.

Description

Create a valid testing pirouette candidate experiment.

Usage

create_cand_experiment(
  inference_conditions = create_inference_conditions(model_type = "candidate", run_if =
    "best_candidate", do_measure_evidence = TRUE),
  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(store_every = 1000, epsilon = 1e-12)
)

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.

Value

a pirouette experiment.

Author(s)

Richèl J.C. Bilderbeek

Examples

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)
  }

}

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