create_all_bd_experiments: Create all pirouette experiments that have a tree prior that...

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

Create all pirouette experiments that have a tree prior that follows a birth-death model.

Description

These tree priors are both the pure-birth (or Yule) model (as created by create_yule_tree_prior) and the constant-rate birth-death model (as created by create_bd_tree_prior).

Usage

create_all_bd_experiments(
  site_models = beautier::create_site_models(),
  clock_models = beautier::create_clock_models(),
  tree_priors = list(beautier::create_bd_tree_prior(),
    beautier::create_yule_tree_prior()),
  mcmc = beautier::create_mcmc(store_every = 1000),
  exclude_model = NA
)

Arguments

site_models	a list of one or more site models, as created by create_site_model
clock_models	a list of one or more clock models, as created by create_clock_model
tree_priors	a list of one or more tree priors, as created by create_tree_prior
mcmc	MCMC options, as created by create_mcmc
exclude_model	an inference model that has to be excluded, as can be created by create_inference_model

Details

These experiments are used in the create_pir_params function

Value

all pirouette experiments.

Author(s)

Richèl J.C. Bilderbeek

See Also

• Use create_all_experiments to create experiments with all combinations of tree model, clock model and tree priors

• Use create_all_bd_experiments to create experiments with all combinations of tree model, clock model and tree priors, except for only using birth-death tree priors

• Use create_all_coal_experiments to create all experiments with all combinations of tree model, clock model and tree priors, except for only coalescent tree priors

Examples

if (rappdirs::app_dir()$os != "win" && beautier::is_on_github_actions()) {
  # it does not work on Windows
  experiments <- create_all_bd_experiments()
  check_experiments(experiments)

  pir_params <- create_pir_params(
    alignment_params = create_test_alignment_params(),
    experiments = experiments,
    evidence_filename = get_temp_evidence_filename()
  )
}

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