pirouette (version 1.6.9)

create_test_pir_params: Create a set of testing parameters for pirouette

Description

Create a set of testing parameters for pirouette

Usage

create_test_pir_params(
  alignment_params = create_test_alignment_params(),
  twinning_params = NA,
  experiments = list(create_test_experiment()),
  error_measure_params = create_error_measure_params(),
  evidence_filename = NA,
  verbose = FALSE
)

Value

a list with all pirouette parameters

Arguments

alignment_params

parameters to simulate an alignment, as can be created by create_alignment_params

twinning_params

can be NA if no twinning is desired, or can be the twinning parameters, as can be created by create_twinning_params

experiments

a list of one or more pirouette experiments, as can be created by create_experiment. If more than one experiment is provided and a "generative" experiment is part of them, the "generative" one has to be the first in the list. See also:

• Use check_experiments to check the list of experiments for validity

• 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

• Use shorten_experiments to shorten the run time of the list of experiments

error_measure_params

parameter set to specify how the error between the given phylogeny and the Bayesian posterior is determined. Use create_error_measure_params to create such a parameter set

evidence_filename

filename to store the estimated evidences (aka marginal likelihoods), as can be created by get_temp_evidence_filename. Must be NA if there is evidence estimation (as determined by will_measure_evidence).

verbose

if TRUE, show more output

Author

Richèl J.C. Bilderbeek

See Also

Use create_test_pir_params_setup to create a test pir_params following a specific setup, such as having a candidate experiemnt and/or use twinning.

Examples

if (rappdirs::app_dir()$os != "win" &&
  beautier::is_on_ci() &&
  beastier::is_beast2_installed()
) {
  pir_params <- create_test_pir_params()
  check_pir_params(pir_params)

  pir_out <- pir_run(
    phylogeny = ape::read.tree(text = "((A:1, B:1):1, C:2);"),
    pir_params = pir_params
  )
  pir_plot(pir_out)
}