errorses_to_data_frame: Convert the collect of errors to a data frame

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

Convert the collect of errors to a data frame

Description

Convert the collect of errors to a data frame

Usage

errorses_to_data_frame(errorses, experiments, marg_liks)

Arguments

errorses	a collection of errors (hence the reduplicated plural)
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
marg_liks	a data frame with marginal likelihoods/evidences. A test data frame can be created by create_test_marg_liks

Value

a data frame

Author(s)

Richèl J.C. Bilderbeek, Giovanni Laudanno

Examples

if (beautier::is_on_ci() && beastier::is_beast2_installed()) {
  phylogeny <- ape::read.tree(text = "(((A:1, B:1):1, C:2):1, D:3);")
  pir_params <- create_test_pir_params()

  # A normal user should not need to call 'phylo_to_errors' directly.
  # For a developer that needs to, the 'pir_params' must be initialized
  pir_params <- init_pir_params(pir_params)

  create_tral_file(
    phylogeny = phylogeny,
    alignment_params = pir_params$alignment_params,
    verbose = FALSE
  )

  errorses <- list()
  errorses[[1]] <- phylo_to_errors(
    phylogeny = phylogeny,
    alignment_params = pir_params$alignment_params,
    error_measure_params = pir_params$error_measure_params,
    experiment = pir_params$experiments[[1]],
    verbose = pir_params$verbose
  )

  errorses_to_data_frame(
    errorses = errorses,
    experiments = list(pir_params$experiments[[1]]),
    marg_liks = create_test_marg_liks(
      site_models = list(beautier::create_jc69_site_model()),
      clock_models = list(beautier::create_strict_clock_model()),
      tree_priors = list(beautier::create_yule_tree_prior())
    )
  )
}

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