phylo_to_errors: Measure the error BEAST2 makes from a true phylogeny.

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

Measure the error BEAST2 makes from a true phylogeny.

Description

The supplied phylogeny (phylogeny) is the true/known phylogeny. From the phylogeny, already an alignment is simulated and saved as a FASTA file with name alignment_params$fasta_filename.

Usage

phylo_to_errors(
  phylogeny,
  alignment_params,
  experiment,
  error_measure_params = create_error_measure_params(),
  verbose = FALSE
)

Arguments

phylogeny	a phylogeny of class phylo
alignment_params	parameters to simulate an alignment, as can be created by create_alignment_params
experiment	a pirouette experiment, as can be created by create_experiment
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
verbose	if TRUE, show more output

Details

The posterior phylogenies are compared to the true/known phylogeny using the nLTT statistics. These nLTT statistics, all with values betweem (including) zero and (including) one, are returned.

Value

a numerical vector of error values

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci()) {

  phylogeny <- ape::read.tree(text = "(((A:1, B:1):1, C:2):1, D:3);")

  # 'phylo_to_errors' expects an alignment file to be present
  alignment_params <- create_test_alignment_params()

  # Create the alignment
  create_tral_file(
    phylogeny = phylogeny,
    alignment_params = alignment_params
  )
  experiment <- create_test_gen_experiment()

  # A normal user should never need to initialize the experiment,
  # as this is done by 'pir_run'.
  # A develop, however, that wants to call 'phylo_to_errors',
  # should initialaze as such
  experiment <- init_experiment(
    experiment = experiment,
    alignment_params = alignment_params
  )

  experiments <- list(experiment)

  if (rappdirs::app_dir()$os != "win" && beastier::is_beast2_installed()) {
    phylo_to_errors(
      phylogeny = phylogeny,
      alignment_params = alignment_params,
      experiment = experiment
    )
  }
}

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