pir_run: Measure the error BEAST2 makes from a known phylogeny.

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

Measure the error BEAST2 makes from a known phylogeny.

Description

From a phylogeny of (un)known speciation model, an alignment is created using a known site model and clock model, as given by alignment_params.

Usage

pir_run(
  phylogeny,
  pir_params = create_pir_params(alignment_params = create_alignment_params(),
    twinning_params = create_twinning_params())
)

Arguments

phylogeny	a phylogeny of class phylo
pir_params	the parameters of pirouette. They are created by create_pir_params.

Value

a data frame with errors, with as many rows as model selection parameter sets. The output can be checked using check_pir_out.

Author(s)

Richèl J.C. Bilderbeek, Giovanni Laudanno

See Also

• Use pir_plot to display the output of pir_run as a figure.

• Use create_test_pir_run_output to create a test output of pir_run.

• Use pir_runs to do multiple pirouette runs.

Examples

if (beautier::is_on_ci()) {

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

  errors <- NA
  if (
    rappdirs::app_dir()$os != "win" &&
    beastier::is_beast2_installed()
  ) {
    pir_run(
      phylogeny = phylogeny,
      pir_params = pir_params
    )
  } else {
    create_test_pir_run_output()
  }
}

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