pirouette (version 1.6.9)

pir_run: 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())
)

Value

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

Arguments

phylogeny

a phylogeny of class phylo

pir_params

the parameters of pirouette. They are created by create_pir_params.

Author

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()
  }
}