create_error_measure_params: Create the parameters to specify how the error between the...

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

Create the parameters to specify how the error between the given phylogeny and the Bayesian posterior trees is measured.

Description

Create the parameters to specify how the error between the given phylogeny and the Bayesian posterior trees is measured.

Usage

create_error_measure_params(
  burn_in_fraction = 0.1,
  error_fun = get_nltt_error_fun()
)

Arguments

burn_in_fraction

the fraction of the posterior trees (starting from the ones generated first) that will be discarded, must be a value from 0.0 (keep all), to 1.0 (discard all).

error_fun

function that determines the error between a given phylogeny and a the trees in a Bayesian posterior. The function must have two arguments: the one given phylogeny, of class phylo one or more posterior trees, of class multiphylo The function must return as many errors as there are posterior trees given. The error must be lowest between identical trees. Example functions are: get_gamma_error_fun: use the absolute difference in gamma statistic get_nltt_error_fun: use the nLTT statistic

Value

an error measurement parameter set

Author(s)

Richèl J.C. Bilderbeek, Giovanni Laudanno

Examples

if (beautier::is_on_ci()) {

  # Default
  error_measure_params <- create_error_measure_params()

  # Use the nLTT statistic with a burn-in of 10%
  error_measure_params <- create_error_measure_params(
    burn_in_fraction = 0.1,
    error_fun = get_nltt_error_fun()
  )

  # Use the gamma statistic with a burn-in of 20%
  error_measure_params <- create_error_measure_params(
    burn_in_fraction = 0.2,
    error_fun = get_gamma_error_fun()
  )

  pir_params <- create_pir_params(
    alignment_params = create_test_alignment_params(),
    experiments = list(create_test_gen_experiment()),
    error_measure_params = error_measure_params
  )

  if (rappdirs::app_dir()$os != "win" &&
    beautier::is_on_ci() && beastier::is_beast2_installed()
  ) {
    pir_out <- pir_run(
      phylogeny = ape::read.tree(text = "((A:2, B:2):1, C:3);"),
      pir_params = pir_params
    )
    pir_plot(pir_out)
  }
}

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