pirouette-package: pirouette: A package to estimate the error BEAST2 makes in...

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

pirouette: A package to estimate the error BEAST2 makes in inferring a phylogeny.

Description

'pirouette' is an R package that estimates the error BEAST2 makes from a given phylogeny. This phylogeny can be created using any (non-BEAST) speciation model, for example the Protracted Birth-Death or Multiple-Birth-Death models. 'pirouette' is presented in the article (in press) "pirouette: the error BEAST2 makes in inferring a phylogeny" authored by R. J. C. Bilderbeek, G. Laudanno and R. S. Etienne.

Note

These abbeviations are commonly used throughout the package:

• 'nsm' Nucleotide Substitution Model

• 'tral': TRue ALignment

• 'trtr': TRue TRee

• 'twal': TWin ALignment

• 'twtr': TWin TRee

Author(s)

Richèl J.C. Bilderbeek

See Also

• To simulate an alignment, use sim_alignment_with_std_nsm or sim_alignment_with_n_mutations.

• To simulate a true alignment, see check_sim_tral_fun for an overview of functions.

• To simulate a twin alignment, see check_sim_twal_fun for an overview of functions.

• To simulate a twin tree, see check_sim_twin_tree_fun for an overview of functions.

These are packages associated with pirouette:

• babette: work with BEAST2

• beautier: create BEAST2 input files

• beastier: run BEAST2

• mauricer: install BEAST2 packages

• mcbette: compare inference models

• tracerer: parse and analyse BEAST2 output

Examples

if (beautier::is_on_ci()) {

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

  # Select all experiments with 'run_if' is 'always'
  experiment <- create_test_gen_experiment()
  experiments <- list(experiment)

  pir_params <- create_pir_params(
    alignment_params = create_test_alignment_params(),
    experiments = experiments
  )

  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.