babette: babette: A package for Bayesian phylogenetics.

babetteR Documentation

babette: A package for Bayesian phylogenetics.

Description

'babette' provides for an alternative workflow of using the popular phylogenetics tool 'BEAST2', including it peripheral tools. From an alignment and inference model, a posterior of jointly estimated phylogenies and parameter estimates is generated.

Note

the imports are created by script 'scripts/create_imports.R'

Author(s)

Richèl J.C. Bilderbeek

See Also

Use bbt_self_test to do verify babette is installed correctly.

These are packages associated with 'babette':

  • 'beautier' creates 'BEAST2' input files.

  • 'beastier' runs 'BEAST2'.

  • 'mauricer' does 'BEAST2' package management.

  • 'tracerer' parses 'BEAST2' output files.

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  inference_model <- create_test_inference_model()
  beast2_options <- create_beast2_options()

  bbt_run_from_model(
    fasta_filename = get_babette_path("anthus_aco.fas"),
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  # Clean up temporary files created by babette
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}
beastier::remove_beaustier_folders()

richelbilderbeek/rbeast2 documentation built on Aug. 15, 2022, 1:10 a.m.