beautier: A package to create a BEAST2 input file.

beautier allows to create a BEAST2 input file, using an R interface. beautier closely follows the interface of BEAUti 2, a GUI tool bundled with BEAST2, including its default settings.

Details

See the documentation of create_inference_model to see the features of BEAST2 that beautier supports.

See also

These are packages associated with beautier:

• The package beastier can run BEAST2 from R

• The package tracerer can parse BEAST2 output files from R

• The package mauricer manages BEAST2 packages from R

• The package babette combines the functionality of beautier, beastier, mauricer and tracerer into a single workflow

Author

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  # Get an example FASTA file
  input_filename <- get_fasta_filename()

  # The file created by beautier, a BEAST2 input file
  output_filename <- get_beautier_tempfilename()

  # Use the default BEAUti settings to create a BEAST2 input file
  create_beast2_input_file_from_model(
    input_filename,
    output_filename,
    inference_model = create_inference_model()
  )

  # Remove the folder that contains the beautier temporary files
  remove_beautier_folder()
  check_empty_beautier_folder()
}