beautier-package: 'beautier': A package to create a 'BEAST2' input file.

In beautier: 'BEAUti' from R

beautier: A package to create a BEAST2 input file.

Description

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.

Author(s)

Richèl J.C. Bilderbeek

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

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()
}

beautier documentation built on Nov. 2, 2023, 5:08 p.m.