create_beast2_input_beast: Creates the XML text for the 'beast' tag of a BEAST2...

In beautier: 'BEAUti' from R

Creates the XML text for the beast tag of a BEAST2 parameter file.

Description

Creates the XML text for the beast tag of a BEAST2 parameter file, which is directly after the XML declaration (created by create_xml_declaration.

Usage

create_beast2_input_beast(
  input_filename,
  inference_model = create_inference_model()
)

Arguments

input_filename	A FASTA filename. Use get_fasta_filename to obtain a testing FASTA filename.
inference_model	a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.

Details

The beast tag has these elements:

  <beast[...]>
      <data
      [...]
      </data>
      [map names]
      <run[...]>
      [...]
      </run>
  </beast>

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_from_model to create the complete XML text. Use create_beast2_input_data to create the XML text for the data tag only. Use create_beast2_input_map to create the XML text for the [map names] part. Use create_beast2_input_run to create the XML text for the run tag only.

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