Creates the three logger sections of a BEAST2 XML parameter file

The logger section has these elements:

 <logger id="tracelog" [...]>
     [...]
 </logger>
 <logger id="screenlog" [...]>
     [...]
 </logger>
 <logger id="treelog.t:[alignment ID]"  [...]>
     [...]
 </logger>

Usage

create_loggers_xml(input_filename, 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.

Value

lines of XML text

See also

Use create_tracelog_xml to create the XML text of the logger with the tracelog ID. Use create_screenlog_xml to create the XML text of the logger with the screenlog ID. Use create_treelog_xml to create the XML text of the loggers with the treelog ID.

Author

Richèl J.C. Bilderbeek