Creates the tree section (part of the state section) when there is tip-dating

tipdate_taxa_to_xml_tree(
  inference_model,
  id = "deprecated",
  tipdates_filename = "deprecated"
)

Arguments

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.

id

an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids_from_fasta_filenames)

tipdates_filename

name of the file containing the tip dates. This file is assumed to have two columns, separated by a tab. The first column contains the taxa names, the second column contains the date.

Value

the random phylogeny as XML text

Author

Richèl J.C. Bilderbeek