create_site_model_xml: Internal function to creates the XML text for the 'siteModel'...

In beautier: 'BEAUti' from R

Internal function to creates the XML text for the siteModel tag of a BEAST2 parameter file.

Description

Creates the XML text for the siteModel tag of a BEAST2 parameter file, which is part of the distribution node for the treeLikelihood ID.

Usage

create_site_model_xml(inference_model)

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.

Details

The siteModel tag has these elements:

  <siteModel[...]>

      [parameters]

      <substModel[...]>
        [...]
      </substModel>
  </siteModel>

The parameter section is created by create_site_model_parameters_xml The substModel section is created by create_subst_model_xml

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()
 # <distribution id="posterior"[...]">
 #     <distribution id="likelihood" [...]>
 #       <siteModel...>
 #         [parameters]
 #       </siteModel>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

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