Creates the XML text for the distribution tag with the treeLikelihood ID, of a BEAST2 parameter file.

Creates the XML text for the distribution tag with the treeLikelihood ID, of a BEAST2 parameter file, in an unindented form

Usage

create_tree_likelihood_distr_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.

Value

lines of XML text

Details

The distribution tag (with ID equals treeLikelihood) has these elements:

   <distribution id="treeLikelihood"[...]>
      <siteModel[...]>
        [...]
      </siteModel>
      <branchRateModel[...]>
        [...]
      </branchRateModel>
   </distribution>

The siteModel section is created by create_site_model_xml. The branchRateModel section is created by create_branch_rate_model_xml.

Zooming out:

  <beast[...]>
    <run[...]>
      <distribution id="posterior"[...]>
        <distribution id="likelihood"[...]>
          [this section]
        </distribution>
      </distribution>
    </run>
  </beast>

Note

this function is not intended for regular use, thus its long name length is accepted

See also

this function is called by create_beast2_input_distr, together with create_beast2_input_distr_prior

Author

Richèl J.C. Bilderbeek