create_tree_likelihood_distr_xml: Creates the XML text for the 'distribution' tag with the...

In beautier: 'BEAUti' from R

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

Description

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.

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>

Value

lines of XML text

Note

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

Author(s)

Richèl J.C. Bilderbeek

See Also

this function is called by create_beast2_input_distr, together with create_beast2_input_distr_prior

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