create_branch_rate_model_xml: Internal function to create the 'branchRateModel' section of...

In richelbilderbeek/beastscriptr: 'BEAUti' from R

Internal function to create the branchRateModel section of the XML as text.

Description

Creates the branchRateModel section of the XML as text.

Usage

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

  <branchRateModel[...]>
    [...]
  </branchRateModel>

When there is a strict clock, create_strict_clock_branch_rate_model_xml is called. When there is an RLN clock, create_rln_clock_branch_rate_model_xml is called.

Zooming out:

  <beast[...]>
    <run[...]>
      <distribution id="posterior"[...]>
        <distribution id="likelihood"[...]>
          <distribution id="treeLikelihood"[...]>
             [...]

             [this section]
          </distribution>
        </distribution>
      </distribution>
    </run>
  </beast>

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

richelbilderbeek/beastscriptr documentation built on April 9, 2024, 2:28 p.m.