Examples with SpeciesTreeBMPrior dr.evomodel.speciation.SpeciesTreeBMPrior used on opensource projects

Example 1 with SpeciesTreeBMPrior

use of dr.evomodel.speciation.SpeciesTreeBMPrior in project beast-mcmc by beast-dev.

the class SpeciesTreeBMPriorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final SpeciesTreeModel st = (SpeciesTreeModel) xo.getChild(SpeciesTreeModel.class);
    //ParametricDistributionModel pr = (ParametricDistributionModel) xo.getChild(ParametricDistributionModel.class);
    final Object child = xo.getChild(SIGMA);
    Parameter popSigma = child != null ? (Parameter) ((XMLObject) child).getChild(Parameter.class) : null;
    Parameter stSigma = (Parameter) ((XMLObject) xo.getChild(STSIGMA)).getChild(Parameter.class);
    final XMLObject cxo = (XMLObject) xo.getChild(TIPS);
    final ParametricDistributionModel tipsPrior = (ParametricDistributionModel) cxo.getChild(ParametricDistributionModel.class);
    final boolean logRoot = xo.getAttribute(LOG_ROOT, false);
    return new SpeciesTreeBMPrior(st, popSigma, stSigma, tipsPrior, logRoot);
}