Examples with BirthDeathGernhard08Model dr.evomodel.speciation.BirthDeathGernhard08Model used on opensource projects

Example 6 with BirthDeathGernhard08Model

use of dr.evomodel.speciation.BirthDeathGernhard08Model in project beast-mcmc by beast-dev.

the class YuleModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    final XMLObject cxo = xo.getChild(BIRTH_RATE);
    final boolean conditonalOnRoot = xo.getAttribute(BirthDeathModelParser.CONDITIONAL_ON_ROOT, false);
    final Parameter brParameter = (Parameter) cxo.getChild(Parameter.class);
    Logger.getLogger("dr.evomodel").info("\nUsing Yule prior on tree");
    return new BirthDeathGernhard08Model(xo.getId(), brParameter, null, null, BirthDeathGernhard08Model.TreeType.UNSCALED, units, conditonalOnRoot);
}

Example 7 with BirthDeathGernhard08Model

use of dr.evomodel.speciation.BirthDeathGernhard08Model in project beast-mcmc by beast-dev.

the class YuleLikelihoodTest method yuleLikelihoodTester.

private void yuleLikelihoodTester(Tree tree, double birthRate, double logL) {
    Parameter b = new Parameter.Default("b", birthRate, 0.0, Double.MAX_VALUE);
    Parameter d = new Parameter.Default("d", 0.0, 0.0, Double.MAX_VALUE);
    SpeciationModel speciationModel = new BirthDeathGernhard08Model(b, d, null, BirthDeathGernhard08Model.TreeType.TIMESONLY, Units.Type.YEARS);
    Likelihood likelihood = new SpeciationLikelihood(tree, speciationModel, "yule.like");
    assertEquals(likelihood.getLogLikelihood(), logL);
}