Examples with AlloppNetworkPriorModel dr.evomodel.alloppnet.speciation.AlloppNetworkPriorModel used on opensource projects

Example 1 with AlloppNetworkPriorModel

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

the class AlloppNetworkPriorParser method parseXMLObject.

/*
	<apspNetworkPrior id="apspnetwork.prior" units="substitutions">
    <eventRate>
      <parameter id="apspnetwork.prior.eventRate" value="0.1" lower="0.0" upper="Infinity"/>
    </eventRate>
    <apspNetwork>
      <apspNetwork idref="apspnetwork"/>
		</apspNetwork>
	</apspNetworkPrior>
*/
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final XMLObject mxo = xo.getChild(MODEL);
    final AlloppNetworkPriorModel anpm = (AlloppNetworkPriorModel) mxo.getChild(AlloppNetworkPriorModel.class);
    final XMLObject asnmxo = xo.getChild(APSPNETWORK);
    final AlloppSpeciesNetworkModel asnm = (AlloppSpeciesNetworkModel) asnmxo.getChild(AlloppSpeciesNetworkModel.class);
    return new AlloppNetworkPrior(anpm, asnm);
}

Example 2 with AlloppNetworkPriorModel

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

the class AlloppNetworkPriorModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    final XMLObject erXo = xo.getChild(EVENTRATE);
    final Parameter eventrate = (Parameter) erXo.getChild(Parameter.class);
    final XMLObject psfXo = xo.getChild(POPULATION_SCALING_FACTOR);
    final Parameter popscalingfactor = (Parameter) psfXo.getChild(Parameter.class);
    final XMLObject tpdXo = xo.getChild(TIP_POPULATION_DISTRIBUTION);
    ParametricDistributionModel tippopmodel = (ParametricDistributionModel) tpdXo.getChild(ParametricDistributionModel.class);
    final XMLObject rpdXo = xo.getChild(ROOT_POPULATION_DISTRIBUTION);
    ParametricDistributionModel rootpopmodel = (ParametricDistributionModel) rpdXo.getChild(ParametricDistributionModel.class);
    final XMLObject hpdXo = xo.getChild(HYBRID_POPULATION_DISTRIBUTION);
    ParametricDistributionModel hybpopmodel = (ParametricDistributionModel) hpdXo.getChild(ParametricDistributionModel.class);
    return new AlloppNetworkPriorModel(eventrate, popscalingfactor, tippopmodel, rootpopmodel, hybpopmodel, units);
}