/*
* ConjugateRootTraitPrior.java
*
* Copyright (c) 2002-2016 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evomodel.treedatalikelihood.continuous;
import dr.inference.distribution.MultivariateDistributionLikelihood;
import dr.inference.model.Parameter;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
import static dr.evomodelxml.treedatalikelihood.ContinuousDataLikelihoodParser.CONJUGATE_ROOT_PRIOR;
import static dr.evomodelxml.treedatalikelihood.ContinuousDataLikelihoodParser.PRIOR_SAMPLE_SIZE;
/**
* @author Marc A. Suchard
*/
public class ConjugateRootTraitPrior {
private final double[] mean;
private final double pseudoObservations;
ConjugateRootTraitPrior(double[] mean, double pseudoObservations) {
this.mean = mean;
this.pseudoObservations = pseudoObservations;
}
public double[] getMean() { return mean; }
public double getPseudoObservations() { return pseudoObservations; }
public static ConjugateRootTraitPrior parseConjugateRootTraitPrior(XMLObject xo,
final int dim) throws XMLParseException {
XMLObject cxo = xo.getChild(CONJUGATE_ROOT_PRIOR);
Parameter meanParameter = (Parameter) cxo.getChild(MultivariateDistributionLikelihood.MVN_MEAN)
.getChild(Parameter.class);
if (meanParameter.getDimension() != dim) {
throw new XMLParseException("Root prior mean dimension does not match trait diffusion dimension");
}
Parameter sampleSizeParameter = (Parameter) cxo.getChild(PRIOR_SAMPLE_SIZE).getChild(Parameter.class);
return new ConjugateRootTraitPrior(meanParameter.getParameterValues(),
sampleSizeParameter.getParameterValue(0));
}
public static final XMLSyntaxRule[] rules = {
new ElementRule(MultivariateDistributionLikelihood.MVN_MEAN,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(PRIOR_SAMPLE_SIZE,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
};
}