/*
* MultivariateOUModelParser.java
*
* Copyright (c) 2002-2015 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.oldevomodelxml.substmodel;
import dr.inference.distribution.MultivariateOUModel;
import dr.oldevomodel.substmodel.SubstitutionModel;
import dr.inference.distribution.GeneralizedLinearModel;
import dr.inference.model.DesignMatrix;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.inferencexml.distribution.GeneralizedLinearModelParser;
import dr.xml.*;
/**
*
*/
public class MultivariateOUModelParser extends AbstractXMLObjectParser {
public static final String MVOU_MODEL = "multivariateOUModel";
public static final String MVOU_TYPE = "MVOU";
public static final String DATA = "data";
public static final String TIME = "times";
public static final String DESIGN = "design";
public String getParserName() {
return MVOU_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
Parameter effectParameter = (Parameter) ((XMLObject) xo.getChild(DATA)).getChild(Parameter.class);
Parameter timesParameter = (Parameter) ((XMLObject) xo.getChild(TIME)).getChild(Parameter.class);
Parameter designParameter = (Parameter) ((XMLObject) xo.getChild(DESIGN)).getChild(Parameter.class);
MatrixParameter gammaParameter = (MatrixParameter) xo.getChild(MatrixParameter.class);
if (effectParameter.getDimension() != timesParameter.getDimension() ||
effectParameter.getDimension() != designParameter.getDimension()) {
// System.err.println("dim(effect) " +effectParameter.getDimension());
// System.err.println("dim(times) "+timesParameter.getDimension());
// System.err.println("dim(design) "+designParameter.getDimension());
throw new XMLParseException("dim(" + effectParameter.getStatisticName() +
") != dim(" + timesParameter.getStatisticName() + ") != dim(" + designParameter.getStatisticName() +
") in " + xo.getName() + " element");
}
MultivariateOUModel glm = new MultivariateOUModel(substitutionModel, effectParameter, gammaParameter,
timesParameter.getParameterValues(), designParameter.getParameterValues());
addIndependentParameters(xo, glm, effectParameter);
// todo Confirm that design vector is consistent with substitution model
// todo Confirm that design vector is ordered 1,\ldots,K,1,\ldots,K, etc.
return glm;
}
public void addIndependentParameters(XMLObject xo, GeneralizedLinearModel glm,
Parameter dependentParam) throws XMLParseException {
int totalCount = xo.getChildCount();
for (int i = 0; i < totalCount; i++) {
if (xo.getChildName(i).compareTo(GeneralizedLinearModelParser.INDEPENDENT_VARIABLES) == 0) {
XMLObject cxo = (XMLObject) xo.getChild(i);
Parameter independentParam = (Parameter) cxo.getChild(Parameter.class);
DesignMatrix designMatrix = (DesignMatrix) cxo.getChild(DesignMatrix.class);
checkDimensions(independentParam, dependentParam, designMatrix);
glm.addIndependentParameter(independentParam, designMatrix, null);
}
}
}
private void checkDimensions(Parameter independentParam, Parameter dependentParam, DesignMatrix designMatrix)
throws XMLParseException {
if ((dependentParam.getDimension() != designMatrix.getRowDimension()) ||
(independentParam.getDimension() != designMatrix.getColumnDimension())) {
System.err.println(dependentParam.getDimension());
System.err.println(independentParam.getDimension());
System.err.println(designMatrix.getRowDimension() + " rows");
System.err.println(designMatrix.getColumnDimension() + " cols");
throw new XMLParseException(
"dim(" + dependentParam.getId() + ") != dim(" + designMatrix.getId() + " %*% " + independentParam.getId() + ")"
);
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(SubstitutionModel.class),
new ElementRule(MatrixParameter.class),
new ElementRule(DATA, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)}),
new ElementRule(TIME, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)}),
new ElementRule(DESIGN, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)}),
new ElementRule(GeneralizedLinearModelParser.INDEPENDENT_VARIABLES,
new XMLSyntaxRule[]{new ElementRule(MatrixParameter.class)}, 0, 3),
};
public String getParserDescription() {
return "Describes a multivariate OU process";
}
public Class getReturnType() {
return MultivariateOUModel.class;
}
}