/*
* BinomialLikelihood.java
*
* Copyright (C) 2002-2009 Alexei Drummond and Andrew Rambaut
*
* 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 test.dr.inference.distribution;
import dr.inference.distribution.DirichletProcessLikelihood;
import dr.inference.model.*;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
/**
* A test suit for the Dirichlet Process likelihood.
*
* @author Andrew Rambaut
* @author Trevor Bedford
* @version $Id: BinomialLikelihood.java,v 1.5 2005/05/24 20:25:59 rambaut Exp $
*/
public class DirichletProcessTest extends TestCase {
public DirichletProcessTest(String name) {
super(name);
}
public void setUp() throws Exception {
super.setUp();
}
public void testDirichletProcess() {
// these are expected results calculated manually...
testDirichletProcess(new double[] {1, 1, 1}, 1.0, -Math.log(6.0)); // log 1/6
testDirichletProcess(new double[] {2, 1}, 1.0, -Math.log(6.0)); // log 1/6
testDirichletProcess(new double[] {3}, 1.0, -Math.log(3.0)); // log 1/3
// check the unoccupied groups are not counted
testDirichletProcess(new double[] {2, 1, 0}, 1.0, -Math.log(6.0)); // log 1/6
testDirichletProcess(new double[] {3, 0, 0}, 1.0, -Math.log(3.0)); // log 1/3
// these are results calculated by the method but confirmed against an independent implementation...
testDirichletProcess(new double[] {1, 1, 1, 1, 1}, 0.5, -6.851184927493743);
testDirichletProcess(new double[] {2, 1, 1, 1, 0}, 0.5, -6.158037746933798);
testDirichletProcess(new double[] {3, 1, 1, 0, 0}, 0.5, -4.771743385813907);
testDirichletProcess(new double[] {4, 1, 0, 0, 0}, 0.5, -2.9799839165858524);
testDirichletProcess(new double[] {5, 0, 0, 0, 0}, 0.5, -0.9005423749060166);
testDirichletProcess(new double[] {1, 1, 1, 1, 1}, 1.0, -4.787491742782046);
testDirichletProcess(new double[] {2, 1, 1, 1, 0}, 1.0, -4.787491742782046);
testDirichletProcess(new double[] {3, 1, 1, 0, 0}, 1.0, -4.0943445622221);
testDirichletProcess(new double[] {4, 1, 0, 0, 0}, 1.0, -2.995732273553991);
testDirichletProcess(new double[] {5, 0, 0, 0, 0}, 1.0, -1.6094379124341005);
testDirichletProcess(new double[] {1, 1, 1, 1, 1}, 2.0, -3.1135153092103747);
testDirichletProcess(new double[] {2, 1, 1, 1, 0}, 2.0, -3.80666248977032);
testDirichletProcess(new double[] {3, 1, 1, 0, 0}, 2.0, -3.80666248977032);
testDirichletProcess(new double[] {4, 1, 0, 0, 0}, 2.0, -3.401197381662156);
testDirichletProcess(new double[] {5, 0, 0, 0, 0}, 2.0, -2.7080502011022105);
testDirichletProcess(new double[] {1, 1, 1, 1, 1}, 5.0, -1.5765840875630222);
testDirichletProcess(new double[] {2, 1, 1, 1, 0}, 5.0, -3.1860219999971227);
testDirichletProcess(new double[] {3, 1, 1, 0, 0}, 5.0, -4.102312731871278);
testDirichletProcess(new double[] {4, 1, 0, 0, 0}, 5.0, -4.613138355637268);
testDirichletProcess(new double[] {5, 0, 0, 0, 0}, 5.0, -4.836281906951478);
}
private void testDirichletProcess(double[] eta, double chi, double expectedLogL) {
Parameter etaParameter = new Parameter.Default("eta", eta);
Parameter chiParameter = new Parameter.Default("chi", chi, 0.0, Double.MAX_VALUE);
DirichletProcessLikelihood dirichlet = new DirichletProcessLikelihood(etaParameter, chiParameter);
assertEquals(expectedLogL, dirichlet.getLogLikelihood(), 1E-10);
}
public static Test suite() {
return new TestSuite(DirichletProcessTest.class);
}
}