/*
* MCMCCriterion.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.inference.mcmc;
import dr.math.MathUtils;
import dr.inference.markovchain.Acceptor;
/**
* This class encapsulates the acceptance criterion for an MCMC proposal.
*
* @author Alexei Drummond
*
* @version $Id: MCMCCriterion.java,v 1.12 2005/05/24 20:25:59 rambaut Exp $
*/
public class MCMCCriterion implements Acceptor {
// this parameter is actually 1/T, when the temperature parameter is 0.0, then the distribution
// is flat and will always accept (symmetric) proposals, i.e. hastings ratio of 0 in log space.
// As this temperature parameter increases, the posterior gets more peaked.
protected double temperature = 1.0;
public MCMCCriterion() {
temperature = 1.0;
}
public MCMCCriterion(double t) {
temperature = t;
}
public double getAcceptanceValue(double oldScore, double hastingsRatio) {
final double acceptanceValue =
(MathUtils.randomLogDouble() + (oldScore * temperature) - hastingsRatio) / temperature;
return acceptanceValue;
}
public boolean accept(double oldScore, double newScore, double hastingsRatio, double[] logr) {
logr[0] = (newScore - oldScore) * temperature + hastingsRatio;
// for coercedAcceptanceProbability
if (logr[0] > 0) logr[0] = 0.0;
final double v = MathUtils.randomLogDouble();
final boolean accept = v < logr[0];
return accept;
}
public double getTemperature() {
return temperature;
}
public void setTemperature(double temperature) {
this.temperature = temperature;
}
}