RateSampleOperator.java

/*
 * RateSampleOperator.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.evomodel.operators;

import dr.evolution.tree.NodeRef;
import dr.oldevomodel.clock.RateEvolutionLikelihood;
import dr.evomodel.tree.TreeModel;
import dr.evomodelxml.operators.RateSampleOperatorParser;
import dr.inference.operators.SimpleMCMCOperator;
import dr.math.MathUtils;

/**
 * A special operator for sampling rates in a subtree
 * according to a RateEvolutionLikelihood such as the autocorrelated clock model
 *
 * @author Michael Defoin Platel
 */
public class RateSampleOperator extends SimpleMCMCOperator {

    private TreeModel tree;

    private boolean sampleAll;

    RateEvolutionLikelihood rateEvolution;

    public RateSampleOperator(TreeModel tree, boolean sampleAll, RateEvolutionLikelihood rateEvolution) {

        this.tree = tree;
        this.sampleAll = sampleAll;
        this.rateEvolution = rateEvolution;
    }

    /**
     * sample the rates of a subtree and return the hastings ratio.
     */
    public final double doOperation() {

        int index;
        if (sampleAll) {
            index = tree.getRoot().getNumber();
        } else {
            do {
                index = MathUtils.nextInt(tree.getNodeCount());
            } while (tree.isExternal(tree.getNode(index)));
        }


        double logBackward = rateEvolution.getLogLikelihood();

        //sampleOne(tree.getNode(index));

        //sampleSubtree(tree.getNode(index));
        sampleNode(tree.getNode(index));

        //sampleSister(tree.getNode(index));

        double logForward = rateEvolution.getLogLikelihood();

        return logBackward - logForward;
    }

    void sampleSubtree(NodeRef parent) {

        int nbChildren = tree.getChildCount(parent);
        for (int c = 0; c < nbChildren; c++) {
            final NodeRef node = tree.getChild(parent, c);
            rateEvolution.sampleRate(node);
            sampleSubtree(node);
        }
    }

    void sampleSister(NodeRef parent) {

        int nbChildren = tree.getChildCount(parent);
        for (int c = 0; c < nbChildren; c++) {
            final NodeRef node = tree.getChild(parent, c);
            rateEvolution.sampleRate(node);
        }

    }

    void sampleNode(NodeRef parent) {

        int nbChildren = tree.getChildCount(parent);

        if (nbChildren > 0) {
            final int c = MathUtils.nextInt(nbChildren);

            final NodeRef node = tree.getChild(parent, c);
            rateEvolution.sampleRate(node);
        }

    }

    void sampleOne(NodeRef parent) {

        int nbChildren = tree.getChildCount(parent);

        if (nbChildren > 0) {

            final NodeRef node = tree.getChild(parent, 0);
            rateEvolution.sampleRate(node);
        }

    }

    /**
     * This method should be overridden by operators that need to do something just before the return of doOperation.
     *
     * @param newValue the proposed parameter value
     * @param oldValue the old parameter value
     */
    void cleanupOperation(double newValue, double oldValue) {
        // DO NOTHING
    }

    //MCMCOperator INTERFACE
    public final String getOperatorName() {
        return "rateSample";
    }


    public double getTargetAcceptanceProbability() {
        return 0.234;
    }

    public double getMinimumAcceptanceLevel() {
        return 0.1;
    }

    public double getMaximumAcceptanceLevel() {
        return 0.4;
    }

    public double getMinimumGoodAcceptanceLevel() {
        return 0.20;
    }

    public double getMaximumGoodAcceptanceLevel() {
        return 0.30;
    }

    public final String getPerformanceSuggestion() {

        return "No suggestions";
    }

    public String toString() {
        return RateSampleOperatorParser.SAMPLE_OPERATOR + "(";
    }

    //PRIVATE STUFF

}