ARGReassortmentOperator.java

/*
 * ARGReassortmentOperator.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.arg.operators;

import dr.evomodel.arg.ARGModel;
import dr.evomodelxml.tree.TreeModelParser;
import dr.inference.model.CompoundParameter;
import dr.inference.operators.SimpleMCMCOperator;
import dr.math.MathUtils;

import java.util.logging.Logger;

public class ARGReassortmentOperator extends SimpleMCMCOperator {

    public static final String ADD_PROBABILITY = "addProbability";
    public static final String ARG_REASSORTMENT_OPERATOR = "argReassortmentOperator";
    public static final String INTERNAL_NODES = "internalNodes";
    public static final String INTERNAL_AND_ROOT = "internalNodesPlusRoot";
    public static final String NODE_RATES = TreeModelParser.NODE_RATES;
    public static final String CHOOSE_BRANCHES_FIRST = "chooseBranchesFirst";
    public static final double LOG_TWO = Math.log(2.0);

    private double singlePartitionProbability = 0.0;
    private double probBelowRoot = 0.9;
    private double size = 0.0; //Used to choose add step
    private boolean branchesFirst;

    private ARGModel arg;

    private CompoundParameter internalNodeParameters;
    private CompoundParameter internalAndRootNodeParameters;
    private CompoundParameter nodeRates;

    public ARGReassortmentOperator(ARGModel arg, int weight, boolean branchesFirst,
                                   double singlePartProb, double addProbability,
                                   CompoundParameter internalNodeParameters,
                                   CompoundParameter internalAndRootNodeParameters,
                                   CompoundParameter nodeRates) {
        this.arg = arg;
        this.internalNodeParameters = internalNodeParameters;
        this.internalAndRootNodeParameters = internalAndRootNodeParameters;
        this.nodeRates = nodeRates;

        this.branchesFirst = branchesFirst;
        this.singlePartitionProbability = singlePartProb;

        setWeight(weight);

        this.size = addProbability;

        //Transformed for computation reasons
        probBelowRoot = -Math.log(1 - Math.sqrt(probBelowRoot));
    }


    public double doOperation() {
        double logHastings = 0;

        if (MathUtils.nextDouble() < 1.0 / (1 + Math.exp(-size)))
            logHastings = addOperation() - size;
        else
            logHastings = removeOperation() + size;

        return logHastings;
    }

    private double addOperation() {
        if (branchesFirst)
            return addOperationBranchesFirst();

        return addOperationHeightsFirst();
    }

    private double addOperationBranchesFirst() {

        double logHastings = 0;
        double treeHeight = arg.getNodeHeight(arg.getRoot());
        double newBifurcationHeight = Double.POSITIVE_INFINITY;
        double newReassortmentHeight = Double.POSITIVE_INFINITY;

        double theta = probBelowRoot / treeHeight;

        while (newBifurcationHeight > treeHeight && newReassortmentHeight > treeHeight) {
            newBifurcationHeight = MathUtils.nextExponential(theta);
            newReassortmentHeight = MathUtils.nextExponential(theta);
        }

        logHastings += theta * (newBifurcationHeight + newReassortmentHeight) - LOG_TWO
                - 2.0 * Math.log(theta) + Math.log(1 - Math.exp(-2.0 * treeHeight * theta));

        if (newBifurcationHeight < newReassortmentHeight) {
            double temp = newBifurcationHeight;
            newBifurcationHeight = newReassortmentHeight;
            newReassortmentHeight = temp;
        }

        return 0;
    }

    private double addOperationHeightsFirst() {

        return 0;
    }

    private double removeOperation() {

        return 0;
    }

    public String getOperatorName() {
        return ARG_REASSORTMENT_OPERATOR;
    }

    public String getPerformanceSuggestion() {
        return "Try changing the add probability probability";
    }

    private class NoReassortmentEventException extends Exception {
        private static final long serialVersionUID = 1L;

        public NoReassortmentEventException() {
            super("");
        }
    }
}