LeastSquaresClockTree.java

/*
 * LeastSquaresClockTree.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.evolution.tree;

import dr.math.ConjugateDirectionSearch;
import dr.math.MultivariateFunction;
import dr.math.MultivariateMinimum;

/**
 *
 * @version $Id: LeastSquaresClockTree.java,v 1.4 2005/05/24 20:25:56 rambaut Exp $
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 */
public class LeastSquaresClockTree extends SimpleTree {

	/**
	 * constructor 
	 */
	public LeastSquaresClockTree(Tree sourceTree) {
	
		super(sourceTree);
		this.sourceTree = sourceTree;
		this.mu = 1.0;
		this.optimizeMu = true;
	}

	/**
	 * constructor with a specific mutation rate
	 */
	public LeastSquaresClockTree(Tree sourceTree, double mu) {
	
		this.sourceTree = sourceTree;
		this.mu = mu;
		this.optimizeMu = false;
	}

	public double getMu() { return mu; }
	
	public void optimize() {
		nodeCount = getInternalNodeCount();
		int argumentCount = nodeCount;
		
		if (optimizeMu) {
			argumentCount++;
			muIndex = nodeCount;
		}
		
		MultivariateMinimum optimizer = new ConjugateDirectionSearch();
		
		nodeValues = new double[nodeCount];
		
		double[] xvec = new double[argumentCount];
		for (int i = 0; i < nodeCount; i++) { 
			xvec[i] = 1.0;
		}
		if (optimizeMu) {
			xvec[muIndex] = mu;
		}
		
		optimizer.optimize(leastSquaresClock, xvec, 1E-8, 1E-8);
	}

	public double getSumOfSquares() {
	
		double[] score = new double[] { 0.0 };
		
		NodeRef root = getRoot();
		
		if (getChildCount(root) != 2) {
			throw new IllegalArgumentException("The tree must have a bifurcating root node");
		}
		
		NodeRef node1 = getChild(root, 0);
		NodeRef node2 = getChild(root, 1);
		
		if (!isExternal(node1)) {
			getSumOfSquaresAtNode(node1, score);
		}
		if (!isExternal(node2)) {
			getSumOfSquaresAtNode(node2, score);
		}
		
		double dist1 = sourceTree.getBranchLength(sourceTree.getNode(node1.getNumber())) +
						sourceTree.getBranchLength(sourceTree.getNode(node2.getNumber()));
		
		double time = getNodeHeight(root) - getNodeHeight(node1) +
						getNodeHeight(root) - getNodeHeight(node2);
		double dist2 = time * mu;
		
		double diff = dist1 - dist2;

		score[0] += diff * diff;

		return score[0];
	}

	//
	// Private stuff
	//	
	
	private void getSumOfSquaresAtNode(NodeRef node, double[] score) {
		
		if (!isExternal(node)) {
			for (int i = 0; i < getChildCount(node); i++) {
				NodeRef child = getChild(node, i);
				if (!isExternal(child)) {
					getSumOfSquaresAtNode(child, score);
					score[0] += getScoreAtNode(child);
				}
			}
		}
	}

	/**
	 * returns the rate on the branch to the node above.
	 */
	private double getScoreAtNode(NodeRef node) {
		double dist1 = sourceTree.getBranchLength(sourceTree.getNode(node.getNumber()));
		
		double time = getNodeHeight(getParent(node)) - getNodeHeight(node);
		double dist2 = time * mu;
		
		double diff = dist1 - dist2;

		return diff * diff;
	}

	private double setNodeHeightsFromValues(NodeRef node) {
		
		if (!isExternal(node)) {
			double maxHeight = setNodeHeightsFromValues(getChild(node, 0));

			for (int i = 1; i < getChildCount(node); i++) {
				double height = setNodeHeightsFromValues(getChild(node, i));
				if (height > maxHeight) maxHeight = height;
			}
			
			setNodeHeight(node, maxHeight + nodeValues[node.getNumber() - getExternalNodeCount()]);
		}
		
		return getNodeHeight(node);
	}

	private MultivariateFunction leastSquaresClock = new MultivariateFunction() {
	
		public double evaluate(double[] argument) {
			for (int i = 0; i < getInternalNodeCount(); i++) {
				nodeValues[i] = argument[i];
			}
			
			setNodeHeightsFromValues(getRoot());
			
			if (optimizeMu) {
				mu = argument[muIndex];
			}
			
			double score = getSumOfSquares();
			return score;
		}
		
		public int getNumArguments() { 
			if (optimizeMu) {
				return getInternalNodeCount() + 1; 
			} else {
				return getInternalNodeCount(); 
			}
		}
		
		public double getLowerBound(int n) {
		
			if (optimizeMu && n == muIndex) {
				return Double.MIN_VALUE;
			} else {
				return 0.0;
			}
		}
		
		public double getUpperBound(int n) {

			if (optimizeMu && n == muIndex) {
				return Double.MAX_VALUE;
			} else {
				return Double.MAX_VALUE;
			}
		}
	};

	private int nodeCount;
	private double[] nodeValues;
	private Tree sourceTree;
	private double mu;
	private boolean optimizeMu;
	private int muIndex;
}