/*
* SubtreeSlideOperator.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.evolution.tree.Tree;
import dr.evomodel.tree.TreeModel;
import dr.evomodelxml.operators.SubtreeSlideOperatorParser;
import dr.inference.operators.*;
import dr.math.MathUtils;
import java.util.ArrayList;
import java.util.List;
/**
* Implements the subtree slide move.
*
* @author Alexei Drummond
* @version $Id: SubtreeSlideOperator.java,v 1.15 2005/06/14 10:40:34 rambaut Exp $
*/
public class SubtreeSlideOperator extends AbstractTreeOperator implements CoercableMCMCOperator {
private static final boolean DEBUG = false;
private TreeModel tree = null;
private double size = 1.0;
private boolean gaussian = false;
private final boolean swapInRandomRate;
private final boolean swapInRandomTrait;
private final boolean scaledDirichletBranches;
private CoercionMode mode = CoercionMode.DEFAULT;
public SubtreeSlideOperator(TreeModel tree, double weight, double size, boolean gaussian,
boolean swapRates, boolean swapTraits, boolean scaleDirichletBranches, CoercionMode mode) {
this.tree = tree;
setWeight(weight);
if (size == 0.0) {
double b = 0.0;
for (int k = 0; k < tree.getNodeCount(); ++k) {
b += tree.getBranchLength(tree.getNode(k));
}
size = b / (2 * tree.getNodeCount());
}
this.size = size;
this.gaussian = gaussian;
this.swapInRandomRate = swapRates;
this.swapInRandomTrait = swapTraits;
this.scaledDirichletBranches = scaleDirichletBranches;
this.mode = mode;
}
/**
* Do a probablistic subtree slide move.
*
* @return the log-transformed hastings ratio
*/
public double doOperation() {
double logq;
final NodeRef root = tree.getRoot();
final double oldTreeHeight = tree.getNodeHeight(root);
NodeRef i;
// 1. choose a random node avoiding root
do {
i = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
} while (root == i);
final NodeRef iP = tree.getParent(i);
final NodeRef CiP = getOtherChild(tree, iP, i);
final NodeRef PiP = tree.getParent(iP);
// 2. choose a delta to move
final double delta = getDelta();
final double oldHeight = tree.getNodeHeight(iP);
final double newHeight = oldHeight + delta;
if (DEBUG) {
System.out.println("\nSubTreeSlideOperator: oldTreeHeight = " + oldTreeHeight);
System.out.println("Node selected: " + i + " ; delta = " + delta);
}
// 3. if the move is up
if (delta > 0) {
// 3.1 if the topology will change
if (PiP != null && tree.getNodeHeight(PiP) < newHeight) {
// find new parent
NodeRef newParent = PiP;
NodeRef newChild = iP;
while (tree.getNodeHeight(newParent) < newHeight) {
newChild = newParent;
newParent = tree.getParent(newParent);
if (newParent == null) break;
}
tree.beginTreeEdit();
// 3.1.1 if creating a new root
if (tree.isRoot(newChild)) {
tree.removeChild(iP, CiP);
tree.removeChild(PiP, iP);
tree.addChild(iP, newChild);
tree.addChild(PiP, CiP);
tree.setRoot(iP);
//System.err.println("Creating new root!");
if (tree.hasNodeTraits()) {
// **********************************************
// swap traits and rates so that root keeps it trait and rate values
// **********************************************
tree.swapAllTraits(newChild, iP);
}
if (tree.hasRates()) {
final double rootNodeRate = tree.getNodeRate(newChild);
tree.setNodeRate(newChild, tree.getNodeRate(iP));
tree.setNodeRate(iP, rootNodeRate);
}
// **********************************************
}
// 3.1.2 no new root
else {
tree.removeChild(iP, CiP);
tree.removeChild(PiP, iP);
tree.removeChild(newParent, newChild);
tree.addChild(iP, newChild);
tree.addChild(PiP, CiP);
tree.addChild(newParent, iP);
//System.err.println("No new root!");
}
tree.setNodeHeight(iP, newHeight);
tree.endTreeEdit();
// 3.1.3 count the hypothetical sources of this destination.
final int possibleSources = intersectingEdges(tree, newChild, oldHeight, null);
//System.out.println("possible sources = " + possibleSources);
logq = -Math.log(possibleSources);
} else {
// just change the node height
tree.setNodeHeight(iP, newHeight);
logq = 0.0;
}
}
// 4 if we are sliding the subtree down.
else {
// 4.0 is it a valid move?
if (tree.getNodeHeight(i) > newHeight) {
return Double.NEGATIVE_INFINITY;
}
// 4.1 will the move change the topology
if (tree.getNodeHeight(CiP) > newHeight) {
List<NodeRef> newChildren = new ArrayList<NodeRef>();
final int possibleDestinations = intersectingEdges(tree, CiP, newHeight, newChildren);
if (DEBUG) {
System.out.println("possibleDestinations = " + possibleDestinations);
}
// if no valid destinations then return a failure
if (newChildren.size() == 0) {
return Double.NEGATIVE_INFINITY;
}
// pick a random parent/child destination edge uniformly from options
final int childIndex = MathUtils.nextInt(newChildren.size());
if (DEBUG) {
for (NodeRef ref : newChildren) {
System.out.println("child: " + ref.getNumber());
}
}
NodeRef newChild = newChildren.get(childIndex);
NodeRef newParent = tree.getParent(newChild);
if (DEBUG) {
System.out.println("childIndex: " + childIndex);
System.out.println(newChild);
System.out.println(newParent);
}
tree.beginTreeEdit();
// 4.1.1 if iP was root
if (tree.isRoot(iP)) {
if (DEBUG) {
System.out.println("isRoot");
}
// new root is CiP
tree.removeChild(iP, CiP);
tree.removeChild(newParent, newChild);
tree.addChild(iP, newChild);
tree.addChild(newParent, iP);
tree.setRoot(CiP);
if (tree.hasNodeTraits()) {
// **********************************************
// swap traits and rates, so that root keeps it trait and rate values
// **********************************************
tree.swapAllTraits(iP, CiP);
}
if (tree.hasRates()) {
final double rootNodeRate = tree.getNodeRate(iP);
tree.setNodeRate(iP, tree.getNodeRate(CiP));
tree.setNodeRate(CiP, rootNodeRate);
}
// **********************************************
//System.err.println("DOWN: Creating new root!");
} else {
tree.removeChild(iP, CiP);
tree.removeChild(PiP, iP);
tree.removeChild(newParent, newChild);
tree.addChild(iP, newChild);
tree.addChild(PiP, CiP);
tree.addChild(newParent, iP);
//System.err.println("DOWN: no new root!");
}
tree.setNodeHeight(iP, newHeight);
tree.endTreeEdit();
logq = Math.log(possibleDestinations);
} else {
tree.setNodeHeight(iP, newHeight);
logq = 0.0;
}
}
if (swapInRandomRate) {
final NodeRef j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
if (j != i) {
final double tmp = tree.getNodeRate(i);
tree.setNodeRate(i, tree.getNodeRate(j));
tree.setNodeRate(j, tmp);
}
}
if (swapInRandomTrait) {
final NodeRef j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
if (j != i) {
tree.swapAllTraits(i, j);
// final double tmp = tree.getNodeTrait(i, TRAIT);
// tree.setNodeTrait(i, TRAIT, tree.getNodeTrait(j, TRAIT));
// tree.setNodeTrait(j, TRAIT, tmp);
}
}
// just return -Inf
//if (logq == Double.NEGATIVE_INFINITY) throw new OperatorFailedException("invalid slide");
if (scaledDirichletBranches) {
if (oldTreeHeight != tree.getNodeHeight(tree.getRoot()))
throw new UnsupportedOperationException("Temporarily disabled."); // TODO calculate Hastings ratio
}
return logq;
}
private double getDelta() {
if (DEBUG) {
System.out.println("size = " + size);
}
if (!gaussian) {
return (MathUtils.nextDouble() * size) - (size / 2.0);
} else {
return MathUtils.nextGaussian() * size;
}
}
private int intersectingEdges(Tree tree, NodeRef node, double height, List<NodeRef> directChildren) {
final NodeRef parent = tree.getParent(node);
/*if (DEBUG) {
System.out.println("intersectingEdges");
System.out.println("parent: " + parent);
}*/
if (tree.getNodeHeight(parent) < height) return 0;
if (tree.getNodeHeight(node) < height) {
if (directChildren != null) directChildren.add(node);
return 1;
}
int count = 0;
for (int i = 0; i < tree.getChildCount(node); i++) {
count += intersectingEdges(tree, tree.getChild(node, i), height, directChildren);
}
return count;
}
public double getSize() {
return size;
}
public void setSize(double size) {
this.size = size;
}
public double getCoercableParameter() {
return Math.log(getSize());
}
public void setCoercableParameter(double value) {
setSize(Math.exp(value));
}
public double getRawParameter() {
return getSize();
}
public CoercionMode getMode() {
return mode;
}
public double getTargetAcceptanceProbability() {
return 0.234;
}
public String getPerformanceSuggestion() {
double prob = MCMCOperator.Utils.getAcceptanceProbability(this);
double targetProb = getTargetAcceptanceProbability();
double ws = OperatorUtils.optimizeWindowSize(getSize(), Double.MAX_VALUE, prob, targetProb);
if (prob < getMinimumGoodAcceptanceLevel()) {
return "Try decreasing size to about " + ws;
} else if (prob > getMaximumGoodAcceptanceLevel()) {
return "Try increasing size to about " + ws;
} else return "";
}
public String getOperatorName() {
return SubtreeSlideOperatorParser.SUBTREE_SLIDE + "(" + tree.getId() + ")";
}
}