/*
* ContinuousBranchRates.java
*
* Copyright (C) 2002-2009 Alexei Drummond and Andrew Rambaut
*
* 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.branchratemodel;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.SimpleTree;
import dr.evolution.tree.Tree;
import dr.evomodel.tree.TreeModel;
import dr.evomodel.tree.TreeParameterModel;
import dr.evomodelxml.branchratemodel.ContinuousBranchRatesParser;
import dr.inference.distribution.ParametricDistributionModel;
import dr.inference.model.*;
/**
*
* Uses the implementation of continuous branch rates described in:
* Li, W.L.S. and A.J. Drummond, Model Averaging and Bayes Factor
* Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics.
* Molecular Biology and Evolution, 2012. 29(2): p. 751-761.
*
* @author Wai Lok Sibon Li
* @version $Id: ContinuousBranchRates.java,v 1.11 2006/01/09 17:44:30 rambaut Exp $
*/
public class ContinuousBranchRates extends AbstractBranchRateModel {
private final ParametricDistributionModel distributionModel;
// The rate categories of each branch
//d final TreeParameterModel rateCategories;
final TreeParameterModel rateCategoryQuantiles;
//private final int categoryCount;
//private final double step;
private final double[] rates;
private boolean normalize = false;
private double normalizeBranchRateTo = Double.NaN;
private double scaleFactor = 1.0;
private TreeModel treeModel;
private Tree tree;
//overSampling control the number of effective categories
public ContinuousBranchRates(
TreeModel tree,
/*Parameter rateCategoryParameter, */
Parameter rateCategoryQuantilesParameter,
ParametricDistributionModel model
/*int overSampling*/) {
this(tree, /* rateCategoryParameter, */rateCategoryQuantilesParameter, model, /*overSampling, */false, Double.NaN);
}
public ContinuousBranchRates(
TreeModel tree,
/* Parameter rateCategoryParameter, */
Parameter rateCategoryQuantilesParameter,
ParametricDistributionModel model,
/*int overSampling,*/
boolean normalize,
double normalizeBranchRateTo) {
super(ContinuousBranchRatesParser.CONTINUOUS_BRANCH_RATES);
//d this.rateCategories = new TreeParameterModel(tree, rateCategoryParameter, false);
this.rateCategoryQuantiles = new TreeParameterModel(tree, rateCategoryQuantilesParameter, false);
rates = new double[tree.getNodeCount()];
this.normalize = normalize;
this.treeModel = tree;
this.distributionModel = model;
this.normalizeBranchRateTo = normalizeBranchRateTo;
this.tree = new SimpleTree(tree);
//Force the boundaries of rateCategoryParameter to match the category count
//d Parameter.DefaultBounds bound = new Parameter.DefaultBounds(categoryCount - 1, 0, rateCategoryParameter.getDimension());
//d rateCategoryParameter.addBounds(bound);
//rateCategoryQuantilesParameter.;
Parameter.DefaultBounds bound = new Parameter.DefaultBounds(1.0, 0.0, rateCategoryQuantilesParameter.getDimension());
rateCategoryQuantilesParameter.addBounds(bound);
/*if(rateCategoryQuantilesParameter.getBounds()==null) {
System.out.println("oh NO!!! " + rateCategoryQuantilesParameter.getBounds().getLowerLimit(0) + "\t"
+ rateCategoryQuantilesParameter.getBounds().getUpperLimit(1));
}*/
/* for (int i = 0; i < rateCategoryParameter.getDimension(); i++) {
int index = (int) Math.floor((i + 0.5) * overSampling);
rateCategoryParameter.setParameterValue(i, index);
} */
addModel(model);
// AR - commented out: changes to the tree are handled by model changed events fired by rateCategories
// addModel(tree);
//d addModel(rateCategories);
addModel(rateCategoryQuantiles);
//addModel(treeModel); // Maybe
// AR - commented out: changes to rateCategoryParameter are handled by model changed events fired by rateCategories
// addVariable(rateCategoryParameter);
if (normalize) {
tree.addModelListener(new ModelListener() {
public void modelChangedEvent(Model model, Object object, int index) {
computeFactor();
}
public void modelRestored(Model model) {
computeFactor();
}
});
}
setupRates();
}
// compute scale factor
private void computeFactor() {
//scale mean rate to 1.0 or separate parameter
double treeRate = 0.0;
double treeTime = 0.0;
//normalizeBranchRateTo = 1.0;
for (int i = 0; i < treeModel.getNodeCount(); i++) {
NodeRef node = treeModel.getNode(i);
if (!treeModel.isRoot(node)) {
//d int rateCategory = (int) Math.round(rateCategories.getNodeValue(treeModel, node));
//d treeRate += rates[rateCategory] * treeModel.getBranchLength(node);
treeTime += treeModel.getBranchLength(node);
// d System.out.println("rates and time\t" + rates[rateCategory] + "\t" + treeModel.getBranchLength(node));
}
}
//treeRate /= treeTime;
scaleFactor = normalizeBranchRateTo / (treeRate / treeTime);
System.out.println("scaleFactor\t\t\t\t\t" + scaleFactor);
}
public void handleModelChangedEvent(Model model, Object object, int index) {
if (model == distributionModel) {
setupRates();
fireModelChanged();
} //else if (model == rateCategories) {
// AR - commented out: if just the rate categories have changed the rates will be the same
// setupRates();
// fireModelChanged(null, index);
//}
else if (model == rateCategoryQuantiles) {
setupRates(); // Maybe
//rateCategories.fireModelChanged();
fireModelChanged(null, index);
} /*else if (model == treeModel) {
setupRates(); // Maybe
}*/
}
protected final void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
// AR - commented out: changes to rateCategoryParameter are handled by model changed events
//setupRates(); // Maybe
}
protected void storeState() {
//setupRates(); // Maybe
}
protected void restoreState() {
setupRates();
}
protected void acceptState() {
//setupRates(); // Maybe
}
public double getBranchRate(final Tree tree, final NodeRef node) {
assert !tree.isRoot(node) : "root node doesn't have a rate!";
//int rateCategory = (int) Math.round(rateCategories.getNodeValue(tree, node));
//System.out.println("dslkjafsdf " + node.getNumber());
return rates[node.getNumber()] * scaleFactor;
}
/**
* Calculates the actual rates corresponding to the category indices.
*/
protected void setupRates() {
//rateCategoryQuantiles.
//double z = step / 2.0;
for (int i = 0; i < tree.getNodeCount(); i++) {
//rates[i] = distributionModel.quantile(rateCategoryQuantiles.getNodeValue(rateCategoryQuantiles.getTreeModel(), rateCategoryQuantiles.getTreeModel().getNode(i) ));
if (!tree.isRoot(tree.getNode(i))) {
//System.out.println(rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i)));
rates[tree.getNode(i).getNumber()] = distributionModel.quantile(rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i)));
}
// System.out.println("road " + i + "\t" + rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i) ) + "\t" + tree.toString() + "\t" + tree.toString());
//System.out.println("road " + i + "\t" + rateCategoryQuantiles.getNodeValue(rateCategoryQuantiles.getTreeModel(), rateCategoryQuantiles.getTreeModel().getNode(i) ) + "\t" + rateCategoryQuantiles.getTreeModel().toString() + "\t" + treeModel.toString());
//System.out.print(rates[i]+"\t");
//z += step;
//rates[i] = distributionModel.quantile(z);
//System.out.println("ape " + tree);
}
//System.out.println("\n");
//System.out.println();
if (normalize) computeFactor();
}
}