/*
* DecayingRateModel.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.branchratemodel;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Andrew Rambaut
* @version $Id: DecayingRateModel.java,v 1.3 2006/01/10 16:48:27 rambaut Exp $
*/
public class DecayingRateModel extends AbstractBranchRateModel {
public static final String DECAYING_RATE_MODEL = "decayingRateModel";
public static final String MUTATION_RATE = "mutationRate";
public static final String HALF_LIFE = "halfLife";
public static final String SUBSTITUTION_RATE = "substitutionRate";
public static final String PROPORTION = "proportion";
public static final String AVERAGE = "average";
private final Parameter mutationRateParameter;
private final Parameter substitutionRateParameter;
private final Parameter proportionParameter;
private final Parameter halfLifeParameter;
private final boolean useAveraging;
private final double[] rates;
private boolean ratesCalculated = false;
public DecayingRateModel(TreeModel treeModel, Parameter mutationRateParameter, Parameter substitutionRateParameter,
Parameter proportionParameter, Parameter halfLifeParameter, boolean useAveraging) {
super(DECAYING_RATE_MODEL);
rates = new double[treeModel.getNodeCount()];
addModel(treeModel);
this.mutationRateParameter = mutationRateParameter;
this.substitutionRateParameter = substitutionRateParameter;
this.proportionParameter = proportionParameter;
this.halfLifeParameter = halfLifeParameter;
addVariable(mutationRateParameter);
if (proportionParameter != null) {
addVariable(proportionParameter);
} else {
addVariable(substitutionRateParameter);
}
addVariable(halfLifeParameter);
this.useAveraging = useAveraging;
}
public void handleModelChangedEvent(Model model, Object object, int index) {
// TreeModel has changed...
ratesCalculated = false;
fireModelChanged();
}
protected final void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
// Parameters have changed
ratesCalculated = false;
fireModelChanged();
}
protected void storeState() {
// nothing to do
}
protected void restoreState() {
ratesCalculated = false;
// nothing to do
}
protected void acceptState() {
// nothing to do
}
public double getBranchRate(final Tree tree, final NodeRef node) {
if (!ratesCalculated) {
double mu = mutationRateParameter.getParameterValue(0);
double k;
if (proportionParameter != null) {
k = mu * proportionParameter.getParameterValue(0);
} else {
k = substitutionRateParameter.getParameterValue(0);
}
double lambda = Math.log(2) / halfLifeParameter.getParameterValue(0);
calculateNodeRates(tree, tree.getRoot(), mu, k, lambda);
ratesCalculated = true;
}
return rates[node.getNumber()];
}
/**
* Traverse the tree calculating partial likelihoods.
*
* @return whether the partials for this node were recalculated.
*/
private final double calculateNodeRates(Tree tree, NodeRef node, double mu, double k, double lambda) {
NodeRef parent = tree.getParent(node);
double time0 = 0.0;
if (!tree.isExternal(node)) {
// Traverse down the two child nodes
NodeRef child1 = tree.getChild(node, 0);
double t1 = calculateNodeRates(tree, child1, mu, k, lambda);
NodeRef child2 = tree.getChild(node, 1);
double t2 = calculateNodeRates(tree, child2, mu, k, lambda);
if (useAveraging) {
time0 = (t1 + t2) / 2.0;
} else {
// pick larger of the two
if (t1 > t2) {
time0 = t1;
} else {
time0 = t2;
}
}
}
// don't bother if you are at the root because rate at root is ignored
if (parent == null) return 0;
double branchTime = tree.getNodeHeight(parent) - tree.getNodeHeight(node);
double time1 = time0 + branchTime;
double branchRate = rateIntegral(time1, mu, k, lambda);
if (time0 > 0.0) {
branchRate -= rateIntegral(time0, mu, k, lambda);
}
rates[node.getNumber()] = branchRate / branchTime;
return time1;
}
private static double rateIntegral(double time, double mu, double k, double lambda) {
return ((k * time) + (((mu - k) / lambda) * (1.0 - Math.exp(-lambda * time))));
}
private static double rate(double time, double mu, double k, double lambda) {
return k + ((mu - k) * Math.exp(-lambda * time));
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return DECAYING_RATE_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean useAveraging = xo.getBooleanAttribute(AVERAGE);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
Parameter mutationRateParameter = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
Parameter proportionParameter = null;
Parameter substitutionRateParameter = null;
if (xo.hasChildNamed(PROPORTION)) {
proportionParameter = (Parameter) xo.getElementFirstChild(PROPORTION);
} else {
substitutionRateParameter = (Parameter) xo.getElementFirstChild(SUBSTITUTION_RATE);
}
Parameter halfLifeParameter = (Parameter) xo.getElementFirstChild(HALF_LIFE);
Logger.getLogger("dr.evomodel").info("Using decaying-rate clock model.");
return new DecayingRateModel(treeModel, mutationRateParameter, substitutionRateParameter, proportionParameter, halfLifeParameter, useAveraging);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return
"This element provides a clock model in which the rate of " +
"molecular evolution decays to a substitution rate in the past.";
}
public Class getReturnType() {
return DecayingRateModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(AVERAGE, false),
new ElementRule(TreeModel.class, "The tree model"),
new ElementRule(MUTATION_RATE, Parameter.class, "The mutation rate parameter", false),
new XORRule(
new ElementRule(PROPORTION, Parameter.class, "The proportion of neutral mutations", false),
new ElementRule(SUBSTITUTION_RATE, Parameter.class, "The long-term substitution", false)
),
new ElementRule(HALF_LIFE, Parameter.class, "The half-life of a deleterious mutation", false)
};
};
public static void main(String[] argv) {
double mu = 1E-4;
double k = 1E-5;
double lambda = Math.log(2) / 1.0;
double time1 = 0.000001;
for (int i = 0; i < 100; i++) {
System.out.println(time1 + "\t" + rate(time1, mu, k, lambda) + "\t" + (rateIntegral(time1, mu, k, lambda)) / time1);
time1 += 1.0;
}
}
}