/*
* TransmissionExchangeOperatorA.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.epidemiology.casetocase.operators;
import dr.evolution.tree.NodeRef;
import dr.evomodel.epidemiology.casetocase.AbstractCase;
import dr.evomodel.epidemiology.casetocase.BranchMapModel;
import dr.evomodel.epidemiology.casetocase.CaseToCaseTreeLikelihood;
import dr.evomodel.operators.AbstractTreeOperator;
import dr.evomodel.tree.TreeModel;
import dr.inference.operators.MCMCOperator;
import dr.math.MathUtils;
import dr.xml.*;
import java.util.ArrayList;
/**
* Implements branch exchange operations that leave the transmission tree unchanged. As this already severely
* restricts the set of eligible pairs of nodes, this is set up as special case of Wide Exchange.
*
* todo For both exchange operators, and the Type B STS and WB moves, you can actually keep the infection times.
* This likely helps both speed and convergence.
*
*
* @author Matthew Hall
*/
public class TransmissionExchangeOperatorA extends AbstractTreeOperator {
private final CaseToCaseTreeLikelihood c2cLikelihood;
public static final String TRANSMISSION_EXCHANGE_OPERATOR_A = "transmissionExchangeOperatorA";
private final boolean resampleInfectionTimes;
public TransmissionExchangeOperatorA(CaseToCaseTreeLikelihood c2cLikelihood, double weight,
boolean resampleInfectionTimes) {
this.c2cLikelihood = c2cLikelihood;
setWeight(weight);
this.resampleInfectionTimes = resampleInfectionTimes;
}
public double doOperation() {
TreeModel tree = c2cLikelihood.getTreeModel();
double hr = exchange();
final int tipCount = tree.getExternalNodeCount();
assert tree.getExternalNodeCount() == tipCount : "Lost some tips";
return hr;
}
public double exchange() {
TreeModel tree = c2cLikelihood.getTreeModel();
final int nodeCount = tree.getNodeCount();
final NodeRef root = tree.getRoot();
NodeRef i = root;
// find a node
while(root == i){
i = tree.getNode(MathUtils.nextInt(nodeCount));
}
ArrayList<NodeRef> candidates = getPossibleExchanges(tree, i);
int candidateCount = candidates.size();
if(candidateCount==0){
// throw new OperatorFailedException("No valid exchanges for this node");
return Double.NEGATIVE_INFINITY;
}
NodeRef j = candidates.get(MathUtils.nextInt(candidates.size()));
int jFirstCandidateCount = getPossibleExchanges(tree, j).size();
double HRDenom = (1/((double)candidateCount)) + (1/((double)jFirstCandidateCount));
NodeRef iP = tree.getParent(i);
NodeRef jP = tree.getParent(j);
if(resampleInfectionTimes){
BranchMapModel branchMap = c2cLikelihood.getBranchMap();
AbstractCase iCase = branchMap.get(i.getNumber());
AbstractCase jCase = branchMap.get(j.getNumber());
AbstractCase parentCase = branchMap.get(iP.getNumber());
if(iCase!=parentCase){
iCase.setInfectionBranchPosition(MathUtils.nextDouble());
}
if(jCase!=parentCase){
jCase.setInfectionBranchPosition(MathUtils.nextDouble());
}
}
exchangeNodes(tree, i, j, iP, jP);
ArrayList<NodeRef> reverseCandidatesIfirst = getPossibleExchanges(tree, i);
ArrayList<NodeRef> reverseCandidatesJfirst = getPossibleExchanges(tree, j);
double HRNum = (1/(double)reverseCandidatesIfirst.size()) + (1/(double)reverseCandidatesJfirst.size());
return Math.log(HRNum/HRDenom);
}
// get a set of candidates for an exchange of a given node. Does not include the node itself or its sibling, so
// the check for a failed move will be if this set is of size 0
public ArrayList<NodeRef> getPossibleExchanges(TreeModel tree, NodeRef node){
ArrayList<NodeRef> out = new ArrayList<NodeRef>();
NodeRef parent = tree.getParent(node);
if(parent==null){
throw new RuntimeException("Can't exchange the root node");
}
Integer[] possibleParentSwaps = c2cLikelihood.getTreeModel().samePartitionElement(parent);
for(Integer index: possibleParentSwaps){
NodeRef newParent = tree.getNode(index);
if(!tree.isExternal(newParent) && newParent!=parent){
for(int i=0; i<2; i++){
NodeRef candidate = tree.getChild(newParent, i);
if(candidate != parent
&& node != newParent
&& tree.getNodeHeight(candidate) < tree.getNodeHeight(parent)
&& tree.getNodeHeight(node) < tree.getNodeHeight(newParent)){
if(out.contains(candidate) || candidate==node){
throw new RuntimeException("Adding a candidate that already exists in the list or" +
" the node itself");
}
out.add(candidate);
}
}
}
}
return out;
}
public String getPerformanceSuggestion() {
return "Not implemented";
}
public String getOperatorName() {
return "Transmission tree exchange operator type A (" + c2cLikelihood.getTreeModel().getId() +")";
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public static final String RESAMPLE_INFECTION_TIMES = "resampleInfectionTimes";
public String getParserName() {
return TRANSMISSION_EXCHANGE_OPERATOR_A;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final CaseToCaseTreeLikelihood c2cL
= (CaseToCaseTreeLikelihood) xo.getChild(CaseToCaseTreeLikelihood.class);
if (c2cL.getTreeModel().getExternalNodeCount() <= 2) {
throw new XMLParseException("Tree with fewer than 3 taxa");
}
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
boolean resampleInfectionTimes = false;
if(xo.hasAttribute(RESAMPLE_INFECTION_TIMES)) {
resampleInfectionTimes = xo.getBooleanAttribute(RESAMPLE_INFECTION_TIMES);
}
return new TransmissionExchangeOperatorA(c2cL, weight, resampleInfectionTimes);
}
// ************************************************************************
// AbstractXMLObjectParser implementation
// ************************************************************************
public String getParserDescription(){
return "This element represents a exchange operator, swapping two random subtrees in such a way that the" +
"transmission tree is unaffected.";
}
public Class getReturnType(){
return TransmissionExchangeOperatorA.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules;{
rules = new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newBooleanRule(RESAMPLE_INFECTION_TIMES, true),
new ElementRule(CaseToCaseTreeLikelihood.class)
};
}
};
}