/*
* SpeciationLikelihood.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.speciation;
import dr.evolution.tree.Tree;
import dr.evolution.util.Taxon;
import dr.evolution.util.Units;
import dr.evomodelxml.speciation.SpeciationLikelihoodParser;
import dr.inference.model.AbstractModelLikelihood;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
import java.util.Set;
/**
* A likelihood function for speciation processes. Takes a tree and a speciation model.
* <p/>
* Parts of this class were derived from C++ code provided by Oliver Pybus.
*
* @author Andrew Rambaut
* @author Alexei Drummond
* @version $Id: SpeciationLikelihood.java,v 1.10 2005/05/18 09:51:11 rambaut Exp $
*/
public class SpeciationLikelihood extends AbstractModelLikelihood implements Units {
// PUBLIC STUFF
/**
* @param tree the tree
* @param speciationModel the model of speciation
* @param id a unique identifier for this likelihood
* @param exclude taxa to exclude from this model
*/
public SpeciationLikelihood(Tree tree, SpeciationModel speciationModel, Set<Taxon> exclude, String id) {
this(SpeciationLikelihoodParser.SPECIATION_LIKELIHOOD, tree, speciationModel, exclude);
setId(id);
}
public SpeciationLikelihood(Tree tree, SpeciationModel speciationModel, String id) {
this(tree, speciationModel, null, id);
}
public SpeciationLikelihood(String name, Tree tree, SpeciationModel speciationModel, Set<Taxon> exclude) {
super(name);
this.tree = tree;
this.speciationModel = speciationModel;
this.exclude = exclude;
if (tree instanceof Model) {
addModel((Model) tree);
}
if (speciationModel != null) {
addModel(speciationModel);
}
}
public SpeciationLikelihood(Tree tree, SpeciationModel specModel, String id, CalibrationPoints calib) {
this(tree, specModel, id);
this.calibration = calib;
}
// **************************************************************
// ModelListener IMPLEMENTATION
// **************************************************************
protected final void handleModelChangedEvent(Model model, Object object, int index) {
likelihoodKnown = false;
}
// **************************************************************
// VariableListener IMPLEMENTATION
// **************************************************************
protected final void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
} // No parameters to respond to
// **************************************************************
// Model IMPLEMENTATION
// **************************************************************
/**
* Stores the precalculated state: likelihood
*/
protected final void storeState() {
storedLikelihoodKnown = likelihoodKnown;
storedLogLikelihood = logLikelihood;
}
/**
* Restores the precalculated state: computed likelihood
*/
protected final void restoreState() {
likelihoodKnown = storedLikelihoodKnown;
logLikelihood = storedLogLikelihood;
}
protected final void acceptState() {
} // nothing to do
// **************************************************************
// Likelihood IMPLEMENTATION
// **************************************************************
public final Model getModel() {
return this;
}
public final double getLogLikelihood() {
if (!likelihoodKnown) {
logLikelihood = calculateLogLikelihood();
likelihoodKnown = true;
}
return logLikelihood;
}
public final void makeDirty() {
likelihoodKnown = false;
}
/**
* Calculates the log likelihood of this set of coalescent intervals,
* given a demographic model.
*
* @return the log likelihood
*/
private double calculateLogLikelihood() {
if (exclude != null) {
return speciationModel.calculateTreeLogLikelihood(tree, exclude);
}
if ( calibration != null ) {
return speciationModel.calculateTreeLogLikelihood(tree, calibration);
}
return speciationModel.calculateTreeLogLikelihood(tree);
}
// **************************************************************
// Loggable IMPLEMENTATION
// **************************************************************
/**
* @return the log columns.
*/
public final dr.inference.loggers.LogColumn[] getColumns() {
String columnName = getId();
if (columnName == null) columnName = getModelName() + ".likelihood";
return new dr.inference.loggers.LogColumn[]{
new LikelihoodColumn(columnName)
};
}
private final class LikelihoodColumn extends dr.inference.loggers.NumberColumn {
public LikelihoodColumn(String label) {
super(label);
}
public double getDoubleValue() {
return getLogLikelihood();
}
}
// **************************************************************
// Units IMPLEMENTATION
// **************************************************************
/**
* Sets the units these coalescent intervals are
* measured in.
*/
public final void setUnits(Type u) {
speciationModel.setUnits(u);
}
/**
* Returns the units these coalescent intervals are
* measured in.
*/
public final Type getUnits() {
return speciationModel.getUnits();
}
@Override
public String prettyName() {
String s = speciationModel.getClass().getName();
String[] parts = s.split("\\.");
s = parts[parts.length - 1];
if( speciationModel.getId() != null ) {
s = s + '/' + speciationModel.getId();
}
s = s + '(' + tree.getId() + ')';
return s;
}
// ****************************************************************
// Private and protected stuff
// ****************************************************************
/**
* The speciation model.
*/
SpeciationModel speciationModel = null;
/**
* The tree.
*/
Tree tree = null;
private final Set<Taxon> exclude;
private CalibrationPoints calibration;
private double logLikelihood;
private double storedLogLikelihood;
private boolean likelihoodKnown = false;
private boolean storedLikelihoodKnown = false;
}