/*
* MetaPopulationModel.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.coalescent.structure;
import dr.evolution.coalescent.structure.MetaPopulation;
import dr.evomodel.coalescent.DemographicModel;
import dr.inference.model.*;
import dr.xml.*;
import java.util.ArrayList;
/**
* A wrapper for ConstantPopulation.
*
* @author Andrew Rambaut
* @author Alexei Drummond
* @version $Id: MetaPopulationModel.java,v 1.3 2006/09/11 09:33:01 gerton Exp $
*/
public class MetaPopulationModel extends AbstractModel implements MetaPopulation {
//
// Public stuff
//
public static final String META_POPULATION_MODEL = "metaPopulationModel";
/**
* Construct demographic model with default settings
*/
public MetaPopulationModel(ArrayList<DemographicModel> demographicModels, Parameter populationProportions) {
this(META_POPULATION_MODEL, demographicModels, populationProportions);
}
/**
* Construct demographic model with default settings
*/
public MetaPopulationModel(String name, ArrayList<DemographicModel> demographicModelList, Parameter populationProportions) {
super(name);
this.populationProportions = populationProportions;
if (populationProportions != null) {
// Single demographic, each with a different weight
addVariable(populationProportions);
populationProportions.addBounds(new Parameter.DefaultBounds(1.0, 0.0, populationProportions.getDimension()));
populationCount = populationProportions.getDimension() + 1;
// Add copies of the demographicModel to the array
for (int i = 1; i < populationCount; i++) {
demographicModelList.add(demographicModelList.get(0));
}
demographicModels = demographicModelList.toArray(new DemographicModel[0]);
addModel(demographicModels[0]);
} else {
// Several demographic models
populationCount = demographicModelList.size();
demographicModels = demographicModelList.toArray(new DemographicModel[0]);
for (int i = 0; i < populationCount; i++) {
addModel(demographicModels[i]);
}
}
addStatistic(populationSizesStatistic);
}
// general functions
private double getProportion(int population) {
if (populationProportions == null) {
return 1.0;
}
if (population > 0) {
return populationProportions.getParameterValue(population - 1);
}
double proportion = 1.0;
for (int i = 1; i < populationCount; i++) {
proportion -= populationProportions.getParameterValue(i - 1);
}
return proportion;
}
public int getPopulationCount() {
return populationCount;
}
public double[] getPopulationSizes(double time) {
// make population size array
double[] N = new double[populationCount];
for (int i = 0; i < populationCount; i++) {
N[i] = demographicModels[i].getDemographicFunction().getDemographic(time) * getProportion(i);
}
return N;
}
/* returns value of demographic function at time t (population size; one entry of double[] getPopulationSizes)
* (This function mirrors an equivalent function in DemographicFunction)
*/
public double getDemographic(double time, int population) {
return demographicModels[population].getDemographicFunction().getDemographic(time) * getProportion(population);
}
/* calculates the integral 1/N(x) dx from start to finish, for one of the populations
* (This function mirrors an equivalent function in DemographicFunction)
*/
public double getIntegral(double start, double finish, int population) {
double integral = demographicModels[population].getDemographicFunction().getIntegral(start, finish);
return integral / getProportion(population);
}
// **************************************************************
// Model IMPLEMENTATION
// **************************************************************
protected void handleModelChangedEvent(Model model, Object object, int index) {
fireModelChanged();
}
protected void storeState() {
} // no additional state needs storing
protected void restoreState() {
fireModelChanged();
} // no additional state needs restoring
protected void acceptState() {
} // no additional state needs accepting
public void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
// nothing to do
}
private Statistic populationSizesStatistic = new Statistic.Abstract() {
public String getStatisticName() {
return "populationSizes";
}
public int getDimension() {
return populationCount;
}
public double getStatisticValue(int dim) {
double metaN0 = demographicModels[dim].getDemographicFunction().getDemographic(0);
return metaN0 * getProportion(dim);
}
};
/**
* Parses an element from an DOM document into a ConstantPopulation.
*/
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return MetaPopulationModel.META_POPULATION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
ArrayList<DemographicModel> demographics = new ArrayList<DemographicModel>(0);
Parameter populationProportions = null;
for (int i = 0; i < xo.getChildCount(); ++i) {
final Object o = xo.getChild(i);
if (o instanceof DemographicModel) {
demographics.add((DemographicModel) o);
} else if (o instanceof Parameter) {
if (populationProportions != null) {
throw new Error("Allowed at most one Parameter in a MetaPopulationModel");
}
populationProportions = (Parameter) o;
} else {
throw new Error("A MetaPopulationModel may only have children of type Parameter or DemographicModel");
}
}
// Do sanity checking.
if (populationProportions == null) {
if (demographics.size() < 2) {
throw new Error("A MetaPopulationModel must have at least 2 DemographicModels (or a Parameter)");
}
} else {
if (demographics.size() != 1) {
throw new Error("A MetaPopulationModel with a Parameter must have exactly one DemographicModel");
}
}
return new MetaPopulationModel(demographics, populationProportions);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A model that represents a subdivided population.";
}
public Class getReturnType() {
return MetaPopulationModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(DemographicModel.class, 1, 999), // at least one required
new ElementRule(Parameter.class, true) // optional
};
};
//
// protected stuff
//
private int populationCount;
private Parameter populationProportions;
private DemographicModel[] demographicModels;
}