ConstExpConstModel.java

/*
 * ConstExpConstModel.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.coalescent;

import dr.evolution.coalescent.ConstExpConst;
import dr.evolution.coalescent.DemographicFunction;
import dr.evomodelxml.coalescent.ConstExpConstModelParser;
import dr.inference.model.Parameter;

/**
 * Exponential growth from a constant ancestral population size.
 *
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @version $Id: ConstantExponentialModel.java,v 1.8 2005/10/28 02:49:17 alexei Exp $
 */
public class ConstExpConstModel extends DemographicModel {

    //
    // Public stuff
    //

    /**
     * Construct demographic model with default settings
     */
    public ConstExpConstModel(Parameter N0Parameter, Parameter N1Parameter, Parameter timeParameter,
                              Parameter growthRateParameter, Type units, boolean usingGrowthRate) {

        this(ConstExpConstModelParser.CONST_EXP_CONST_MODEL, N0Parameter, N1Parameter, timeParameter, growthRateParameter, units, usingGrowthRate);
    }

    /**
     * Construct demographic model with default settings
     */
    public ConstExpConstModel(String name, Parameter N0Parameter, Parameter N1Parameter, Parameter timeParameter,
                              Parameter growthRateParameter, Type units, boolean usingGrowthRate) {

        super(name);

        constExpConst = new ConstExpConst(units);

        this.N0Parameter = N0Parameter;
        addVariable(N0Parameter);
        N0Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));

        this.N1Parameter = N0Parameter;
        addVariable(N1Parameter);
        N1Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));

        this.timeParameter = timeParameter;
        addVariable(timeParameter);
        timeParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));

        this.growthRateParameter = growthRateParameter;
        addVariable(growthRateParameter);
        growthRateParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));

        this.usingGrowthRate = usingGrowthRate;

        setUnits(units);
    }


    // general functions

    public DemographicFunction getDemographicFunction() {

        double time = timeParameter.getParameterValue(0);
        double N0 = N0Parameter.getParameterValue(0);
        double N1 = N1Parameter.getParameterValue(0);
        double growthRate = growthRateParameter.getParameterValue(0);

        if (!usingGrowthRate) {
            double doublingTime = growthRate;
            growthRate = Math.log(2) / doublingTime;
        }

        constExpConst.setGrowthRate(growthRate);
        constExpConst.setN0(N0);
        constExpConst.setN1(N1);
        constExpConst.setTime1(time);

        return constExpConst;
    }

    //
    // protected stuff
    //

    private final Parameter N0Parameter;
    private final Parameter N1Parameter;
    private final Parameter timeParameter;
    private final Parameter growthRateParameter;
    private final ConstExpConst constExpConst;
    private final boolean usingGrowthRate;
}