/*
* LogisticGrowthModel.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;
import dr.evolution.coalescent.DemographicFunction;
import dr.evolution.coalescent.LogisticGrowth;
import dr.evomodelxml.coalescent.LogisticGrowthModelParser;
import dr.inference.model.Parameter;
import dr.util.Author;
import dr.util.Citable;
import dr.util.Citation;
import java.util.Collections;
import java.util.List;
/**
* Logistic growth.
*
* @author Alexei Drummond
* @author Andrew Rambaut
* @version $Id: LogisticGrowthModel.java,v 1.21 2005/05/24 20:25:57 rambaut Exp $
*/
public class LogisticGrowthModel extends DemographicModel implements Citable {
//
// Public stuff
//
/**
* Construct demographic model with default settings
*/
public LogisticGrowthModel(Parameter N0Parameter, Parameter growthRateParameter,
Parameter shapeParameter, double alpha, Type units,
boolean usingGrowthRate) {
this(LogisticGrowthModelParser.LOGISTIC_GROWTH_MODEL, N0Parameter, growthRateParameter, shapeParameter, alpha, units, usingGrowthRate);
}
/**
* Construct demographic model with default settings
*/
public LogisticGrowthModel(String name, Parameter N0Parameter, Parameter growthRateParameter, Parameter shapeParameter, double alpha, Type units, boolean usingGrowthRate) {
super(name);
logisticGrowth = new LogisticGrowth(units);
this.N0Parameter = N0Parameter;
addVariable(N0Parameter);
N0Parameter.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.shapeParameter = shapeParameter;
addVariable(shapeParameter);
shapeParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.alpha = alpha;
this.usingGrowthRate = usingGrowthRate;
setUnits(units);
}
// general functions
public DemographicFunction getDemographicFunction() {
logisticGrowth.setN0(N0Parameter.getParameterValue(0));
if (usingGrowthRate) {
double r = growthRateParameter.getParameterValue(0);
logisticGrowth.setGrowthRate(r);
} else {
double doublingTime = growthRateParameter.getParameterValue(0);
logisticGrowth.setDoublingTime(doublingTime);
}
logisticGrowth.setTime50(shapeParameter.getParameterValue(0));
return logisticGrowth;
}
//
// protected stuff
//
Parameter N0Parameter = null;
Parameter growthRateParameter = null;
Parameter shapeParameter = null;
double alpha = 0.5;
LogisticGrowth logisticGrowth = null;
boolean usingGrowthRate = true;
@Override
public Citation.Category getCategory() {
return Citation.Category.TREE_PRIORS;
}
@Override
public String getDescription() {
return "Logistic Growth Coalescent";
}
@Override
public List<Citation> getCitations() {
return Collections.singletonList(CITATION);
}
public static Citation CITATION = new Citation(
new Author[]{
new Author("OG", "Pybus"),
new Author("A", "Rambaut")
},
"GENIE: estimating demographic history from molecular phylogenies",
2001,
"Bioinformatics",
18, 1404, 1405
);
}