LogisticGrowthN0Model.java

/*
 * LogisticGrowthN0Model.java
 *
 * Daniel Wilson 4th October 2011
 *
 */

package dr.evomodel.epidemiology;

import dr.evomodel.coalescent.*;
import dr.evolution.coalescent.DemographicFunction;
import dr.inference.model.Parameter;

/**
 * Logistic growth.
 * 
 * @version $Id: LogisticGrowthN0Model.java,v 1.21 2008/03/21 20:25:57 rambaut Exp $
 *
 * @author Daniel Wilson
 * @author Alexei Drummond
 * @author Andrew Rambaut
 */
public class LogisticGrowthN0Model extends DemographicModel
{
	//
	// Public stuff
	//
	
	/**
	 * Construct demographic model with default settings
	 */
	public LogisticGrowthN0Model(Parameter N0Parameter, Parameter growthRateParameter, 
								Parameter t50Parameter, Type units, boolean usingGrowthRate) {
		this(LogisticGrowthN0ModelParser.LOGISTIC_GROWTH_MODEL, N0Parameter, growthRateParameter, t50Parameter, units, usingGrowthRate);
	}

	/**
	 * Construct demographic model with default settings
	 */
	public LogisticGrowthN0Model(String name, Parameter N0Parameter, Parameter growthRateParameter, Parameter t50Parameter, Type units, boolean usingGrowthRate) {	
		super(name);
		
		logisticGrowthN0 = new LogisticGrowthN0(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.t50Parameter = t50Parameter;
		addVariable(t50Parameter);
		t50Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY, 1));

		this.usingGrowthRate = usingGrowthRate;

		setUnits(units);
	}


	// general functions

	public DemographicFunction getDemographicFunction() {
		logisticGrowthN0.setN0(N0Parameter.getParameterValue(0));
		if (usingGrowthRate) {
			double r = growthRateParameter.getParameterValue(0);
			logisticGrowthN0.setGrowthRate(r);
		} else {
			double doublingTime = growthRateParameter.getParameterValue(0);
			logisticGrowthN0.setDoublingTime(doublingTime);
		}
		logisticGrowthN0.setT50(t50Parameter.getParameterValue(0));
		
		return logisticGrowthN0;
	}
	
	//
	// protected stuff
	//

	Parameter N0Parameter = null;	
	Parameter growthRateParameter = null;	
	Parameter t50Parameter = null;	
	LogisticGrowthN0 logisticGrowthN0 = null;
	boolean usingGrowthRate = true;
}