/*
* LogisticGrowthN0ModelParser.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.epidemiology;
import dr.evolution.util.Units;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Parses an element from an XMLObject into LogisticGrowthN0Model.
* @author Daniel Wilson
*/
public class LogisticGrowthN0ModelParser extends AbstractXMLObjectParser
{
public static String POPULATION_SIZE = "populationSize";
public static String LOGISTIC_GROWTH_MODEL = "logisticGrowthN0";
public static String GROWTH_RATE = "growthRate";
public static String DOUBLING_TIME = "doublingTime";
public static String TIME_50 = "t50";
public String getParserName() { return LOGISTIC_GROWTH_MODEL; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
XMLObject cxo = (XMLObject)xo.getChild(POPULATION_SIZE);
Parameter N0Param = (Parameter)cxo.getChild(Parameter.class);
boolean usingGrowthRate = true;
Parameter rParam = null;
if (xo.getChild(GROWTH_RATE) != null) {
cxo = (XMLObject)xo.getChild(GROWTH_RATE);
rParam = (Parameter)cxo.getChild(Parameter.class);
} else {
cxo = (XMLObject)xo.getChild(DOUBLING_TIME);
rParam = (Parameter)cxo.getChild(Parameter.class);
usingGrowthRate = false;
}
cxo = (XMLObject)xo.getChild(TIME_50);
Parameter t50Param = (Parameter)cxo.getChild(Parameter.class);
return new LogisticGrowthN0Model(N0Param, rParam, t50Param, units, usingGrowthRate);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Logistic growth demographic model.";
}
public Class getReturnType() { return LogisticGrowthN0Model.class; }
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
XMLUnits.SYNTAX_RULES[0],
new ElementRule(POPULATION_SIZE,
new XMLSyntaxRule[] { new ElementRule(Parameter.class) },
"This parameter represents the present day population size."),
new XORRule(
new ElementRule(GROWTH_RATE,
new XMLSyntaxRule[] { new ElementRule(Parameter.class) },
"This parameter determines the rate of growth during the exponential phase. " +
"See exponentialGrowth for details."),
new ElementRule(DOUBLING_TIME,
new XMLSyntaxRule[] { new ElementRule(Parameter.class) },
"This parameter determines the doubling time at peak growth rate.")
),
new ElementRule(TIME_50,
new XMLSyntaxRule[] { new ElementRule(Parameter.class) },
"This parameter represents the time in the past (or future) when the population had (or will have) " +
"half of the carrying capacity (maximum population size). " +
"It is a positive number if half the carrying capacity was attained in the past " +
"or a negative number if it will be attained in the future.")
};
}