/*
* HierarchicalTransmissionDemographicModel.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.transmission;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* A demographic model for within patient evolution in a transmission history with a hierarchical parameterization.
*
* @author Marc A. Suchard
* @author Andrew Rambaut
* @version $Id: TransmissionDemographicModel.java,v 1.7 2005/05/24 20:25:58 rambaut Exp $
*/
public class HierarchicalTransmissionDemographicModel extends TransmissionDemographicModel {
//
// Public stuff
//
public static String HIERARCHICAL_TRANSMISSION_MODEL = "hierarchicalTransmissionModel";
public static String CONSTANT = TransmissionDemographicModel.CONSTANT;
public static String EXPONENTIAL = TransmissionDemographicModel.EXPONENTIAL;
public static String LOGISTIC = TransmissionDemographicModel.LOGISTIC;
public static String POPULATION_SIZE = TransmissionDemographicModel.POPULATION_SIZE;
public static String ANCESTRAL_PROPORTION = TransmissionDemographicModel.ANCESTRAL_PROPORTION;
public static String GROWTH_RATE = TransmissionDemographicModel.GROWTH_RATE;
public static String DOUBLING_TIME = TransmissionDemographicModel.DOUBLING_TIME;
public static final String HOST_COUNT = "hostCount";
public HierarchicalTransmissionDemographicModel(int model,
Parameter N0Parameter, Parameter N1Parameter,
Parameter growthRateParameter, Parameter doublingTimeParameter, Type units) {
this(HIERARCHICAL_TRANSMISSION_MODEL, model, N0Parameter, N1Parameter, growthRateParameter, doublingTimeParameter, units);
}
public HierarchicalTransmissionDemographicModel(String name, int model,
Parameter N0Parameter, Parameter N1Parameter,
Parameter growthRateParameter, Parameter doublingTimeParameter, Type units) {
super(name, model, N0Parameter, N1Parameter, growthRateParameter, doublingTimeParameter, units);
}
public void resizeHierarchicalParameters(int hostCount) {
if (N0Parameter != null) {
N0Parameter.setDimension(hostCount);
// N0Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, hostCount));
}
if (N1Parameter != null) {
N1Parameter.setDimension(hostCount);
// N1Parameter.addBounds(new Parameter.DefaultBounds(1.0, 0.0, 1));
}
if (growthRateParameter != null) {
growthRateParameter.setDimension(hostCount);
// growthRateParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, hostCount));
}
if (doublingTimeParameter != null) {
doublingTimeParameter.setDimension(hostCount);
// doublingTimeParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, hostCount));
}
}
protected int getIndexFromHost(int host) {
return host - 1;
}
/**
* Parses an element from an DOM document into a ExponentialGrowth.
*/
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return HIERARCHICAL_TRANSMISSION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Type units = XMLUnits.Utils.getUnitsAttr(xo);
int model = 0;
Parameter N0Param = null;
Parameter N1Param = null;
Parameter rParam = null;
Parameter dParam = null;
if (xo.hasChildNamed(CONSTANT)) {
XMLObject cxo = xo.getChild(CONSTANT);
N0Param = (Parameter) cxo.getElementFirstChild(POPULATION_SIZE);
model = 0;
} else if (xo.hasChildNamed(EXPONENTIAL)) {
XMLObject cxo = xo.getChild(EXPONENTIAL);
N1Param = (Parameter) cxo.getElementFirstChild(ANCESTRAL_PROPORTION);
if (cxo.hasChildNamed(GROWTH_RATE)) {
rParam = (Parameter) cxo.getElementFirstChild(GROWTH_RATE);
} else {
dParam = (Parameter) cxo.getElementFirstChild(DOUBLING_TIME);
}
model = 1;
} else if (xo.hasChildNamed(LOGISTIC)) {
XMLObject cxo = xo.getChild(LOGISTIC);
N0Param = (Parameter) cxo.getElementFirstChild(POPULATION_SIZE);
N1Param = (Parameter) cxo.getElementFirstChild(ANCESTRAL_PROPORTION);
if (cxo.hasChildNamed(GROWTH_RATE)) {
rParam = (Parameter) cxo.getElementFirstChild(GROWTH_RATE);
} else {
dParam = (Parameter) cxo.getElementFirstChild(DOUBLING_TIME);
}
model = 2;
}
HierarchicalTransmissionDemographicModel demoModel =
new HierarchicalTransmissionDemographicModel(model, N0Param, N1Param, rParam, dParam, units);
demoModel.resizeHierarchicalParameters(xo.getAttribute(HOST_COUNT, 1));
return demoModel;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A SiteModel that has a gamma distributed rates across sites";
}
public Class getReturnType() {
return HierarchicalTransmissionDemographicModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
XMLUnits.UNITS_RULE,
AttributeRule.newIntegerRule(HOST_COUNT, false),
new XORRule(
new ElementRule(CONSTANT,
new XMLSyntaxRule[]{
new ElementRule(POPULATION_SIZE,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"This parameter represents the carrying capacity (maximum population size). " +
"If the shape is very large then the current day population size will be very close to the carrying capacity."),
}
),
new XORRule(
new ElementRule(EXPONENTIAL,
new XMLSyntaxRule[]{
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(ANCESTRAL_PROPORTION,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"This parameter determines the populaation size at transmission.")
}
),
new ElementRule(LOGISTIC,
new XMLSyntaxRule[]{
new ElementRule(POPULATION_SIZE,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"This parameter represents the carrying capacity (maximum population size). " +
"If the shape is very large then the current day population size will be very close to the carrying capacity."),
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(ANCESTRAL_PROPORTION,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"This parameter determines the populaation size at transmission.")
}
)
)
)
};
};
}