/*
* BirthDeathSerialSamplingModelParser.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.evomodelxml.speciation;
import dr.evolution.util.Units;
import dr.evomodel.speciation.BirthDeathSerialSamplingModel;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Alexei Drummond
* @author Joseph Heled
*/
public class BirthDeathSerialSamplingModelParser extends AbstractXMLObjectParser {
public static final String BIRTH_DEATH_SERIAL_MODEL = "birthDeathSerialSampling";
public static final String LAMBDA = "birthRate";
public static final String MU = "deathRate";
public static final String RELATIVE_MU = "relativeDeathRate";
public static final String PSI = "psi";
public static final String SAMPLE_PROBABILITY = "sampleProbability"; // default to fix to 0
public static final String SAMPLE_BECOMES_NON_INFECTIOUS = "sampleBecomesNonInfectiousProb";
public static final String R = "r";
// public static final String FINAL_TIME_INTERVAL = "finalTimeInterval";
public static final String ORIGIN = "origin";
public static final String TREE_TYPE = "type";
public static final String BDSS = "bdss";
public static final String HAS_FINAL_SAMPLE = "hasFinalSample";
public String getParserName() {
return BIRTH_DEATH_SERIAL_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final String modelName = xo.getId();
final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
boolean hasFinalSample = xo.getAttribute(HAS_FINAL_SAMPLE, false);
final Parameter lambda = (Parameter) xo.getElementFirstChild(LAMBDA);
boolean relativeDeath = xo.hasChildNamed(RELATIVE_MU);
Parameter mu;
if (relativeDeath) {
mu = (Parameter) xo.getElementFirstChild(RELATIVE_MU);
} else {
mu = (Parameter) xo.getElementFirstChild(MU);
}
final Parameter psi = (Parameter) xo.getElementFirstChild(PSI);
//Issue 656: fix p=0
final Parameter p = xo.hasChildNamed(SAMPLE_PROBABILITY) ?
(Parameter) xo.getElementFirstChild(SAMPLE_PROBABILITY) : new Parameter.Default(0.0);
Parameter origin = null;
if (xo.hasChildNamed(ORIGIN)) {
origin = (Parameter) xo.getElementFirstChild(ORIGIN);
}
final Parameter r = xo.hasChildNamed(SAMPLE_BECOMES_NON_INFECTIOUS) ?
(Parameter) xo.getElementFirstChild(SAMPLE_BECOMES_NON_INFECTIOUS) : new Parameter.Default(0.0);
// r.setParameterValueQuietly(0, 1 - r.getParameterValue(0)); // donot use it, otherwise log is changed improperly
// final Parameter finalTimeInterval = xo.hasChildNamed(FINAL_TIME_INTERVAL) ?
// (Parameter) xo.getElementFirstChild(FINAL_TIME_INTERVAL) : new Parameter.Default(0.0);
Logger.getLogger("dr.evomodel").info(xo.hasChildNamed(SAMPLE_BECOMES_NON_INFECTIOUS) ? getCitationRT() : getCitationPsiOrg());
return new BirthDeathSerialSamplingModel(modelName, lambda, mu, psi, p, relativeDeath,
r, hasFinalSample, origin, units);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public static String getCitationPsiOrg() {
// return "Stadler, T; Sampling-through-time in birth-death trees; JOURNAL OF THEORETICAL BIOLOGY (2010) 267:396-404";
return "Stadler T (2010) J Theor Biol 267, 396-404 [Birth-Death with Serial Samples].";
}
public static String getCitationRT() {
return "Stadler et al (2011) : Estimating the basic reproductive number from viral sequence data, " +
"Mol.Biol.Evol., doi: 10.1093/molbev/msr217, 2011";
}
public String getParserDescription() {
return "Stadler et al (2010) model of speciation.";
}
public Class getReturnType() {
return BirthDeathSerialSamplingModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newStringRule(TREE_TYPE, true),
AttributeRule.newBooleanRule(HAS_FINAL_SAMPLE, true),
// new ElementRule(FINAL_TIME_INTERVAL, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true),
new ElementRule(ORIGIN, Parameter.class, "The origin of the infection, x0 > tree.rootHeight", true),
new ElementRule(LAMBDA, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new XORRule(
new ElementRule(MU, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(RELATIVE_MU, new XMLSyntaxRule[]{new ElementRule(Parameter.class)})),
new ElementRule(PSI, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(SAMPLE_BECOMES_NON_INFECTIOUS, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true),
//Issue 656
// new ElementRule(SAMPLE_PROBABILITY, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
// XMLUnits.SYNTAX_RULES[0]
};
}