/*
* BirthDeathModelParser.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.BirthDeathGernhard08Model;
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 BirthDeathModelParser extends AbstractXMLObjectParser {
public static final String BIRTH_DEATH_MODEL = "birthDeathModel";
public static final String BIRTHDIFF_RATE = "birthMinusDeathRate";
public static final String RELATIVE_DEATH_RATE = "relativeDeathRate";
public static final String SAMPLE_PROB = "sampleProbability";
public static final String TREE_TYPE = "type";
public static final String CONDITIONAL_ON_ROOT = "conditionalOnRoot";
public static final String BIRTH_DEATH = "birthDeath";
public static final String MEAN_GROWTH_RATE_PARAM_NAME = BIRTH_DEATH + ".meanGrowthRate";
public static final String RELATIVE_DEATH_RATE_PARAM_NAME = BIRTH_DEATH + "." + RELATIVE_DEATH_RATE;
public String getParserName() {
return BIRTH_DEATH_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
final String s = xo.getAttribute(TREE_TYPE, BirthDeathGernhard08Model.TreeType.UNSCALED.toString());
final BirthDeathGernhard08Model.TreeType treeType = BirthDeathGernhard08Model.TreeType.valueOf(s);
final boolean conditonalOnRoot = xo.getAttribute(CONDITIONAL_ON_ROOT, false);
final Parameter birthParameter = (Parameter) xo.getElementFirstChild(BIRTHDIFF_RATE);
final Parameter deathParameter = (Parameter) xo.getElementFirstChild(RELATIVE_DEATH_RATE);
final Parameter sampleProbability = xo.hasChildNamed(SAMPLE_PROB) ?
(Parameter) xo.getElementFirstChild(SAMPLE_PROB) : null;
Logger.getLogger("dr.evomodel").info(xo.hasChildNamed(SAMPLE_PROB) ? getCitationRHO() : getCitation());
final String modelName = xo.getId();
return new BirthDeathGernhard08Model(modelName, birthParameter, deathParameter, sampleProbability,
treeType, units, conditonalOnRoot);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public static String getCitationRHO() {
return "Stadler, T; On incomplete sampling under birth-death models and connections to the sampling-based coalescent;\n" +
"JOURNAL OF THEORETICAL BIOLOGY (2009) 261:58-66";
}
public static String getCitation() {
return "Using birth-death model on tree: Gernhard T (2008) J Theor Biol, Volume 253, Issue 4, Pages 769-778 In press";
}
public String getParserDescription() {
return "Gernhard (2008) model of speciation (equation at bottom of page 19 of draft).";
}
public Class getReturnType() {
return BirthDeathGernhard08Model.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newStringRule(TREE_TYPE, true),
AttributeRule.newBooleanRule(CONDITIONAL_ON_ROOT, true),
new ElementRule(BIRTHDIFF_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(RELATIVE_DEATH_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(SAMPLE_PROB, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true),
XMLUnits.SYNTAX_RULES[0]
};
}