/*
* BirthDeathCollapseModel.java
*
* Copyright (c) 2002-2017 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
*/
/*
This file is part of BEAST.
BEAST is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with DISSECT. If not, see <http://www.gnu.org/licenses/>.
*/
package dr.evomodel.alloppnet.speciation;
/**
*
* Model for prior for species delimitation in multispecies coalescent model.
*
* @author Graham Jones
* Date: 01/09/2013
*/
import dr.evolution.util.Taxon;
import dr.evolution.util.Units;
import dr.evolution.tree.Tree;
import dr.evomodel.speciation.SpeciationModel;
import dr.inference.model.Parameter;
import dr.util.Author;
import dr.util.Citable;
import dr.util.Citation;
import java.util.*;
import java.util.logging.Logger;
public class BirthDeathCollapseModel extends SpeciationModel implements Citable {
private Parameter birthDiffRate; // lambda - mu
private Parameter relativeDeathRate; // mu/lambda
private Parameter originHeight;
private Parameter collapseWeight;
private final double collapseHeight;
public BirthDeathCollapseModel(String modelName, Tree tree, Units.Type units,
Parameter birthDiffRate, Parameter relativeDeathRate,
Parameter originHeight, Parameter collapseWeight, double collH) {
super(modelName, units);
this.collapseHeight = collH;
this.birthDiffRate = birthDiffRate;
addVariable(birthDiffRate);
birthDiffRate.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.relativeDeathRate = relativeDeathRate;
addVariable(relativeDeathRate);
relativeDeathRate.addBounds(new Parameter.DefaultBounds(1.0, 0.0, 1));
this.originHeight = originHeight;
originHeight.setParameterValue(0, 1.05 * tree.getNodeHeight(tree.getRoot()));
addVariable(originHeight);
originHeight.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.collapseWeight = collapseWeight;
addVariable(collapseWeight);
collapseWeight.addBounds(new Parameter.DefaultBounds(1.0, 0.0, 1));
Logger.getLogger("dr.evomodel.speciation").info("\tConstructing a birth-death-collapse model, please cite:\n"
+ Citable.Utils.getCitationString(this));
}
public double getCollapseHeight() {
return collapseHeight;
}
// provided to help avoid inconsistent treatment of h == collapseHeight
public static boolean belowCollapseHeight(double h, double collapseHeight) {
return (h < collapseHeight);
}
@Override
public double calculateTreeLogLikelihood(Tree tree) {
double logpt = 0.0;
int ninodes = tree.getInternalNodeCount();
int ntips = tree.getExternalNodeCount();
double alpha = birthDiffRate.getParameterValue(0);
double beta = relativeDeathRate.getParameterValue(0);
double tor = originHeight.getParameterValue(0);
double w = collapseWeight.getParameterValue(0);
double rooth = tree.getNodeHeight(tree.getRoot());
if (rooth > tor) {
return Double.NEGATIVE_INFINITY;
}
logpt += originHeightLogLikelihood(tor, alpha, beta, w, ntips);
for (int n = 0; n < ninodes; n++) {
final double height = tree.getNodeHeight(tree.getInternalNode(n));
double usualpn = nodeHeightLikelihood(height, tor, alpha, beta);
double collapsedpn = (height < collapseHeight) ? 1.0 / collapseHeight : 0.0;
logpt += Math.log((1.0 - w) * usualpn + w * collapsedpn);
}
return logpt;
}
private double originHeightLogLikelihood(double t, double a, double b, double w, int n) {
double E = Math.exp(-a * t);
double B = (1 - E) / (1-b*E);
double z = 0.0;
z += Math.log(a);
z += Math.log(1 - b);
z -= a * t;
z -= 2 * Math.log(1 - b * E);
z += (n-2) * Math.log(w + (1 - w) * B);
z += Math.log(w + n * (1 - w) * B);
return z;
}
private double nodeHeightLikelihood(double s, double t, double a, double b) {
double Es = Math.exp(-a * s);
double Et = Math.exp(-a * t);
double z = 0.0;
if (s < t) {
z = a;
z *= (1 - b);
z *= Es;
z /= (1 - b * Es) * (1 - b * Es);
z *= (1 - b * Et);
z /= (1 - Et);
}
return z;
}
@Override
public double calculateTreeLogLikelihood(Tree tree, Set<Taxon> exclude) {
// not implemented.
return Double.NEGATIVE_INFINITY;
}
@Override
public Citation.Category getCategory() {
return Citation.Category.SPECIES_MODELS;
}
@Override
public String getDescription() {
return "DISSECT species delimitation model";
}
@Override
public List<Citation> getCitations() {
return Collections.singletonList(
new Citation(
new Author[]{
new Author("Graham", "Jones"),
new Author("Bengt", "Oxelman")
},
"DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent",
2014,
"BIORXIV/2014/003178",
-1,
-1,
-1,
Citation.Status.IN_SUBMISSION
));
}
}