/*
* AlloppHybPopSizesScale.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
*/
package dr.evomodel.alloppnet.operators;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesNetworkModel;
import dr.evomodel.alloppnet.parsers.AlloppHybPopSizesScaleParser;
import dr.inference.operators.SimpleMCMCOperator;
import dr.math.MathUtils;
/**
* @author Graham Jones
* Date: 03/08/12
*/
public class AlloppHybPopSizesScale extends SimpleMCMCOperator {
private final AlloppSpeciesNetworkModel apspnet;
private final AlloppSpeciesBindings apsp;
private final double scalingFactor;
public AlloppHybPopSizesScale(AlloppSpeciesNetworkModel apspnet, AlloppSpeciesBindings apsp, double scalingFactor, double weight) {
this.apspnet = apspnet;
this.apsp = apsp;
this.scalingFactor = scalingFactor;
setWeight(weight);
}
public String getPerformanceSuggestion() {
return "None";
}
@Override
public String getOperatorName() {
return AlloppHybPopSizesScaleParser.HYB_POP_SIZES_SCALE + "(" + apspnet.getId() +
"," + apsp.getId() + ")";
}
@Override
public double doOperation() {
apspnet.beginNetworkEdit();
double b = (1.0-scalingFactor) * (1.0-scalingFactor) / scalingFactor;
double c = scalingFactor / (1.0-scalingFactor);
double y = MathUtils.nextDouble();
double s = b * (y+c) * (y+c);
int i = MathUtils.nextInt(apspnet.getNumberOfTetraTrees());
apspnet.setOneHybPopValue(i, s * apspnet.getOneHybPopValue(i));
apspnet.endNetworkEdit();
return 0.0; // this way of scaling, with proposal proportional to x^-(1/2) has hastings ratio 1
}
}