/*
* OneOnX3Prior.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.inference.model;
import java.util.ArrayList;
/**
* @author Chieh-Hsi Wu
*
* This an improper prior 1/(x_i^3) which is the Jeffrey's prior for parameters of Normal distribution
* (and Log-normal distribution?)
*
*/
public class OneOnX3Prior extends Likelihood.Abstract{
public OneOnX3Prior() {
super(null);
}
/**
* Adds a statistic, this is the data for which the Prod_i (1/x_i^3) prior is calculated.
*
* @param data the statistic to compute density of
*/
public void addData(Statistic data) {
dataList.add(data);
}
protected ArrayList<Statistic> dataList = new ArrayList<Statistic>();
/**
* Overridden to always return false.
*/
protected boolean getLikelihoodKnown() {
return false;
}
/**
* Calculate the log likelihood of the current state.
*
* @return the log likelihood.
*/
public double calculateLogLikelihood() {
double logL = 0.0;
for (Statistic statistic : dataList) {
for (int j = 0; j < statistic.getDimension(); j++) {
logL -= 3*Math.log(statistic.getStatisticValue(j));
}
}
return logL;
}
public String prettyName() {
String s = "OneOnX3" + "(";
for (Statistic statistic : dataList) {
s = s + statistic.getStatisticName() + ",";
}
return s.substring(0, s.length() - 1) + ")";
}
}