/*
* PearsonCorrelation.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 dr.stats.DiscreteStatistics;
/**
* @author Simon Greenhill
* @author Alexei Drummond
*/
public class PearsonCorrelation extends Statistic.Abstract {
Parameter X, Y;
boolean log = false;
public PearsonCorrelation(Parameter X, Parameter Y, boolean log) {
if (X.getDimension() != Y.getDimension()) throw new IllegalArgumentException();
this.X = X;
this.Y = Y;
this.log = log;
}
public int getDimension() {
return 1;
}
public double getStatisticValue(int dim) {
double[] xvalues = X.getParameterValues();
double[] yvalues = Y.getParameterValues();
if (log) {
for (int i = 0; i < xvalues.length; i++) {
xvalues[i] = Math.log(xvalues[i]);
yvalues[i] = Math.log(yvalues[i]);
}
}
double meanX = DiscreteStatistics.mean(xvalues);
double meanY = DiscreteStatistics.mean(yvalues);
double stdevX = DiscreteStatistics.stdev(xvalues);
double stdevY = DiscreteStatistics.stdev(yvalues);
double corr = 0;
for (int i = 0; i < xvalues.length; i++) {
double deviateX = xvalues[i] - meanX;
double deviateY = yvalues[i] - meanY;
corr += deviateX*deviateY;
}
corr /= X.getDimension();
corr /= (stdevX*stdevY);
return corr;
}
}