/*
* GammaStatistic.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.app.treestat.statistics;
import dr.evolution.tree.Tree;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* @author Alexei Drummond
*
* @version $Id: GammaStatistic.java,v 1.5 2006/05/09 10:24:27 rambaut Exp $
*/
public class GammaStatistic extends AbstractTreeSummaryStatistic {
private GammaStatistic() { }
public double[] getSummaryStatistic(Tree tree) {
int n = tree.getExternalNodeCount();
double[] g = getIntervals(tree);
double T = 0; // total branch length
for (int j = 2; j <= n; j++) {
T += j * g[j-2];
}
double sum = 0.0;
for (int i = 2; i < n; i++) {
for (int k = 2; k <= i; k++) {
sum += k * g[k-2];
}
}
double gamma = ((sum / (n-2.0)) - (T / 2.0)) / (T * Math.sqrt(1.0 / (12.0 * (n - 2.0))));
return new double[] { gamma };
}
/**
* @return the intervals in an ultrametric tree in order from root to tips.
*/
private static double[] getIntervals(Tree tree) {
List<Double> heights = new ArrayList<Double>();
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
heights.add(tree.getNodeHeight(tree.getInternalNode(i)));
}
Collections.sort(heights, Collections.reverseOrder());
double[] intervals = new double[heights.size()];
for (int i = 0; i < intervals.length - 1; i++) {
double height1 = heights.get(i);
double height2 = heights.get(i + 1);
intervals[i] = height1 - height2;
}
intervals[intervals.length - 1] = heights.get(intervals.length - 1);
return intervals;
}
public String getSummaryStatisticName() { return FACTORY.getSummaryStatisticName(); }
public String getSummaryStatisticDescription() { return FACTORY.getSummaryStatisticDescription(); }
public String getSummaryStatisticReference() { return FACTORY.getSummaryStatisticReference(); }
public boolean allowsPolytomies() { return FACTORY.allowsPolytomies(); }
public boolean allowsNonultrametricTrees() { return FACTORY.allowsNonultrametricTrees(); }
public boolean allowsUnrootedTrees() { return FACTORY.allowsUnrootedTrees(); }
public SummaryStatisticDescription.Category getCategory() { return FACTORY.getCategory(); }
public static final TreeSummaryStatistic.Factory FACTORY = new TreeSummaryStatistic.Factory() {
public TreeSummaryStatistic createStatistic() {
return new GammaStatistic();
}
public String getSummaryStatisticName() {
return "Gamma";
}
public String getSummaryStatisticDescription() {
return "The gamma-statistic is a summary of the information contained in the inter-node " +
"intervals of a phylogeny; under the assumption that the clade diversified " +
"with constant rates, it follows a normal distribution with mean of zero and a standard-deviation " +
"of one " +
"(Pybus and Harvey 2000). Thus, the null hypothesis that the clade diversified with constant " +
"rates may be tested with 1 - 2*pnorm(abs(gamma.stat(phy))) for a two-tailed test, " +
"or 1 - pnorm(abs(gamma.stat(phy))) for a one-tailed test, both returning the corresponding P-value.";
}
public String getSummaryStatisticReference() {
return "Pybus & Harvey (2000)";
}
public boolean allowsPolytomies() { return true; }
public boolean allowsNonultrametricTrees() { return false; }
public boolean allowsUnrootedTrees() { return false; }
public SummaryStatisticDescription.Category getCategory() { return SummaryStatisticDescription.Category.SPECIATION; }
};
}