/*
* Nbar.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.NodeRef;
import dr.evolution.tree.Tree;
/**
*
* @version $Id: Nbar.java,v 1.2 2005/09/28 13:50:56 rambaut Exp $
*
* @author Alexei Drummond
*/
public class Nbar extends AbstractTreeSummaryStatistic {
private Nbar() { }
public double[] getSummaryStatistic(Tree tree) {
double NBar = 0.0;
for (int i =0; i < tree.getExternalNodeCount(); i++) {
NodeRef node = tree.getExternalNode(i);
while (!tree.isRoot(node)) {
node = tree.getParent(node);
NBar += 1.0;
}
}
return new double[] { NBar / tree.getExternalNodeCount() };
}
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 Nbar();
}
public String getSummaryStatisticName() {
return "N_bar";
}
public String getSummaryStatisticDescription() {
return "The mean number of nodes above an external node.";
}
public String getSummaryStatisticReference() {
return "Kirkpatrick & Slatkin (1992)";
}
public boolean allowsPolytomies() { return true; }
public boolean allowsNonultrametricTrees() { return true; }
public boolean allowsUnrootedTrees() { return false; }
public SummaryStatisticDescription.Category getCategory() { return SummaryStatisticDescription.Category.TREE_SHAPE; }
};
}