/*
* B1Statistic.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: B1Statistic.java,v 1.2 2005/09/28 13:50:56 rambaut Exp $
*
* @author Alexei Drummond
*/
public class B1Statistic extends AbstractTreeSummaryStatistic {
private B1Statistic() { }
public double[] getSummaryStatistic(Tree tree) {
double B1 = 0.0;
int n = tree.getInternalNodeCount();
for (int i =0; i < n; i++) {
NodeRef node = tree.getInternalNode(i);
if (!tree.isRoot(node)) {
B1 += 1.0/getMi(tree, node);
}
}
return new double[] { B1 };
}
/**
* Assumes strictly bifurcating tree
*/
private static int getMi(Tree tree, NodeRef node) {
int childCount = tree.getChildCount(node);
if (childCount == 0) return 0;
int Mi = 0;
for (int i =0; i < childCount; i++) {
int mi = getMi(tree, tree.getChild(node, i));
if (mi > Mi) Mi = mi;
}
Mi += 1;
return Mi;
}
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 B1Statistic();
}
public String getSummaryStatisticName() {
return "B1";
}
public String getSummaryStatisticDescription() {
return "The sum of the reciprocals of the maximum number of nodes between " +
"each interior node and a tip (Mi) for all internal nodes except the " +
"root.";
}
public String getSummaryStatisticReference() {
return "see Kirkpatrick & Slatkin (1992)";
}
public boolean allowsPolytomies() { return false; }
public boolean allowsNonultrametricTrees() { return true; }
public boolean allowsUnrootedTrees() { return false; }
public SummaryStatisticDescription.Category getCategory() { return SummaryStatisticDescription.Category.TREE_SHAPE; }
};
}