/*
* TreeShape.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.evolution.tree;
import dr.evolution.io.NexusImporter;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.Collections;
/**
* A collection of tree shape summary statistics.
*
* @version $Id: TreeShape.java,v 1.7 2005/05/24 20:25:57 rambaut Exp $
*
* @author Alexei Drummond
*/
public class TreeShape {
/**
* The NBar statistic is the average number of nodes above a terminal node.
* see Kirkpatrick & Slatkin (1992)
*/
public static double getNBarStatistic(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 NBar / tree.getExternalNodeCount();
}
/**
* The varNBar statistic is the average number of nodes above a terminal node.
* see Kirkpatrick & Slatkin (1992)
*/
public static double getVarNBarStatistic(Tree tree) {
double[] N = new double[tree.getExternalNodeCount()];
for (int i =0; i < N.length; i++) {
NodeRef node = tree.getExternalNode(i);
while (!tree.isRoot(node)) {
node = tree.getParent(node);
N[i] += 1.0;
}
}
return dr.stats.DiscreteStatistics.variance(N);
}
/**
* The C statistic is the normalized sum of differences of
* number of children in left and right subtrees over all
* internal nodes.
* see Kirkpatrick & Slatkin (1992)
*/
public static double getCStatistic(Tree tree) {
double C = 0.0;
int n = tree.getExternalNodeCount();
for (int i =0; i < n-1; i++) {
NodeRef node = tree.getInternalNode(i);
int r = TreeUtils.getLeafCount(tree, tree.getChild(node, 0));
int s = TreeUtils.getLeafCount(tree, tree.getChild(node, 1));
C += Math.abs(r-s);
}
C *= 2.0 / (n * (n - 3) + 2);
return C;
}
/**
* The B1 statistic measures the maximum number of nodes between
* each interior node and a tip (Mi) for all internal nodes except the
* root. THe statistic is the sum of the reciprocals of this Mi
* statistic.
* see Kirkpatrick & Slatkin (1992)
*/
public static double getB1Statistic(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 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 static double getTreeness(Tree tree) {
double noise = 0.0;
double signal = 0.0;
for (int i = 0; i < tree.getExternalNodeCount(); i++) {
NodeRef node = tree.getExternalNode(i);
NodeRef parent = tree.getParent(node);
noise += tree.getNodeHeight(parent) - tree.getNodeHeight(node);
}
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef node = tree.getInternalNode(i);
if (!tree.isRoot(node)) {
NodeRef parent = tree.getParent(node);
signal += tree.getNodeHeight(parent) - tree.getNodeHeight(node);
}
}
return signal/noise;
}
/**
* @return the gamma statistic of tree shape (see Pybus & Harvey, 2000).
* Assumes a strictly bifurcating tree and contemporaneous sequences.
*/
public static double getGammaStatistic(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 gamma = 0.0;
for (int i = 2; i < n; i++) {
for (int k = 2; k <= i; k++) {
gamma += k * g[k-2];
}
}
gamma *= (1.0 / n-2.0);
gamma -= T/2.0;
gamma /= T * Math.sqrt(1.0/(12.0*(n-2.0)));
return gamma;
}
/**
* @return the intervals in an ultrametric tree in order from root to tips.
*/
private static double[] getIntervals(Tree tree) {
ArrayList<Double> heights = new ArrayList<Double>();
if (TreeUtils.isUltrametric(tree)) {
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
heights.add(tree.getNodeHeight(tree.getInternalNode(i)));
}
Collections.sort(heights);
// for (int i = 0; i < heights.size(); i++) {
// System.out.print(heights.get(i)+" ");
// }
// System.out.println();
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;
} else
throw new IllegalArgumentException("Expecting ultrametric tree.");
}
public static void main(String[] args) throws Exception {
NexusImporter importer = new NexusImporter(new FileReader(args[0]));
Tree[] trees = importer.importTrees(null);
System.out.println("File = " + args[0]);
double[] treeness = new double[trees.length];
for (int i = 0; i < treeness.length; i++) {
treeness[i] = getTreeness(trees[i]);
}
System.out.println("Mean treeness = " + dr.stats.DiscreteStatistics.mean(treeness));
System.out.println("Lower (95%) treeness = " + dr.stats.DiscreteStatistics.quantile(0.025, treeness));
System.out.println("Upper (95%) treeness = " + dr.stats.DiscreteStatistics.quantile(0.975, treeness));
}
}