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REPTree.java

/*
 *    This program is free software; you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation; either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    This program 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 General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with this program; if not, write to the Free Software
 *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 *    REPTree.java
 *    Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.classifiers.trees;

import weka.classifiers.Classifier;
import weka.classifiers.Sourcable;
import weka.classifiers.rules.ZeroR;
import weka.core.AdditionalMeasureProducer;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.ContingencyTables;
import weka.core.Drawable;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;
import weka.core.Utils;
import weka.core.WeightedInstancesHandler;
import weka.core.Capabilities.Capability;

import java.io.Serializable;
import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;

/**
 <!-- globalinfo-start -->
 * Fast decision tree learner. Builds a decision/regression tree using information gain/variance and prunes it using reduced-error pruning (with backfitting).  Only sorts values for numeric attributes once. Missing values are dealt with by splitting the corresponding instances into pieces (i.e. as in C4.5).
 * <p/>
 <!-- globalinfo-end -->
 *
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -M &lt;minimum number of instances&gt;
 *  Set minimum number of instances per leaf (default 2).</pre>
 * 
 * <pre> -V &lt;minimum variance for split&gt;
 *  Set minimum numeric class variance proportion
 *  of train variance for split (default 1e-3).</pre>
 * 
 * <pre> -N &lt;number of folds&gt;
 *  Number of folds for reduced error pruning (default 3).</pre>
 * 
 * <pre> -S &lt;seed&gt;
 *  Seed for random data shuffling (default 1).</pre>
 * 
 * <pre> -P
 *  No pruning.</pre>
 * 
 * <pre> -L
 *  Maximum tree depth (default -1, no maximum)</pre>
 * 
 <!-- options-end -->
 *
 * @author Eibe Frank (eibe@cs.waikato.ac.nz)
 * @version $Revision: 1.26 $ 
 */
00081 public class REPTree 
  extends Classifier 
  implements OptionHandler, WeightedInstancesHandler, Drawable, 
           AdditionalMeasureProducer, Sourcable {

  /** for serialization */
00087   static final long serialVersionUID = -8562443428621539458L;
  
  /** ZeroR model that is used if no attributes are present. */
00090   protected ZeroR m_zeroR;

  /**
   * Returns a string describing classifier
   * @return a description suitable for
   * displaying in the explorer/experimenter gui
   */
00097   public String globalInfo() {

    return  "Fast decision tree learner. Builds a decision/regression tree using "
      + "information gain/variance and prunes it using reduced-error pruning "
      + "(with backfitting).  Only sorts values for numeric attributes "
      + "once. Missing values are dealt with by splitting the corresponding "
      + "instances into pieces (i.e. as in C4.5).";
  }

  /** An inner class for building and storing the tree structure */
00107   protected class Tree 
    implements Serializable, RevisionHandler {
    
    /** for serialization */
00111     static final long serialVersionUID = -1635481717888437935L;
    
    /** The header information (for printing the tree). */
00114     protected Instances m_Info = null;

    /** The subtrees of this tree. */ 
00117     protected Tree[] m_Successors;
    
    /** The attribute to split on. */
00120     protected int m_Attribute = -1;

    /** The split point. */
00123     protected double m_SplitPoint = Double.NaN;
    
    /** The proportions of training instances going down each branch. */
00126     protected double[] m_Prop = null;

    /** Class probabilities from the training data in the nominal case. 
      Holds the mean in the numeric case. */
00130     protected double[] m_ClassProbs = null;
    
    /** The (unnormalized) class distribution in the nominal
      case. Holds the sum of squared errors and the weight 
      in the numeric case. */
00135     protected double[] m_Distribution = null;
    
    /** Class distribution of hold-out set at node in the nominal case. 
      Straight sum of weights in the numeric case (i.e. array has
      only one element. */
00140     protected double[] m_HoldOutDist = null;
    
    /** The hold-out error of the node. The number of miss-classified
      instances in the nominal case, the sum of squared errors in the 
      numeric case. */
00145     protected double m_HoldOutError = 0;
  
    /**
     * Computes class distribution of an instance using the tree.
     * 
     * @param instance the instance to compute the distribution for
     * @return the distribution
     * @throws Exception if computation fails
     */
00154     protected double[] distributionForInstance(Instance instance) 
      throws Exception {

      double[] returnedDist = null;
      
      if (m_Attribute > -1) {
      
      // Node is not a leaf
      if (instance.isMissing(m_Attribute)) {
        
        // Value is missing
        returnedDist = new double[m_Info.numClasses()];

        // Split instance up
        for (int i = 0; i < m_Successors.length; i++) {
          double[] help = 
            m_Successors[i].distributionForInstance(instance);
          if (help != null) {
            for (int j = 0; j < help.length; j++) {
            returnedDist[j] += m_Prop[i] * help[j];
            }
          }
        }
      } else if (m_Info.attribute(m_Attribute).isNominal()) {
        
        // For nominal attributes
        returnedDist =  m_Successors[(int)instance.value(m_Attribute)].
          distributionForInstance(instance);
      } else {
        
        // For numeric attributes
        if (instance.value(m_Attribute) < m_SplitPoint) {
          returnedDist = 
            m_Successors[0].distributionForInstance(instance);
        } else {
          returnedDist = 
            m_Successors[1].distributionForInstance(instance);
        }
      }
      }
      if ((m_Attribute == -1) || (returnedDist == null)) {
      
      // Node is a leaf or successor is empty
      return m_ClassProbs;
      } else {
      return returnedDist;
      }
    }

   /**
    * Returns a string containing java source code equivalent to the test
    * made at this node. The instance being tested is called "i". This
    * routine assumes to be called in the order of branching, enabling us to
    * set the >= condition test (the last one) of a numeric splitpoint 
    * to just "true" (because being there in the flow implies that the 
    * previous less-than test failed).
    *
    * @param index index of the value tested
    * @return a value of type 'String'
    */
00214     public final String sourceExpression(int index) {
      
      StringBuffer expr = null;
      if (index < 0) {
        return "i[" + m_Attribute + "] == null";
      }
      if (m_Info.attribute(m_Attribute).isNominal()) {
        expr = new StringBuffer("i[");
      expr.append(m_Attribute).append("]");
      expr.append(".equals(\"").append(m_Info.attribute(m_Attribute)
            .value(index)).append("\")");
      } else {
        expr = new StringBuffer("");
      if (index == 0) {
        expr.append("((Double)i[")
          .append(m_Attribute).append("]).doubleValue() < ")
          .append(m_SplitPoint);
      } else {
        expr.append("true");
      }
      }
      return expr.toString();
    }

   /**
    * Returns source code for the tree as if-then statements. The 
    * class is assigned to variable "p", and assumes the tested 
    * instance is named "i". The results are returned as two stringbuffers: 
    * a section of code for assignment of the class, and a section of
    * code containing support code (eg: other support methods).
    * <p/>
    * TODO: If the outputted source code encounters a missing value
    * for the evaluated attribute, it stops branching and uses the 
    * class distribution of the current node to decide the return value. 
    * This is unlike the behaviour of distributionForInstance(). 
    *
    * @param className the classname that this static classifier has
    * @param parent parent node of the current node 
    * @return an array containing two stringbuffers, the first string containing
    * assignment code, and the second containing source for support code.
    * @throws Exception if something goes wrong
    */
00256     public StringBuffer [] toSource(String className, Tree parent) 
      throws Exception {
    
      StringBuffer [] result = new StringBuffer[2];
      double[] currentProbs;

      if(m_ClassProbs == null)
        currentProbs = parent.m_ClassProbs;
      else
        currentProbs = m_ClassProbs;

      long printID = nextID();

      // Is this a leaf?
      if (m_Attribute == -1) {
        result[0] = new StringBuffer("    p = ");
      if(m_Info.classAttribute().isNumeric())
        result[0].append(currentProbs[0]);
      else {
        result[0].append(Utils.maxIndex(currentProbs));
      }
      result[0].append(";\n");
      result[1] = new StringBuffer("");
      } else {
      StringBuffer text = new StringBuffer("");
      StringBuffer atEnd = new StringBuffer("");

      text.append("  static double N")
        .append(Integer.toHexString(this.hashCode()) + printID)
        .append("(Object []i) {\n")
        .append("    double p = Double.NaN;\n");

        text.append("    /* " + m_Info.attribute(m_Attribute).name() + " */\n");
      // Missing attribute?
      text.append("    if (" + this.sourceExpression(-1) + ") {\n")
        .append("      p = ");
      if(m_Info.classAttribute().isNumeric())
        text.append(currentProbs[0] + ";\n");
      else
        text.append(Utils.maxIndex(currentProbs) + ";\n");
      text.append("    } ");
      
      // Branching of the tree
      for (int i=0;i<m_Successors.length; i++) {
          text.append("else if (" + this.sourceExpression(i) + ") {\n");
        // Is the successor a leaf?
        if(m_Successors[i].m_Attribute == -1) {
          double[] successorProbs = m_Successors[i].m_ClassProbs;
          if(successorProbs == null)
            successorProbs = m_ClassProbs;
          text.append("      p = ");
          if(m_Info.classAttribute().isNumeric()) {
            text.append(successorProbs[0] + ";\n");
          } else {
            text.append(Utils.maxIndex(successorProbs) + ";\n");
          }
        } else {
          StringBuffer [] sub = m_Successors[i].toSource(className, this);
          text.append("" + sub[0]);
            atEnd.append("" + sub[1]);
        }
        text.append("    } ");
        if (i == m_Successors.length - 1) {
          text.append("\n");
        }
        }

        text.append("    return p;\n  }\n");

        result[0] = new StringBuffer("    p = " + className + ".N");
        result[0].append(Integer.toHexString(this.hashCode()) + printID)
          .append("(i);\n");
        result[1] = text.append("" + atEnd);
      }
      return result;
    }

      
    /**
     * Outputs one node for graph.
     * 
     * @param text the buffer to append the output to
     * @param num the current node id
     * @param parent the parent of the nodes
     * @return the next node id
     * @throws Exception if something goes wrong
     */
00343     protected int toGraph(StringBuffer text, int num,
                  Tree parent) throws Exception {
      
      num++;
      if (m_Attribute == -1) {
      text.append("N" + Integer.toHexString(Tree.this.hashCode()) +
                " [label=\"" + num + leafString(parent) +"\"" +
                "shape=box]\n");
      } else {
      text.append("N" + Integer.toHexString(Tree.this.hashCode()) +
                " [label=\"" + num + ": " + 
                m_Info.attribute(m_Attribute).name() + 
                "\"]\n");
      for (int i = 0; i < m_Successors.length; i++) {
        text.append("N" + Integer.toHexString(Tree.this.hashCode()) 
                  + "->" + 
                  "N" + 
                  Integer.toHexString(m_Successors[i].hashCode())  +
                  " [label=\"");
        if (m_Info.attribute(m_Attribute).isNumeric()) {
          if (i == 0) {
            text.append(" < " +
                    Utils.doubleToString(m_SplitPoint, 2));
          } else {
            text.append(" >= " +
                    Utils.doubleToString(m_SplitPoint, 2));
          }
        } else {
          text.append(" = " + m_Info.attribute(m_Attribute).value(i));
        }
        text.append("\"]\n");
        num = m_Successors[i].toGraph(text, num, this);
      }
      }
      
      return num;
    }

    /**
     * Outputs description of a leaf node.
     * 
     * @param parent the parent of the node
     * @return the description of the node
     * @throws Exception if generation fails
     */
00388     protected String leafString(Tree parent) throws Exception {
    
      if (m_Info.classAttribute().isNumeric()) {
      double classMean;
      if (m_ClassProbs == null) {
        classMean = parent.m_ClassProbs[0];
      } else {
        classMean = m_ClassProbs[0];
      }
      StringBuffer buffer = new StringBuffer();
      buffer.append(" : " + Utils.doubleToString(classMean, 2));
      double avgError = 0;
      if (m_Distribution[1] > 0) {
        avgError = m_Distribution[0] / m_Distribution[1];
      }
      buffer.append(" (" +
                  Utils.doubleToString(m_Distribution[1], 2) + "/" +
                  Utils.doubleToString(avgError, 2) 
                  + ")");
      avgError = 0;
      if (m_HoldOutDist[0] > 0) {
        avgError = m_HoldOutError / m_HoldOutDist[0];
      }
      buffer.append(" [" +
                  Utils.doubleToString(m_HoldOutDist[0], 2) + "/" +
                  Utils.doubleToString(avgError, 2) 
                  + "]");
      return buffer.toString();
      } else { 
      int maxIndex;
      if (m_ClassProbs == null) {
        maxIndex = Utils.maxIndex(parent.m_ClassProbs);
      } else {
        maxIndex = Utils.maxIndex(m_ClassProbs);
      }
      return " : " + m_Info.classAttribute().value(maxIndex) + 
        " (" + Utils.doubleToString(Utils.sum(m_Distribution), 2) + 
        "/" + 
        Utils.doubleToString((Utils.sum(m_Distribution) - 
                        m_Distribution[maxIndex]), 2) + ")" +
        " [" + Utils.doubleToString(Utils.sum(m_HoldOutDist), 2) + "/" + 
        Utils.doubleToString((Utils.sum(m_HoldOutDist) - 
                        m_HoldOutDist[maxIndex]), 2) + "]";
      }
    }
  
    /**
     * Recursively outputs the tree.
     * 
     * @param level the current level
     * @param parent the current parent
     * @return the generated substree
     */
00441     protected String toString(int level, Tree parent) {

      try {
      StringBuffer text = new StringBuffer();
      
      if (m_Attribute == -1) {
      
        // Output leaf info
        return leafString(parent);
      } else if (m_Info.attribute(m_Attribute).isNominal()) {
      
        // For nominal attributes
        for (int i = 0; i < m_Successors.length; i++) {
          text.append("\n");
          for (int j = 0; j < level; j++) {
            text.append("|   ");
          }
          text.append(m_Info.attribute(m_Attribute).name() + " = " +
                  m_Info.attribute(m_Attribute).value(i));
          text.append(m_Successors[i].toString(level + 1, this));
        }
      } else {
      
        // For numeric attributes
        text.append("\n");
        for (int j = 0; j < level; j++) {
          text.append("|   ");
        }
        text.append(m_Info.attribute(m_Attribute).name() + " < " +
                  Utils.doubleToString(m_SplitPoint, 2));
        text.append(m_Successors[0].toString(level + 1, this));
        text.append("\n");
        for (int j = 0; j < level; j++) {
          text.append("|   ");
        }
        text.append(m_Info.attribute(m_Attribute).name() + " >= " +
                  Utils.doubleToString(m_SplitPoint, 2));
        text.append(m_Successors[1].toString(level + 1, this));
      }
      
      return text.toString();
      } catch (Exception e) {
      e.printStackTrace();
      return "Decision tree: tree can't be printed";
      }
    }     

    /**
     * Recursively generates a tree.
     * 
     * @param sortedIndices the sorted indices of the instances
     * @param weights the weights of the instances
     * @param data the data to work with
     * @param totalWeight
     * @param classProbs the class probabilities
     * @param header the header of the data
     * @param minNum the minimum number of instances in a leaf
     * @param minVariance
     * @param depth the current depth of the tree
     * @param maxDepth the maximum allowed depth of the tree
     * @throws Exception if generation fails
     */
00503     protected void buildTree(int[][] sortedIndices, double[][] weights,
                       Instances data, double totalWeight, 
                       double[] classProbs, Instances header,
                       double minNum, double minVariance,
                       int depth, int maxDepth) 
      throws Exception {
      
      // Store structure of dataset, set minimum number of instances
      // and make space for potential info from pruning data
      m_Info = header;
      m_HoldOutDist = new double[data.numClasses()];
      
      // Make leaf if there are no training instances
      int helpIndex = 0;
      if (data.classIndex() == 0) {
      helpIndex = 1;
      }
      if (sortedIndices[helpIndex].length == 0) {
      if (data.classAttribute().isNumeric()) {
        m_Distribution = new double[2];
      } else {
        m_Distribution = new double[data.numClasses()];
      }
      m_ClassProbs = null;
      return;
      }
      
      double priorVar = 0;
      if (data.classAttribute().isNumeric()) {

      // Compute prior variance
      double totalSum = 0, totalSumSquared = 0, totalSumOfWeights = 0; 
      for (int i = 0; i < sortedIndices[helpIndex].length; i++) {
        Instance inst = data.instance(sortedIndices[helpIndex][i]);
        totalSum += inst.classValue() * weights[helpIndex][i];
        totalSumSquared += 
          inst.classValue() * inst.classValue() * weights[helpIndex][i];
        totalSumOfWeights += weights[helpIndex][i];
      }
      priorVar = singleVariance(totalSum, totalSumSquared, 
                          totalSumOfWeights);
      }

      // Check if node doesn't contain enough instances, is pure
      // or the maximum tree depth is reached
      m_ClassProbs = new double[classProbs.length];
      System.arraycopy(classProbs, 0, m_ClassProbs, 0, classProbs.length);
      if ((totalWeight < (2 * minNum)) ||

        // Nominal case
        (data.classAttribute().isNominal() &&
         Utils.eq(m_ClassProbs[Utils.maxIndex(m_ClassProbs)],
                Utils.sum(m_ClassProbs))) ||

        // Numeric case
        (data.classAttribute().isNumeric() && 
         ((priorVar / totalWeight) < minVariance)) ||

        // Check tree depth
        ((m_MaxDepth >= 0) && (depth >= maxDepth))) {

      // Make leaf
      m_Attribute = -1;
      if (data.classAttribute().isNominal()) {

        // Nominal case
        m_Distribution = new double[m_ClassProbs.length];
        for (int i = 0; i < m_ClassProbs.length; i++) {
          m_Distribution[i] = m_ClassProbs[i];
        }
        Utils.normalize(m_ClassProbs);
      } else {

        // Numeric case
        m_Distribution = new double[2];
        m_Distribution[0] = priorVar;
        m_Distribution[1] = totalWeight;
      }
      return;
      }

      // Compute class distributions and value of splitting
      // criterion for each attribute
      double[] vals = new double[data.numAttributes()];
      double[][][] dists = new double[data.numAttributes()][0][0];
      double[][] props = new double[data.numAttributes()][0];
      double[][] totalSubsetWeights = new double[data.numAttributes()][0];
      double[] splits = new double[data.numAttributes()];
      if (data.classAttribute().isNominal()) { 

      // Nominal case
      for (int i = 0; i < data.numAttributes(); i++) {
        if (i != data.classIndex()) {
          splits[i] = distribution(props, dists, i, sortedIndices[i], 
                             weights[i], totalSubsetWeights, data);
          vals[i] = gain(dists[i], priorVal(dists[i]));
        }
      }
      } else {

      // Numeric case
      for (int i = 0; i < data.numAttributes(); i++) {
        if (i != data.classIndex()) {
          splits[i] = 
            numericDistribution(props, dists, i, sortedIndices[i], 
                          weights[i], totalSubsetWeights, data, 
                          vals);
        }
      }
      }

      // Find best attribute
      m_Attribute = Utils.maxIndex(vals);
      int numAttVals = dists[m_Attribute].length;

      // Check if there are at least two subsets with
      // required minimum number of instances
      int count = 0;
      for (int i = 0; i < numAttVals; i++) {
      if (totalSubsetWeights[m_Attribute][i] >= minNum) {
        count++;
      }
      if (count > 1) {
        break;
      }
      }

      // Any useful split found?
      if ((vals[m_Attribute] > 0) && (count > 1)) {

      // Build subtrees
      m_SplitPoint = splits[m_Attribute];
      m_Prop = props[m_Attribute];
      int[][][] subsetIndices = 
        new int[numAttVals][data.numAttributes()][0];
      double[][][] subsetWeights = 
        new double[numAttVals][data.numAttributes()][0];
      splitData(subsetIndices, subsetWeights, m_Attribute, m_SplitPoint, 
              sortedIndices, weights, data);
      m_Successors = new Tree[numAttVals];
      for (int i = 0; i < numAttVals; i++) {
        m_Successors[i] = new Tree();
        m_Successors[i].
          buildTree(subsetIndices[i], subsetWeights[i], 
                  data, totalSubsetWeights[m_Attribute][i],
                  dists[m_Attribute][i], header, minNum, 
                  minVariance, depth + 1, maxDepth);
      }
      } else {
      
      // Make leaf
      m_Attribute = -1;
      }

      // Normalize class counts
      if (data.classAttribute().isNominal()) {
      m_Distribution = new double[m_ClassProbs.length];
      for (int i = 0; i < m_ClassProbs.length; i++) {
          m_Distribution[i] = m_ClassProbs[i];
      }
      Utils.normalize(m_ClassProbs);
      } else {
      m_Distribution = new double[2];
      m_Distribution[0] = priorVar;
      m_Distribution[1] = totalWeight;
      }
    }

    /**
     * Computes size of the tree.
     * 
     * @return the number of nodes
     */
00676     protected int numNodes() {
    
      if (m_Attribute == -1) {
      return 1;
      } else {
      int size = 1;
      for (int i = 0; i < m_Successors.length; i++) {
        size += m_Successors[i].numNodes();
      }
      return size;
      }
    }

    /**
     * Splits instances into subsets.
     * 
     * @param subsetIndices the sorted indices in the subset
     * @param subsetWeights the weights of the subset
     * @param att the attribute index
     * @param splitPoint the split point for numeric attributes
     * @param sortedIndices the sorted indices of the whole set
     * @param weights the weights of the whole set
     * @param data the data to work with
     * @throws Exception if something goes wrong
     */
00701     protected void splitData(int[][][] subsetIndices, 
                       double[][][] subsetWeights,
                       int att, double splitPoint, 
                       int[][] sortedIndices, double[][] weights, 
                       Instances data) throws Exception {
    
      int j;
      int[] num;
   
      // For each attribute
      for (int i = 0; i < data.numAttributes(); i++) {
      if (i != data.classIndex()) {
        if (data.attribute(att).isNominal()) {

          // For nominal attributes
          num = new int[data.attribute(att).numValues()];
          for (int k = 0; k < num.length; k++) {
            subsetIndices[k][i] = new int[sortedIndices[i].length];
            subsetWeights[k][i] = new double[sortedIndices[i].length];
          }
          for (j = 0; j < sortedIndices[i].length; j++) {
            Instance inst = data.instance(sortedIndices[i][j]);
            if (inst.isMissing(att)) {

            // Split instance up
            for (int k = 0; k < num.length; k++) {
              if (m_Prop[k] > 0) {
                subsetIndices[k][i][num[k]] = sortedIndices[i][j];
                subsetWeights[k][i][num[k]] = 
                  m_Prop[k] * weights[i][j];
                num[k]++;
              }
            }
            } else {
            int subset = (int)inst.value(att);
            subsetIndices[subset][i][num[subset]] = 
              sortedIndices[i][j];
            subsetWeights[subset][i][num[subset]] = weights[i][j];
            num[subset]++;
            }
          }
        } else {

          // For numeric attributes
          num = new int[2];
          for (int k = 0; k < 2; k++) {
            subsetIndices[k][i] = new int[sortedIndices[i].length];
            subsetWeights[k][i] = new double[weights[i].length];
          }
          for (j = 0; j < sortedIndices[i].length; j++) {
            Instance inst = data.instance(sortedIndices[i][j]);
            if (inst.isMissing(att)) {

            // Split instance up
            for (int k = 0; k < num.length; k++) {
              if (m_Prop[k] > 0) {
                subsetIndices[k][i][num[k]] = sortedIndices[i][j];
                subsetWeights[k][i][num[k]] = 
                  m_Prop[k] * weights[i][j];
                num[k]++;
              }
            }
            } else {
            int subset = (inst.value(att) < splitPoint) ? 0 : 1;
            subsetIndices[subset][i][num[subset]] = 
              sortedIndices[i][j];
            subsetWeights[subset][i][num[subset]] = weights[i][j];
            num[subset]++;
            } 
          }
        }
      
        // Trim arrays
        for (int k = 0; k < num.length; k++) {
          int[] copy = new int[num[k]];
          System.arraycopy(subsetIndices[k][i], 0, copy, 0, num[k]);
          subsetIndices[k][i] = copy;
          double[] copyWeights = new double[num[k]];
          System.arraycopy(subsetWeights[k][i], 0,
                       copyWeights, 0, num[k]);
          subsetWeights[k][i] = copyWeights;
        }
      }
      }
    }

    /**
     * Computes class distribution for an attribute.
     * 
     * @param props
     * @param dists
     * @param att the attribute index
     * @param sortedIndices the sorted indices of the instances
     * @param weights the weights of the instances
     * @param subsetWeights the weights of the subset
     * @param data the data to work with
     * @return the split point
     * @throws Exception if computation fails
     */
00800     protected double distribution(double[][] props,
                          double[][][] dists, int att, 
                          int[] sortedIndices,
                          double[] weights, 
                          double[][] subsetWeights, 
                          Instances data) 
      throws Exception {

      double splitPoint = Double.NaN;
      Attribute attribute = data.attribute(att);
      double[][] dist = null;
      int i;

      if (attribute.isNominal()) {

      // For nominal attributes
      dist = new double[attribute.numValues()][data.numClasses()];
      for (i = 0; i < sortedIndices.length; i++) {
        Instance inst = data.instance(sortedIndices[i]);
        if (inst.isMissing(att)) {
          break;
        }
        dist[(int)inst.value(att)][(int)inst.classValue()] += weights[i];
      }
      } else {

      // For numeric attributes
      double[][] currDist = new double[2][data.numClasses()];
      dist = new double[2][data.numClasses()];

      // Move all instances into second subset
      for (int j = 0; j < sortedIndices.length; j++) {
        Instance inst = data.instance(sortedIndices[j]);
        if (inst.isMissing(att)) {
          break;
        }
        currDist[1][(int)inst.classValue()] += weights[j];
      }
      double priorVal = priorVal(currDist);
      System.arraycopy(currDist[1], 0, dist[1], 0, dist[1].length);

      // Try all possible split points
      double currSplit = data.instance(sortedIndices[0]).value(att);
      double currVal, bestVal = -Double.MAX_VALUE;
      for (i = 0; i < sortedIndices.length; i++) {
        Instance inst = data.instance(sortedIndices[i]);
        if (inst.isMissing(att)) {
          break;
        }
        if (inst.value(att) > currSplit) {
          currVal = gain(currDist, priorVal);
          if (currVal > bestVal) {
            bestVal = currVal;
            splitPoint = (inst.value(att) + currSplit) / 2.0;
            for (int j = 0; j < currDist.length; j++) {
            System.arraycopy(currDist[j], 0, dist[j], 0, 
                         dist[j].length);
            }
          } 
        } 
        currSplit = inst.value(att);
        currDist[0][(int)inst.classValue()] += weights[i];
        currDist[1][(int)inst.classValue()] -= weights[i];
      }
      }

      // Compute weights
      props[att] = new double[dist.length];
      for (int k = 0; k < props[att].length; k++) {
      props[att][k] = Utils.sum(dist[k]);
      }
      if (!(Utils.sum(props[att]) > 0)) {
      for (int k = 0; k < props[att].length; k++) {
        props[att][k] = 1.0 / (double)props[att].length;
      }
      } else {
      Utils.normalize(props[att]);
      }
    
      // Distribute counts
      while (i < sortedIndices.length) {
      Instance inst = data.instance(sortedIndices[i]);
      for (int j = 0; j < dist.length; j++) {
        dist[j][(int)inst.classValue()] += props[att][j] * weights[i];
      }
      i++;
      }

      // Compute subset weights
      subsetWeights[att] = new double[dist.length];
      for (int j = 0; j < dist.length; j++) {
      subsetWeights[att][j] += Utils.sum(dist[j]);
      }

      // Return distribution and split point
      dists[att] = dist;
      return splitPoint;
    }      

    /**
     * Computes class distribution for an attribute.
     * 
     * @param props
     * @param dists
     * @param att the attribute index
     * @param sortedIndices the sorted indices of the instances
     * @param weights the weights of the instances
     * @param subsetWeights the weights of the subset
     * @param data the data to work with
     * @param vals
     * @return the split point
     * @throws Exception if computation fails
     */
00913     protected double numericDistribution(double[][] props, 
                               double[][][] dists, int att, 
                               int[] sortedIndices,
                               double[] weights, 
                               double[][] subsetWeights, 
                               Instances data,
                               double[] vals) 
      throws Exception {

      double splitPoint = Double.NaN;
      Attribute attribute = data.attribute(att);
      double[][] dist = null;
      double[] sums = null;
      double[] sumSquared = null;
      double[] sumOfWeights = null;
      double totalSum = 0, totalSumSquared = 0, totalSumOfWeights = 0;

      int i;

      if (attribute.isNominal()) {

      // For nominal attributes
      sums = new double[attribute.numValues()];
        sumSquared = new double[attribute.numValues()];
      sumOfWeights = new double[attribute.numValues()];
      int attVal;
      for (i = 0; i < sortedIndices.length; i++) {
        Instance inst = data.instance(sortedIndices[i]);
        if (inst.isMissing(att)) {
          break;
        }
        attVal = (int)inst.value(att);
        sums[attVal] += inst.classValue() * weights[i];
        sumSquared[attVal] += 
          inst.classValue() * inst.classValue() * weights[i];
        sumOfWeights[attVal] += weights[i];
      }
      totalSum = Utils.sum(sums);
      totalSumSquared = Utils.sum(sumSquared);
      totalSumOfWeights = Utils.sum(sumOfWeights);
      } else {

      // For numeric attributes
      sums = new double[2];
        sumSquared = new double[2];
      sumOfWeights = new double[2];
      double[] currSums = new double[2];
        double[] currSumSquared = new double[2];
      double[] currSumOfWeights = new double[2];

      // Move all instances into second subset
      for (int j = 0; j < sortedIndices.length; j++) {
        Instance inst = data.instance(sortedIndices[j]);
        if (inst.isMissing(att)) {
          break;
        }
        currSums[1] += inst.classValue() * weights[j];
        currSumSquared[1] += 
          inst.classValue() * inst.classValue() * weights[j];
        currSumOfWeights[1] += weights[j];
        
      }
      totalSum = currSums[1];
      totalSumSquared = currSumSquared[1];
      totalSumOfWeights = currSumOfWeights[1];
      
      sums[1] = currSums[1];
      sumSquared[1] = currSumSquared[1];
      sumOfWeights[1] = currSumOfWeights[1];

      // Try all possible split points
      double currSplit = data.instance(sortedIndices[0]).value(att);
      double currVal, bestVal = Double.MAX_VALUE;
      for (i = 0; i < sortedIndices.length; i++) {
        Instance inst = data.instance(sortedIndices[i]);
        if (inst.isMissing(att)) {
          break;
        }
        if (inst.value(att) > currSplit) {
          currVal = variance(currSums, currSumSquared, currSumOfWeights);
          if (currVal < bestVal) {
            bestVal = currVal;
            splitPoint = (inst.value(att) + currSplit) / 2.0;
            for (int j = 0; j < 2; j++) {
            sums[j] = currSums[j];
            sumSquared[j] = currSumSquared[j];
            sumOfWeights[j] = currSumOfWeights[j];
            }
          } 
        } 

        currSplit = inst.value(att);

        double classVal = inst.classValue() * weights[i];
        double classValSquared = inst.classValue() * classVal;

        currSums[0] += classVal;
        currSumSquared[0] += classValSquared;
        currSumOfWeights[0] += weights[i];

        currSums[1] -= classVal;
        currSumSquared[1] -= classValSquared;
        currSumOfWeights[1] -= weights[i];
      }
      }

      // Compute weights
      props[att] = new double[sums.length];
      for (int k = 0; k < props[att].length; k++) {
      props[att][k] = sumOfWeights[k];
      }
      if (!(Utils.sum(props[att]) > 0)) {
      for (int k = 0; k < props[att].length; k++) {
        props[att][k] = 1.0 / (double)props[att].length;
      }
      } else {
      Utils.normalize(props[att]);
      }
    
      
      // Distribute counts for missing values
      while (i < sortedIndices.length) {
      Instance inst = data.instance(sortedIndices[i]);
      for (int j = 0; j < sums.length; j++) {
        sums[j] += props[att][j] * inst.classValue() * weights[i];
        sumSquared[j] += props[att][j] * inst.classValue() * 
          inst.classValue() * weights[i];
        sumOfWeights[j] += props[att][j] * weights[i];
      }
      totalSum += inst.classValue() * weights[i];
      totalSumSquared += 
        inst.classValue() * inst.classValue() * weights[i]; 
      totalSumOfWeights += weights[i];
      i++;
      }

      // Compute final distribution
      dist = new double[sums.length][data.numClasses()];
      for (int j = 0; j < sums.length; j++) {
      if (sumOfWeights[j] > 0) {
        dist[j][0] = sums[j] / sumOfWeights[j];
      } else {
        dist[j][0] = totalSum / totalSumOfWeights;
      }
      }
      
      // Compute variance gain
      double priorVar =
      singleVariance(totalSum, totalSumSquared, totalSumOfWeights);
      double var = variance(sums, sumSquared, sumOfWeights);
      double gain = priorVar - var;
      
      // Return distribution and split point
      subsetWeights[att] = sumOfWeights;
      dists[att] = dist;
      vals[att] = gain;
      return splitPoint;
    }      

    /**
     * Computes variance for subsets.
     * 
     * @param s
     * @param sS
     * @param sumOfWeights
     * @return the variance
     */
01080     protected double variance(double[] s, double[] sS, 
                      double[] sumOfWeights) {
      
      double var = 0;
      
      for (int i = 0; i < s.length; i++) {
      if (sumOfWeights[i] > 0) {
        var += singleVariance(s[i], sS[i], sumOfWeights[i]);
      }
      }
      
      return var;
    }
    
    /** 
     * Computes the variance for a single set
     * 
     * @param s
     * @param sS
     * @param weight the weight
     * @return the variance
     */
01102     protected double singleVariance(double s, double sS, double weight) {
      
      return sS - ((s * s) / weight);
    }

    /**
     * Computes value of splitting criterion before split.
     * 
     * @param dist
     * @return the splitting criterion
     */
01113     protected double priorVal(double[][] dist) {

      return ContingencyTables.entropyOverColumns(dist);
    }

    /**
     * Computes value of splitting criterion after split.
     * 
     * @param dist
     * @param priorVal the splitting criterion
     * @return the gain after splitting
     */
01125     protected double gain(double[][] dist, double priorVal) {

      return priorVal - ContingencyTables.entropyConditionedOnRows(dist);
    }

    /**
     * Prunes the tree using the hold-out data (bottom-up).
     * 
     * @return the error
     * @throws Exception if pruning fails for some reason
     */
01136     protected double reducedErrorPrune() throws Exception {

      // Is node leaf ? 
      if (m_Attribute == -1) {
      return m_HoldOutError;
      }

      // Prune all sub trees
      double errorTree = 0;
      for (int i = 0; i < m_Successors.length; i++) {
      errorTree += m_Successors[i].reducedErrorPrune();
      }

      // Replace sub tree with leaf if error doesn't get worse
      if (errorTree >= m_HoldOutError) {
      m_Attribute = -1;
      m_Successors = null;
      return m_HoldOutError;
      } else {
      return errorTree;
      }
    }

    /**
     * Inserts hold-out set into tree.
     * 
     * @param data the data to insert
     * @throws Exception if something goes wrong
     */
01165     protected void insertHoldOutSet(Instances data) throws Exception {

      for (int i = 0; i < data.numInstances(); i++) {
      insertHoldOutInstance(data.instance(i), data.instance(i).weight(),
                        this);
      }
    }

    /**
     * Inserts an instance from the hold-out set into the tree.
     * 
     * @param inst the instance to insert
     * @param weight the weight of the instance
     * @param parent the parent of the node
     * @throws Exception if insertion fails
     */
01181     protected void insertHoldOutInstance(Instance inst, double weight, 
                               Tree parent) throws Exception {
      
      // Insert instance into hold-out class distribution
      if (inst.classAttribute().isNominal()) {
      
      // Nominal case
      m_HoldOutDist[(int)inst.classValue()] += weight;
      int predictedClass = 0;
      if (m_ClassProbs == null) {
        predictedClass = Utils.maxIndex(parent.m_ClassProbs);
      } else {
        predictedClass = Utils.maxIndex(m_ClassProbs);
      }
      if (predictedClass != (int)inst.classValue()) {
        m_HoldOutError += weight;
      }
      } else {
      
      // Numeric case
      m_HoldOutDist[0] += weight;
      double diff = 0;
      if (m_ClassProbs == null) {
        diff = parent.m_ClassProbs[0] - inst.classValue();
      } else {
        diff =  m_ClassProbs[0] - inst.classValue();
      }
      m_HoldOutError += diff * diff * weight;
      }     
      
      // The process is recursive
      if (m_Attribute != -1) {
      
      // If node is not a leaf
      if (inst.isMissing(m_Attribute)) {
        
        // Distribute instance
        for (int i = 0; i < m_Successors.length; i++) {
          if (m_Prop[i] > 0) {
            m_Successors[i].insertHoldOutInstance(inst, weight * 
                                        m_Prop[i], this);
          }
        }
      } else {
        
        if (m_Info.attribute(m_Attribute).isNominal()) {
          
          // Treat nominal attributes
          m_Successors[(int)inst.value(m_Attribute)].
            insertHoldOutInstance(inst, weight, this);
        } else {
          
          // Treat numeric attributes
          if (inst.value(m_Attribute) < m_SplitPoint) {
            m_Successors[0].insertHoldOutInstance(inst, weight, this);
          } else {
            m_Successors[1].insertHoldOutInstance(inst, weight, this);
          }
        }
      }
      }
    }
  
    /**
     * Inserts hold-out set into tree.
     * 
     * @param data the data to insert
     * @throws Exception if insertion fails
     */
01250     protected void backfitHoldOutSet(Instances data) throws Exception {
      
      for (int i = 0; i < data.numInstances(); i++) {
      backfitHoldOutInstance(data.instance(i), data.instance(i).weight(),
                         this);
      }
    }
    
    /**
     * Inserts an instance from the hold-out set into the tree.
     * 
     * @param inst the instance to insert
     * @param weight the weight of the instance
     * @param parent the parent node
     * @throws Exception if insertion fails
     */
01266     protected void backfitHoldOutInstance(Instance inst, double weight, 
                                Tree parent) throws Exception {
      
      // Insert instance into hold-out class distribution
      if (inst.classAttribute().isNominal()) {
      
      // Nominal case
      if (m_ClassProbs == null) {
        m_ClassProbs = new double[inst.numClasses()];
      }
      System.arraycopy(m_Distribution, 0, m_ClassProbs, 0, inst.numClasses());
      m_ClassProbs[(int)inst.classValue()] += weight;
      Utils.normalize(m_ClassProbs);
      } else {
      
      // Numeric case
      if (m_ClassProbs == null) {
        m_ClassProbs = new double[1];
      }
      m_ClassProbs[0] *= m_Distribution[1];
      m_ClassProbs[0] += weight * inst.classValue();
      m_ClassProbs[0] /= (m_Distribution[1] + weight);
      }     
      
      // The process is recursive
      if (m_Attribute != -1) {
      
      // If node is not a leaf
      if (inst.isMissing(m_Attribute)) {
        
        // Distribute instance
        for (int i = 0; i < m_Successors.length; i++) {
          if (m_Prop[i] > 0) {
            m_Successors[i].backfitHoldOutInstance(inst, weight * 
                                         m_Prop[i], this);
          }
        }
      } else {
        
        if (m_Info.attribute(m_Attribute).isNominal()) {
          
          // Treat nominal attributes
          m_Successors[(int)inst.value(m_Attribute)].
            backfitHoldOutInstance(inst, weight, this);
        } else {
          
          // Treat numeric attributes
          if (inst.value(m_Attribute) < m_SplitPoint) {
            m_Successors[0].backfitHoldOutInstance(inst, weight, this);
          } else {
            m_Successors[1].backfitHoldOutInstance(inst, weight, this);
          }
        }
      }
      }
    }
    
    /**
     * Returns the revision string.
     * 
     * @return          the revision
     */
01328     public String getRevision() {
      return RevisionUtils.extract("$Revision: 1.26 $");
    }
  }

  /** The Tree object */
01334   protected Tree m_Tree = null;
    
  /** Number of folds for reduced error pruning. */
01337   protected int m_NumFolds = 3;
    
  /** Seed for random data shuffling. */
01340   protected int m_Seed = 1;
    
  /** Don't prune */
01343   protected boolean m_NoPruning = false;

  /** The minimum number of instances per leaf. */
01346   protected double m_MinNum = 2;

  /** The minimum proportion of the total variance (over all the data)
      required for split. */
01350   protected double m_MinVarianceProp = 1e-3;

  /** Upper bound on the tree depth */
01353   protected int m_MaxDepth = -1;
  
  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
01360   public String noPruningTipText() {
    return "Whether pruning is performed.";
  }
  
  /**
   * Get the value of NoPruning.
   *
   * @return Value of NoPruning.
   */
01369   public boolean getNoPruning() {
    
    return m_NoPruning;
  }
  
  /**
   * Set the value of NoPruning.
   *
   * @param newNoPruning Value to assign to NoPruning.
   */
01379   public void setNoPruning(boolean newNoPruning) {
    
    m_NoPruning = newNoPruning;
  }
  
  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
01389   public String minNumTipText() {
    return "The minimum total weight of the instances in a leaf.";
  }

  /**
   * Get the value of MinNum.
   *
   * @return Value of MinNum.
   */
01398   public double getMinNum() {
    
    return m_MinNum;
  }
  
  /**
   * Set the value of MinNum.
   *
   * @param newMinNum Value to assign to MinNum.
   */
01408   public void setMinNum(double newMinNum) {
    
    m_MinNum = newMinNum;
  }
  
  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
01418   public String minVariancePropTipText() {
    return "The minimum proportion of the variance on all the data " +
      "that needs to be present at a node in order for splitting to " +
      "be performed in regression trees.";
  }

  /**
   * Get the value of MinVarianceProp.
   *
   * @return Value of MinVarianceProp.
   */
01429   public double getMinVarianceProp() {
    
    return m_MinVarianceProp;
  }
  
  /**
   * Set the value of MinVarianceProp.
   *
   * @param newMinVarianceProp Value to assign to MinVarianceProp.
   */
01439   public void setMinVarianceProp(double newMinVarianceProp) {
    
    m_MinVarianceProp = newMinVarianceProp;
  }

  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
01449   public String seedTipText() {
    return "The seed used for randomizing the data.";
  }

  /**
   * Get the value of Seed.
   *
   * @return Value of Seed.
   */
01458   public int getSeed() {
    
    return m_Seed;
  }
  
  /**
   * Set the value of Seed.
   *
   * @param newSeed Value to assign to Seed.
   */
01468   public void setSeed(int newSeed) {
    
    m_Seed = newSeed;
  }

  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
01478   public String numFoldsTipText() {
    return "Determines the amount of data used for pruning. One fold is used for "
      + "pruning, the rest for growing the rules.";
  }
  
  /**
   * Get the value of NumFolds.
   *
   * @return Value of NumFolds.
   */
01488   public int getNumFolds() {
    
    return m_NumFolds;
  }
  
  /**
   * Set the value of NumFolds.
   *
   * @param newNumFolds Value to assign to NumFolds.
   */
01498   public void setNumFolds(int newNumFolds) {
    
    m_NumFolds = newNumFolds;
  }
  
  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
01508   public String maxDepthTipText() {
    return "The maximum tree depth (-1 for no restriction).";
  }

  /**
   * Get the value of MaxDepth.
   *
   * @return Value of MaxDepth.
   */
01517   public int getMaxDepth() {
    
    return m_MaxDepth;
  }
  
  /**
   * Set the value of MaxDepth.
   *
   * @param newMaxDepth Value to assign to MaxDepth.
   */
01527   public void setMaxDepth(int newMaxDepth) {
    
    m_MaxDepth = newMaxDepth;
  }
  
  /**
   * Lists the command-line options for this classifier.
   * 
   * @return an enumeration over all commandline options
   */
01537   public Enumeration listOptions() {
    
    Vector newVector = new Vector(5);

    newVector.
      addElement(new Option("\tSet minimum number of instances per leaf " +
                      "(default 2).",
                      "M", 1, "-M <minimum number of instances>"));
    newVector.
      addElement(new Option("\tSet minimum numeric class variance proportion\n" +
                      "\tof train variance for split (default 1e-3).",
                      "V", 1, "-V <minimum variance for split>"));
    newVector.
      addElement(new Option("\tNumber of folds for reduced error pruning " +
                      "(default 3).",
                      "N", 1, "-N <number of folds>"));
    newVector.
      addElement(new Option("\tSeed for random data shuffling (default 1).",
                      "S", 1, "-S <seed>"));
    newVector.
      addElement(new Option("\tNo pruning.",
                      "P", 0, "-P"));
    newVector.
      addElement(new Option("\tMaximum tree depth (default -1, no maximum)",
                      "L", 1, "-L"));

    return newVector.elements();
  } 

  /**
   * Gets options from this classifier.
   * 
   * @return the options for the current setup
   */
01571   public String[] getOptions() {
    
    String [] options = new String [12];
    int current = 0;
    options[current++] = "-M"; 
    options[current++] = "" + (int)getMinNum();
    options[current++] = "-V"; 
    options[current++] = "" + getMinVarianceProp();
    options[current++] = "-N"; 
    options[current++] = "" + getNumFolds();
    options[current++] = "-S"; 
    options[current++] = "" + getSeed();
    options[current++] = "-L"; 
    options[current++] = "" + getMaxDepth();
    if (getNoPruning()) {
      options[current++] = "-P";
    }
    while (current < options.length) {
      options[current++] = "";
    }
    return options;
  }

  /**
   * Parses a given list of options. <p/>
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -M &lt;minimum number of instances&gt;
   *  Set minimum number of instances per leaf (default 2).</pre>
   * 
   * <pre> -V &lt;minimum variance for split&gt;
   *  Set minimum numeric class variance proportion
   *  of train variance for split (default 1e-3).</pre>
   * 
   * <pre> -N &lt;number of folds&gt;
   *  Number of folds for reduced error pruning (default 3).</pre>
   * 
   * <pre> -S &lt;seed&gt;
   *  Seed for random data shuffling (default 1).</pre>
   * 
   * <pre> -P
   *  No pruning.</pre>
   * 
   * <pre> -L
   *  Maximum tree depth (default -1, no maximum)</pre>
   * 
   <!-- options-end -->
   * 
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
01624   public void setOptions(String[] options) throws Exception {
    
    String minNumString = Utils.getOption('M', options);
    if (minNumString.length() != 0) {
      m_MinNum = (double)Integer.parseInt(minNumString);
    } else {
      m_MinNum = 2;
    }
    String minVarString = Utils.getOption('V', options);
    if (minVarString.length() != 0) {
      m_MinVarianceProp = Double.parseDouble(minVarString);
    } else {
      m_MinVarianceProp = 1e-3;
    }
    String numFoldsString = Utils.getOption('N', options);
    if (numFoldsString.length() != 0) {
      m_NumFolds = Integer.parseInt(numFoldsString);
    } else {
      m_NumFolds = 3;
    }
    String seedString = Utils.getOption('S', options);
    if (seedString.length() != 0) {
      m_Seed = Integer.parseInt(seedString);
    } else {
      m_Seed = 1;
    }
    m_NoPruning = Utils.getFlag('P', options);
    String depthString = Utils.getOption('L', options);
    if (depthString.length() != 0) {
      m_MaxDepth = Integer.parseInt(depthString);
    } else {
      m_MaxDepth = -1;
    }
    Utils.checkForRemainingOptions(options);
  }
  
  /**
   * Computes size of the tree.
   * 
   * @return the number of nodes
   */
01665   public int numNodes() {

    return m_Tree.numNodes();
  }

  /**
   * Returns an enumeration of the additional measure names.
   *
   * @return an enumeration of the measure names
   */
01675   public Enumeration enumerateMeasures() {
    
    Vector newVector = new Vector(1);
    newVector.addElement("measureTreeSize");
    return newVector.elements();
  }
 
  /**
   * Returns the value of the named measure.
   *
   * @param additionalMeasureName the name of the measure to query for its value
   * @return the value of the named measure
   * @throws IllegalArgumentException if the named measure is not supported
   */
01689   public double getMeasure(String additionalMeasureName) {
    
    if (additionalMeasureName.equalsIgnoreCase("measureTreeSize")) {
      return (double) numNodes();
    }
    else {throw new IllegalArgumentException(additionalMeasureName 
                        + " not supported (REPTree)");
    }
  }

  /**
   * Returns default capabilities of the classifier.
   *
   * @return      the capabilities of this classifier
   */
01704   public Capabilities getCapabilities() {
    Capabilities result = super.getCapabilities();

    // attributes
    result.enable(Capability.NOMINAL_ATTRIBUTES);
    result.enable(Capability.NUMERIC_ATTRIBUTES);
    result.enable(Capability.DATE_ATTRIBUTES);
    result.enable(Capability.MISSING_VALUES);

    // class
    result.enable(Capability.NOMINAL_CLASS);
    result.enable(Capability.NUMERIC_CLASS);
    result.enable(Capability.DATE_CLASS);
    result.enable(Capability.MISSING_CLASS_VALUES);
    
    return result;
  }

  /**
   * Builds classifier.
   * 
   * @param data the data to train with
   * @throws Exception if building fails
   */
01728   public void buildClassifier(Instances data) throws Exception {

    // can classifier handle the data?
    getCapabilities().testWithFail(data);

    // remove instances with missing class
    data = new Instances(data);
    data.deleteWithMissingClass();
    
    Random random = new Random(m_Seed);

    m_zeroR = null;
    if (data.numAttributes() == 1) {
      m_zeroR = new ZeroR();
      m_zeroR.buildClassifier(data);
      return;
    }

    // Randomize and stratify
    data.randomize(random);
    if (data.classAttribute().isNominal()) {
      data.stratify(m_NumFolds);
    }

    // Split data into training and pruning set
    Instances train = null;
    Instances prune = null;
    if (!m_NoPruning) {
      train = data.trainCV(m_NumFolds, 0, random);
      prune = data.testCV(m_NumFolds, 0);
    } else {
      train = data;
    }

    // Create array of sorted indices and weights
    int[][] sortedIndices = new int[train.numAttributes()][0];
    double[][] weights = new double[train.numAttributes()][0];
    double[] vals = new double[train.numInstances()];
    for (int j = 0; j < train.numAttributes(); j++) {
      if (j != train.classIndex()) {
      weights[j] = new double[train.numInstances()];
      if (train.attribute(j).isNominal()) {

        // Handling nominal attributes. Putting indices of
        // instances with missing values at the end.
        sortedIndices[j] = new int[train.numInstances()];
        int count = 0;
        for (int i = 0; i < train.numInstances(); i++) {
          Instance inst = train.instance(i);
          if (!inst.isMissing(j)) {
            sortedIndices[j][count] = i;
            weights[j][count] = inst.weight();
            count++;
          }
        }
        for (int i = 0; i < train.numInstances(); i++) {
          Instance inst = train.instance(i);
          if (inst.isMissing(j)) {
            sortedIndices[j][count] = i;
            weights[j][count] = inst.weight();
            count++;
          }
        }
      } else {

        // Sorted indices are computed for numeric attributes
        for (int i = 0; i < train.numInstances(); i++) {
          Instance inst = train.instance(i);
          vals[i] = inst.value(j);
        }
        sortedIndices[j] = Utils.sort(vals);
        for (int i = 0; i < train.numInstances(); i++) {
          weights[j][i] = train.instance(sortedIndices[j][i]).weight();
        }
      }
      }
    }

    // Compute initial class counts
    double[] classProbs = new double[train.numClasses()];
    double totalWeight = 0, totalSumSquared = 0;
    for (int i = 0; i < train.numInstances(); i++) {
      Instance inst = train.instance(i);
      if (data.classAttribute().isNominal()) {
      classProbs[(int)inst.classValue()] += inst.weight();
      totalWeight += inst.weight();
      } else {
      classProbs[0] += inst.classValue() * inst.weight();
      totalSumSquared += inst.classValue() * inst.classValue() * inst.weight();
      totalWeight += inst.weight();
      }
    }
    m_Tree = new Tree();
    double trainVariance = 0;
    if (data.classAttribute().isNumeric()) {
      trainVariance = m_Tree.
      singleVariance(classProbs[0], totalSumSquared, totalWeight) / totalWeight;
      classProbs[0] /= totalWeight;
    }

    // Build tree
    m_Tree.buildTree(sortedIndices, weights, train, totalWeight, classProbs,
                 new Instances(train, 0), m_MinNum, m_MinVarianceProp * 
                 trainVariance, 0, m_MaxDepth);
    
    // Insert pruning data and perform reduced error pruning
    if (!m_NoPruning) {
      m_Tree.insertHoldOutSet(prune);
      m_Tree.reducedErrorPrune();
      m_Tree.backfitHoldOutSet(prune);
    }
  }

  /**
   * Computes class distribution of an instance using the tree.
   * 
   * @param instance the instance to compute the distribution for
   * @return the computed class probabilities
   * @throws Exception if computation fails
   */
01848   public double[] distributionForInstance(Instance instance) 
    throws Exception {
      
      if (m_zeroR != null) {
      return m_zeroR.distributionForInstance(instance);
      } else {
      return m_Tree.distributionForInstance(instance);
      }
  }


  /** 
   * For getting a unique ID when outputting the tree source
   * (hashcode isn't guaranteed unique) 
   */
01863   private static long PRINTED_NODES = 0;

  /**
   * Gets the next unique node ID.
   *
   * @return the next unique node ID.
   */
01870   protected static long nextID() {

    return PRINTED_NODES ++;
  }

  /**
   * resets the counter for the nodes
   */
01878   protected static void resetID() {
    PRINTED_NODES = 0;
  }

  /**
   * Returns the tree as if-then statements.
   *
   * @param className the name for the generated class
   * @return the tree as a Java if-then type statement
   * @throws Exception if something goes wrong
   */
01889   public String toSource(String className) 
    throws Exception {
     
    if (m_Tree == null) {
      throw new Exception("REPTree: No model built yet.");
    } 
    StringBuffer [] source = m_Tree.toSource(className, m_Tree);
    return
    "class " + className + " {\n\n"
    +"  public static double classify(Object [] i)\n"
    +"    throws Exception {\n\n"
    +"    double p = Double.NaN;\n"
    + source[0]  // Assignment code
    +"    return p;\n"
    +"  }\n"
    + source[1]  // Support code
    +"}\n";
  }

  /**
   *  Returns the type of graph this classifier
   *  represents.
   *  @return Drawable.TREE
   */   
01913   public int graphType() {
      return Drawable.TREE;
  }

  /**
   * Outputs the decision tree as a graph
   * 
   * @return the tree as a graph
   * @throws Exception if generation fails
   */
01923   public String graph() throws Exception {

    if (m_Tree == null) {
      throw new Exception("REPTree: No model built yet.");
    } 
    StringBuffer resultBuff = new StringBuffer();
    m_Tree.toGraph(resultBuff, 0, null);
    String result = "digraph Tree {\n" + "edge [style=bold]\n" + resultBuff.toString()
      + "\n}\n";
    return result;
  }
  
  /**
   * Outputs the decision tree.
   * 
   * @return a string representation of the classifier 
   */
01940   public String toString() {

    if (m_zeroR != null) {
      return "No attributes other than class. Using ZeroR.\n\n" + m_zeroR.toString();
    }
    if ((m_Tree == null)) {
      return "REPTree: No model built yet.";
    } 
    return     
      "\nREPTree\n============\n" + m_Tree.toString(0, null) + "\n" +
      "\nSize of the tree : " + numNodes();
  }
  
  /**
   * Returns the revision string.
   * 
   * @return            the revision
   */
01958   public String getRevision() {
    return RevisionUtils.extract("$Revision: 1.26 $");
  }

  /**
   * Main method for this class.
   * 
   * @param argv the commandline options
   */
01967   public static void main(String[] argv) {
    runClassifier(new REPTree(), argv);
  }
}

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