+//
+// forest.h
+// Mothur
+//
+// Created by Kathryn Iverson on 10/26/12. Modified abstractrandomforest
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__forest__
+#define __Mothur__forest__
+
+#include <iostream>
+#include "mothurout.h"
+#include "macros.h"
+#include "abstractdecisiontree.hpp"
+/***********************************************************************/
+//this is a re-implementation of the abstractrandomforest class
+
+class Forest{
+public:
+ // intialization with vectors
+ Forest(const std::vector < std::vector<int> > dataSet,
+ const int numDecisionTrees,
+ const string);
+ virtual ~Forest(){ }
+ virtual int populateDecisionTrees() = 0;
+ virtual int calcForrestErrorRate() = 0;
+ virtual int calcForrestVariableImportance(string) = 0;
+
+ /***********************************************************************/
+
+protected:
+
+ // TODO: create a better way of discarding feature
+ // currently we just set FEATURE_DISCARD_SD_THRESHOLD to 0 to solved this
+ // it can be tuned for better selection
+ // also, there might be other factors like Mean or other stuffs
+ // same would apply for createLocalDiscardedFeatureList in the TreeNode class
+
+ // TODO: Another idea is getting an aggregated discarded feature indices after the run, from combining
+ // the local discarded feature indices
+ // this would penalize a feature, even if in global space the feature looks quite good
+ // the penalization would be averaged, so this woould unlikely to create a local optmina
+
+ vector<int> getGlobalDiscardedFeatureIndices();
+
+ int numDecisionTrees;
+ int numSamples;
+ int numFeatures;
+ vector< vector<int> > dataSet;
+ vector<int> globalDiscardedFeatureIndices;
+ vector<double> globalVariableImportanceList;
+ string treeSplitCriterion;
+ // This is a map of each feature to outcome count of each classes
+ // e.g. 1 => [2 7] means feature 1 has 2 outcome of 0 and 7 outcome of 1
+ map<int, vector<int> > globalOutOfBagEstimates;
+
+ // TODO: fix this, do we use pointers?
+ vector<AbstractDecisionTree*> decisionTrees;
+
+ MothurOut* m;
+
+private:
+
+};
+
+#endif /* defined(__Mothur__forest__) */