abstractrandomforest.hpp

//
//  abstractrandomforest.hpp
//  rrf-fs-prototype
//
//  Created by Abu Zaher Faridee on 7/20/12.
//  Copyright (c) 2012 Schloss Lab. All rights reserved.
//

#ifndef rrf_fs_prototype_abstractrandomforest_hpp
#define rrf_fs_prototype_abstractrandomforest_hpp

#include "mothurout.h"
#include "macros.h"
#include "abstractdecisiontree.hpp"

#define DEBUG_MODE

/***********************************************************************/

class AbstractRandomForest{
public:
    // intialization with vectors
    AbstractRandomForest(const std::vector < std::vector<int> > dataSet, 
                       const int numDecisionTrees, 
                       const string);
    virtual ~AbstractRandomForest(){ }
    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