--- /dev/null
+//
+// classifysharedcommand.h
+// Mothur
+//
+// Created by Abu Zaher Md. Faridee on 8/13/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__classifyrfsharedcommand__
+#define __Mothur__classifyrfsharedcommand__
+
+#include "command.hpp"
+#include "inputdata.h"
+
+class ClassifyRFSharedCommand : public Command {
+public:
+ ClassifyRFSharedCommand();
+ ClassifyRFSharedCommand(string);
+ ~ClassifyRFSharedCommand() {};
+
+ vector<string> setParameters();
+ string getCommandName() { return "classifyrf.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Classifyrf.shared\n"; }
+ string getDescription() { return "implements the random forest machine learning algorithm to identify OTUs that can be used to differentiate between various groups of samples"; }
+ int execute();
+
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ bool abort;
+ string outputDir;
+ vector<string> outputNames, Groups;
+
+ string sharedfile, designfile;
+ set<string> labels;
+ bool allLines;
+
+ int processors;
+ bool useTiming;
+
+ GroupMap designMap;
+
+ int numDecisionTrees;
+ string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
+ bool doPruning, discardHighErrorTrees;
+ double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
+
+ void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
+};
+
+#endif /* defined(__Mothur__classifyrfsharedcommand__) */