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#ifndef COOCCURRENCECOMMAND_H
#define COOCCURRENCECOMMAND_H
/*
* COOCCURRENCE.h
* Mothur
*
* Created by westcott on 11/10/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "trialswap2.h"
#include "inputdata.h"
class CooccurrenceCommand : public Command {
public:
CooccurrenceCommand(string);
~CooccurrenceCommand(){}
vector<string> setParameters();
string getCommandName() { return "cooccurrence"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Ulrich W & Gotelli NJ (2010). Null model analysis of species associations using abundance data. Ecology 91:3384.\nhttp://www.mothur.org/wiki/Cooccurrence"; }
string getDescription() { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string metric, matrix;
string label, sharedfile, groups;
bool abort, allLines;
set<string> labels;
vector<string> outputNames, Groups;
int runs;
int getCooccurrence(SharedRAbundVectors*&, ofstream&);
};
#endif
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