1 #ifndef COOCCURRENCECOMMAND_H
2 #define COOCCURRENCECOMMAND_H
8 * Created by westcott on 11/10/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "trialswap2.h"
16 #include "inputdata.h"
17 #include "sharedrabundvector.h"
20 class CooccurrenceCommand : public Command {
24 CooccurrenceCommand(string);
25 CooccurrenceCommand();
26 ~CooccurrenceCommand(){}
28 vector<string> setParameters();
29 string getCommandName() { return "Cooccurrence"; }
30 string getCommandCategory() { return "Hypothesis Testing"; }
32 string getHelpString();
33 string getOutputPattern(string);
34 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"; }
35 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."; }
38 void help() { m->mothurOut(getHelpString()); }
42 string metric, matrix, outputDir;
43 string label, sharedfile, groups;
46 vector<string> outputNames, Groups;
49 int getCooccurrence(vector<SharedRAbundVector*>&, ofstream&);