1 #ifndef CORRAXESCOMMAND_H
2 #define CORRAXESCOMMAND_H
8 * Created by westcott on 12/22/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundfloatvector.h"
15 #include "inputdata.h"
18 class CorrAxesCommand : public Command {
20 CorrAxesCommand(string);
24 vector<string> setParameters();
25 string getCommandName() { return "corr.axes"; }
26 string getCommandCategory() { return "Hypothesis Testing"; }
27 string getOutputFileNameTag(string, string);
28 string getHelpString();
29 string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; }
30 string getDescription() { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
33 void help() { m->mothurOut(getHelpString()); }
36 string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
37 bool abort, pickedGroups;
41 vector<string> outputNames, Groups;
42 vector<SharedRAbundFloatVector*> lookupFloat;
43 vector<string> metadataLabels;
45 int getSharedFloat(InputData*);
47 int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
48 map<string, vector<float> > readAxes();
49 int calcPearson(map<string, vector<float> >&, ofstream&);
50 int calcSpearman(map<string, vector<float> >&, ofstream&);
51 int calcKendall(map<string, vector<float> >&, ofstream&);