1 #ifndef MANTELCOMMAND_H
2 #define MANTELCOMMAND_H
8 * Created by westcott on 2/9/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "linearalgebra.h"
16 class MantelCommand : public Command {
18 MantelCommand(string);
22 vector<string> setParameters();
23 string getCommandName() { return "mantel"; }
24 string getCommandCategory() { return "Hypothesis Testing"; }
26 string getHelpString();
27 string getOutputPattern(string);
28 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/Mantel"; }
29 string getDescription() { return "Mantel’s test for correlation between matrices"; }
32 void help() { m->mothurOut(getHelpString()); }
36 string phylipfile1, phylipfile2, outputDir, method;
40 vector<string> outputNames;