1 #ifndef ANOSIMCOMMAND_H
2 #define ANOSIMCOMMAND_H
8 * Created by westcott on 2/14/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
18 class AnosimCommand : public Command {
21 AnosimCommand(string);
25 vector<string> setParameters();
26 string getCommandName() { return "anosim"; }
27 string getCommandCategory() { return "Hypothesis Testing"; }
28 string getHelpString();
29 string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
30 string getDescription() { return "analysis of similarity"; }
33 void help() { m->mothurOut(getHelpString()); }
38 string outputDir, inputDir, designFileName, phylipFileName;
40 vector<vector<double> > convertToRanks(vector<vector<double> >);
41 double calcR(vector<vector<double> >, map<string, vector<int> >);
42 map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
43 double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
45 vector< vector<double> > distanceMatrix;
46 vector<string> outputNames;
48 double experimentwiseAlpha;
49 vector< vector<string> > namesOfGroupCombos;