X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=cooccurrencecommand.h;h=94930ac2db71fff68a9fb208385a6cdc2c94ade4;hb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;hp=da7cde84a5372acb083e509b0fb0a997039ad835;hpb=597560b3c23f03d0069082cf096ce65e0c087519;p=mothur.git

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
index da7cde8..94930ac 100644
--- a/cooccurrencecommand.h
+++ b/cooccurrencecommand.h
@@ -26,11 +26,13 @@ public:
 	~CooccurrenceCommand(){}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "Cooccurrence";			}
+	string getCommandName()			{ return "cooccurrence";			}
 	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Cooccurrence"; }
-	string getDescription()		{ return "Cooccurrence"; }
+    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()); }