X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cooccurrencecommand.h;h=94930ac2db71fff68a9fb208385a6cdc2c94ade4;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=530db9e2d27cad41cda6dc4f37ad07b01c570009;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
index 530db9e..94930ac 100644
--- a/cooccurrencecommand.h
+++ b/cooccurrencecommand.h
@@ -26,11 +26,12 @@ public:
 	~CooccurrenceCommand(){}
 	
 	vector<string> setParameters();
-	string getCommandName()			{ return "Cooccurrence";			}
+	string getCommandName()			{ return "cooccurrence";			}
 	string getCommandCategory()		{ return "Hypothesis Testing";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/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();