fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it,...

[mothur.git] / spearman.cpp

diff --git a/spearman.cpp b/spearman.cpp
new file mode 100644 (file)
index 0000000..72d5667
--- /dev/null
+++ b/spearman.cpp
@@ -0,0 +1,47 @@
+/*
+ *  spearman.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/15/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "spearman.h"
+
+/***********************************************************************/
+EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               SAbundVector savA = shared[0]->getSAbundVector();
+               SAbundVector savB = shared[1]->getSAbundVector();
+               
+               double sumRanks = 0.0;
+               int numOTUS = shared[0]->getNumBins();
+               
+               //calc the 2 denominators
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+                       
+                       int Aij = shared[0]->getAbundance(i);
+                       int Bij = shared[1]->getAbundance(i);
+                       
+                       int rankA = savA.get(Aij);
+                       int rankB = savB.get(Bij);
+                       
+                       sumRanks += ((rankA - rankB) * (rankA - rankB));
+               }
+               
+               data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * (numOTUS-1)));
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Soergel", "getValues");
+               exit(1);
+       }
+}
+/***********************************************************************/
+