X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=spearman.cpp;fp=spearman.cpp;h=72d5667e97a0e6a0a499464fe529699212ae8a91;hb=75c5a235ac3eb22e0f97d36874f4b2dcf9591f2e;hp=0000000000000000000000000000000000000000;hpb=8f89a92f4ada82a2b3bf51b23b6a977770f2b9e2;p=mothur.git

diff --git a/spearman.cpp b/spearman.cpp
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+++ b/spearman.cpp
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+/*
+ *  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);
+	}
+}
+/***********************************************************************/
+