X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=spearman.cpp;fp=spearman.cpp;h=49d5265259bc2ceb566d6f88f71fda30130b7945;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;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();
+		
+		vector<double> rankVectorA(savA.getMaxRank()+1, 0);
+		int currentRankA = 0;
+		for(int i=savA.getMaxRank();i>0;i--){	
+			int numWithAbundanceI = savA.get(i);
+
+			if(numWithAbundanceI > 1){	rankVectorA[i] = (currentRankA + 1 + currentRankA + numWithAbundanceI) / 2.0;	}
+			else					{	rankVectorA[i] = currentRankA+numWithAbundanceI;	}
+			currentRankA += numWithAbundanceI;
+		}
+		rankVectorA[0] = (numOTUS + currentRankA + 1) / 2.0;
+		
+		
+		vector<double> rankVectorB(savB.getMaxRank()+1, 0);
+		int currentRankB = 0;
+		for(int i=savB.getMaxRank();i>0;i--){	
+			int numWithAbundanceI = savB.get(i);
+			
+			if(numWithAbundanceI > 1){	rankVectorB[i] = (currentRankB + 1 + currentRankB + numWithAbundanceI) / 2.0;	}
+			else					{	rankVectorB[i] = currentRankB+numWithAbundanceI;	}
+			currentRankB += numWithAbundanceI;
+		}
+		rankVectorB[0] = (numOTUS + currentRankB + 1) / 2.0;
+		
+		
+
+		for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+			int Aij = shared[0]->getAbundance(i);
+			int Bij = shared[1]->getAbundance(i);
+			
+			float rankA = rankVectorA[Aij];
+			float rankB = rankVectorB[Bij];
+			
+			sumRanks += ((rankA - rankB) * (rankA - rankB));
+		}
+		data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * ((numOTUS*numOTUS)-1)));
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Spearman", "getValues");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+