X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=spearman.cpp;fp=spearman.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=49d5265259bc2ceb566d6f88f71fda30130b7945;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/spearman.cpp b/spearman.cpp
deleted file mode 100644
index 49d5265..0000000
--- a/spearman.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- *  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);
-	}
-}
-
-/***********************************************************************/
-