X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=spearman.cpp;h=49d5265259bc2ceb566d6f88f71fda30130b7945;hp=72d5667e97a0e6a0a499464fe529699212ae8a91;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=75c5a235ac3eb22e0f97d36874f4b2dcf9591f2e

diff --git a/spearman.cpp b/spearman.cpp
index 72d5667..49d5265 100644
--- a/spearman.cpp
+++ b/spearman.cpp
@@ -10,6 +10,7 @@
 #include "spearman.h"
 
 /***********************************************************************/
+
 EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
 	try {
 		data.resize(1,0);
@@ -20,28 +21,51 @@ EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
 		double sumRanks = 0.0;
 		int numOTUS = shared[0]->getNumBins();
 		
-		//calc the 2 denominators
-		for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+		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);
 			
-			int rankA = savA.get(Aij);
-			int rankB = savB.get(Bij);
+			float rankA = rankVectorA[Aij];
+			float rankB = rankVectorB[Bij];
 			
 			sumRanks += ((rankA - rankB) * (rankA - rankB));
 		}
-		
-		data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * (numOTUS-1)));
+		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, "Soergel", "getValues");
+		m->errorOut(e, "Spearman", "getValues");
 		exit(1);
 	}
 }
+
 /***********************************************************************/