X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=structpearson.cpp;h=a21eb9936aa7799e9d56436a4c513c668148d7d9;hp=9d030ef90742f232a5d0c114b21e5bb8878c83ad;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=7d38edc137a66a33f67f8cf55cce88331290aaf7

diff --git a/structpearson.cpp b/structpearson.cpp
index 9d030ef..a21eb99 100644
--- a/structpearson.cpp
+++ b/structpearson.cpp
@@ -14,17 +14,11 @@ EstOutput StructPearson::getValues(vector<SharedRAbundVector*> shared) {
 	try {
 		data.resize(1,0);
 		
-		double sumA = 0.0;
-		double sumB = 0.0;
 		int numOTUS = shared[0]->getNumBins();
+		double averageA = shared[0]->getNumSeqs() /  (float) numOTUS;
+		double averageB = shared[1]->getNumSeqs() / (float) numOTUS;
 		
-		for (int i = 0; i < shared[0]->getNumBins(); i++) { 
-			sumA += shared[0]->getAbundance(i);
-			sumB += shared[1]->getAbundance(i);
-		}
-		
-		double numTerm1 = 0.0;
-		double numTerm2 = 0.0;
+		double numTerm = 0.0;
 		double denomTerm1 = 0.0;
 		double denomTerm2 = 0.0;
 		
@@ -32,20 +26,18 @@ EstOutput StructPearson::getValues(vector<SharedRAbundVector*> shared) {
 			int Aij =  shared[0]->getAbundance(i);
 			int Bij =  shared[1]->getAbundance(i);
 			
-			numTerm1 += (Aij - (sumA / (float) numOTUS));
-			numTerm2 += (Bij - (sumB / (float) numOTUS));
 			
-			denomTerm1 += ((Aij - (sumA / (float) numOTUS)) * (Aij - (sumA / (float) numOTUS)));
-			denomTerm2 += ((Bij - (sumB / (float) numOTUS)) * (Bij - (sumB / (float) numOTUS)));
+			numTerm += ((Aij - averageA) * (Bij - averageB));
+			denomTerm1 += ((Aij - averageA) * (Aij - averageA));
+			denomTerm2 += ((Bij - averageB) * (Bij - averageB));
 		}
 		
 		denomTerm1 = sqrt(denomTerm1);
 		denomTerm2 = sqrt(denomTerm2);
 		
 		double denom = denomTerm1 * denomTerm2;
-		double numerator = numTerm1 * numTerm2;
 		
-		data[0] = 1.0 - (numerator / denom);
+		data[0] = (numTerm / denom);
 		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }