X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mempearson.cpp;h=2503b5dc1cfc18e253e6042b25931068f3c13054;hp=b39afd86f3d147f54d2e8ad9542c670955da961f;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=7d38edc137a66a33f67f8cf55cce88331290aaf7

diff --git a/mempearson.cpp b/mempearson.cpp
index b39afd8..2503b5d 100644
--- a/mempearson.cpp
+++ b/mempearson.cpp
@@ -24,10 +24,11 @@ EstOutput MemPearson::getValues(vector<SharedRAbundVector*> shared) {
 			if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
 		}
 		
-		double numTerm1 = 0.0;
-		double numTerm2 = 0.0;
+		double numTerm = 0.0;
 		double denomTerm1 = 0.0;
 		double denomTerm2 = 0.0;
+		double averageA = nonZeroA / (float) numOTUS;
+		double averageB = nonZeroB / (float) numOTUS;
 		
 		for (int i = 0; i < shared[0]->getNumBins(); i++) { 
 			int Aij =  shared[0]->getAbundance(i);
@@ -36,21 +37,18 @@ EstOutput MemPearson::getValues(vector<SharedRAbundVector*> shared) {
 			if (Aij > 0) { Aij = 1; }
 			if (Bij > 0) { Bij = 1; }
 			
-			numTerm1 += (Aij - (nonZeroA / (float) numOTUS));
-			numTerm2 += (Bij - (nonZeroB / (float) numOTUS));
-			
-			denomTerm1 += ((Aij - (nonZeroA / (float) numOTUS)) * (Aij - (nonZeroA / (float) numOTUS)));
-			denomTerm2 += ((Bij - (nonZeroB / (float) numOTUS)) * (Bij - (nonZeroB / (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;
-		
+
 		if (denom != 0) { 
-			data[0] = 1.0 - (numerator / denom);
+			data[0] = (numTerm / denom);
 		}else {
 			data[0] = 1.0;
 		}