working on pam

[mothur.git] / mempearson.cpp

diff --git a/mempearson.cpp b/mempearson.cpp
index b39afd86f3d147f54d2e8ad9542c670955da961f..2503b5dc1cfc18e253e6042b25931068f3c13054 100644 (file)
--- 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;
                }