working on pam

[mothur.git] / structpearson.cpp

diff --git a/structpearson.cpp b/structpearson.cpp
index 9d030ef90742f232a5d0c114b21e5bb8878c83ad..a21eb9936aa7799e9d56436a4c513c668148d7d9 100644 (file)
--- 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; }