converted jsd calculation to be based on relative abundance

diff --git a/sharedjsd.cpp b/sharedjsd.cpp
index 46cb9770bcd285fcff10f0df6e8d9da1bb3febda..914c87550ba257689965cb8452a2af49d85d4144 100644 (file)
--- a/sharedjsd.cpp
+++ b/sharedjsd.cpp
@@ -19,21 +19,35 @@ EstOutput JSD::getValues(vector<SharedRAbundVector*> shared) {
         double KLD1 = 0.0;
         double KLD2 = 0.0;
 
+        vector<int> countA = shared[0]->getAbundances();
+        vector<int> countB = shared[1]->getAbundances();
+        double totalA = 0;
+        double totalB = 0;
+        
                for (int i = 0; i < shared[0]->getNumBins(); i++) {
-                       //store in temps to avoid multiple repetitive function calls
-                       double tempA = shared[0]->getAbundance(i);
-                       double tempB = shared[1]->getAbundance(i);
+            totalA += countA[i];
+            totalB += countB[i];
+        }
+
+        for (int i = 0; i < shared[0]->getNumBins(); i++) {
+            double tempA = countA[i] / totalA;
+            double tempB = countB[i] / totalB;
             
+            tempA = countA[i] / totalA;
+            tempB = countB[i] / totalB;
+
             if (tempA == 0) { tempA = 0.000001; }
             if (tempB == 0) { tempB = 0.000001; }
-            
+
             double denom = (tempA+tempB)/(double)2.0;
-           
+
             if (tempA != 0) {  KLD1 += tempA * log(tempA/denom); } //KLD(x,m)
             if (tempB != 0) {  KLD2 += tempB * log(tempB/denom); } //KLD(y,m)
+
         }
-        
-               data[0] = sqrt((0.5*KLD1) + (0.5*KLD2));
+
+            
+        data[0] = ((0.5*KLD1) + (0.5*KLD2));
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }