+//
+// sharedrjsd.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 1/21/14.
+// Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#include "sharedrjsd.h"
+
+/***********************************************************************/
+//KLD <- function(x,y) sum(x *log(x/y))
+//JSD<- function(x,y) sqrt(0.5 * KLD(x, (x+y)/2) + 0.5 * KLD(y, (x+y)/2))
+EstOutput RJSD::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+
+ data.resize(1,0);
+
+ 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++) {
+ 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));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RJSD", "getValues");
+ exit(1);
+ }
+}
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