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//
// 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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