sharedjsd.cpp

   1 //
   2 //  sharedjsd.cpp
   3 //  Mothur
   4 //
   5 //  Created by SarahsWork on 12/9/13.
   6 //  Copyright (c) 2013 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "sharedjsd.h"
  10
  11 /***********************************************************************/
  12 //KLD <- function(x,y) sum(x *log(x/y))
  13 //JSD<- function(x,y) sqrt(0.5 * KLD(x, (x+y)/2) + 0.5 * KLD(y, (x+y)/2))
  14 EstOutput JSD::getValues(vector<SharedRAbundVector*> shared) {
  15         try {
  16
  17                 data.resize(1,0);
  18
  19         double KLD1 = 0.0;
  20         double KLD2 = 0.0;
  21
  22         vector<int> countA = shared[0]->getAbundances();
  23         vector<int> countB = shared[1]->getAbundances();
  24         double totalA = 0;
  25         double totalB = 0;
  26
  27                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  28             totalA += countA[i];
  29             totalB += countB[i];
  30         }
  31
  32         for (int i = 0; i < shared[0]->getNumBins(); i++) {
  33             double tempA = countA[i] / totalA;
  34             double tempB = countB[i] / totalB;
  35
  36             tempA = countA[i] / totalA;
  37             tempB = countB[i] / totalB;
  38
  39             if (tempA == 0) { tempA = 0.000001; }
  40             if (tempB == 0) { tempB = 0.000001; }
  41
  42             double denom = (tempA+tempB)/(double)2.0;
  43
  44             if (tempA != 0) {  KLD1 += tempA * log(tempA/denom); } //KLD(x,m)
  45             if (tempB != 0) {  KLD2 += tempB * log(tempB/denom); } //KLD(y,m)
  46
  47         }
  48
  49
  50         data[0] = ((0.5*KLD1) + (0.5*KLD2));
  51
  52                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  53
  54                 return data;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "JSD", "getValues");
  58                 exit(1);
  59         }
  60 }
  61
  62 /***********************************************************************/