shannon.cpp

   1 /*
   2  *  shannon.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/7/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "shannon.h"
  11
  12 /***********************************************************************/
  13
  14 EstOutput Shannon::getValues(SAbundVector* rank){
  15         try {
  16                 //vector<double> shannonData(3,0);
  17                 data.resize(3,0);
  18
  19                 double shannon = 0.0000;  //hprime
  20                 double hvara=0.0000;
  21
  22                 double maxRank = rank->getMaxRank();
  23                 int sampled = rank->getNumSeqs();
  24                 int sobs = rank->getNumBins();
  25
  26                 for(int i=1;i<=maxRank;i++){
  27                         double p = ((double) i)/((double)sampled);
  28                         shannon += (double)rank->get(i)*p*log(p); //hprime
  29                         hvara  += (double)rank->get(i)*p*pow(log(p),2);
  30                 }
  31                 shannon = -shannon;
  32
  33                 double hvar = (hvara-pow(shannon,2))/(double)sampled+(double)(sobs-1)/(double)(2*sampled*sampled);
  34
  35                 double ci = 0;
  36
  37                 if(hvar>0){
  38                         ci = 1.96*pow(hvar,0.5);
  39                 }
  40
  41                 double shannonhci = shannon + ci;
  42                 double shannonlci = shannon - ci;
  43
  44                 data[0] = shannon;
  45                 data[1] = shannonlci;
  46                 data[2] = shannonhci;
  47
  48                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  49                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  50                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  51
  52                 return data;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "Shannon", "getValues");
  56                 exit(1);
  57         }
  58 }
  59
  60 /***********************************************************************/