simpson.cpp

   1 /*
   2  *  simpson.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 "simpson.h"
  11
  12 /***********************************************************************/
  13
  14 EstOutput Simpson::getValues(SAbundVector* rank){
  15         try {
  16                 //vector<double> simpsonData(3,0);
  17                 data.resize(3,0);
  18                 double simpson = 0.0000;
  19                 double ci = 0;
  20
  21                 double maxRank = (double)rank->getMaxRank();
  22                 double sampled = (double)rank->getNumSeqs();
  23                 double sobs = (double)rank->getNumBins();
  24
  25                 double firstTerm = 0;
  26                 double secondTerm = 0;
  27
  28                 if(sobs != 0){
  29                         double simnum=0.0000;
  30
  31                         for(unsigned long long i=1;i<=maxRank;i++){
  32                                 simnum += (double)(rank->get(i)*i*(i-1));
  33                         }
  34
  35                         simpson = simnum / (sampled*(sampled-1));
  36
  37                         for(unsigned long long i=1;i<=maxRank;i++){
  38                                 double piI = (double) i / (double)sampled;
  39                                 firstTerm += rank->get(i) * pow(piI, 3);
  40                                 secondTerm += rank->get(i) * pow(piI, 2);
  41                         }
  42
  43                         double var = (4.0 / sampled) * (firstTerm - secondTerm*secondTerm);
  44                         ci = 1.95 * pow(var, 0.5);
  45                 }
  46
  47                 double simpsonlci = simpson - ci;
  48                 double simpsonhci = simpson + ci;
  49
  50                 data[0] = simpson;
  51                 data[1] = simpsonlci;
  52                 data[2] = simpsonhci;
  53
  54                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  55                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  56                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  57
  58                 return data;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "Simpson", "getValues");
  62                 exit(1);
  63         }
  64 }
  65
  66 /***********************************************************************/