chao1.cpp

   1 /*
   2  *  chao1.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 "chao1.h"
  11
  12 /***********************************************************************/
  13 EstOutput Chao1::getValues(SAbundVector* rank){
  14         try {
  15                 data.resize(3,0);
  16
  17                 double sobs = (double)rank->getNumBins();
  18
  19                 double singles = (double)rank->get(1);
  20                 double doubles = (double)rank->get(2);
  21                 double chaovar = 0.0000;
  22
  23                 double chao = sobs + pow(singles,2)/(2*(doubles+1)) - (singles*doubles/(2*pow(doubles+1,2)));
  24
  25                 if(doubles==0){chaovar=0;}
  26                 else{
  27                         double g=singles/doubles;
  28                         chaovar = doubles*(0.25*pow(g,4)+pow(g,3)+0.5*pow(g,2));
  29                 }
  30
  31
  32                 double chaohci, chaolci;
  33
  34                 if(chao==sobs){
  35                         double ci = 1.96*pow(chaovar,0.5);
  36                         chaolci = chao-ci;//chao lci
  37                         chaohci = chao+ci;//chao hci
  38                 }
  39                 else{
  40                         double denom = pow(chao-sobs,2);
  41                         double c = exp(1.96*pow((log(1+chaovar/denom)),0.5));
  42                         chaolci = sobs+(chao-sobs)/c;//chao lci
  43                         chaohci = sobs+(chao-sobs)*c;//chao hci
  44                 }
  45
  46                 data[0] = chao;
  47                 data[1] = chaolci;
  48                 data[2] = chaohci;
  49
  50             if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  51                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  52                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  53
  54                 return data;
  55         }
  56         catch(exception& e) {
  57                 cout << "Standard Error: " << e.what() << " has occurred in the Chao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60         catch(...) {
  61                 cout << "An unknown error has occurred in the Chao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64 };
  65
  66 /***********************************************************************/