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 + singles*(singles-1)/(2*(doubles+1));
  24
  25                 if(singles > 0 && doubles > 0){
  26                         chaovar = singles*(singles-1)/(2*(doubles+1))
  27                                         + singles*pow(2*singles-1, 2)/(4*pow(doubles+1,2))
  28                                         + pow(singles, 2)*doubles*pow(singles-1, 2)/(4*pow(doubles+1,4));
  29                 }
  30                 else if(singles > 0 && doubles == 0){
  31                         chaovar = singles*(singles-1)/2 + singles*pow(2*singles-1, 2)/4 - pow(singles, 4)/(4*chao);
  32                 }
  33                 else if(singles == 0){
  34                         chaovar = sobs*exp(-1*rank->getNumSeqs()/sobs)*(1-exp(-1*rank->getNumSeqs()/sobs));
  35                 }
  36
  37                 double chaohci, chaolci;
  38
  39                 if(singles>0){
  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                 else{
  46                         double p = exp(-1*rank->getNumSeqs()/sobs);
  47                         chaolci = sobs/(1-p)-1.96*pow(sobs*p/(1-p), 0.5);
  48                         chaohci = sobs/(1-p)+1.96*pow(sobs*p/(1-p), 0.5);
  49                         if(chaolci < sobs){     chaolci = sobs; }
  50                 }
  51
  52                 data[0] = chao;
  53                 data[1] = chaolci;
  54                 data[2] = chaohci;
  55
  56             if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  57                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  58                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  59
  60                 return data;
  61         }
  62         catch(exception& e) {
  63                 errorOut(e, "Chao1", "getValues");
  64                 exit(1);
  65         }
  66 }
  67
  68 /***********************************************************************/