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                 //this is a modification do to a vector fill error that occurs when an empty sharedRabund creates a sabund
  20                 //in that case there is no 1 0r 2.
  21                 double singles;
  22                 if (rank->size() > 1) {
  23                         singles = (double)rank->get(1);
  24                 }else{ singles = 0.0;  }
  25
  26                 double doubles;
  27                 if (rank->size() > 2) {
  28                          doubles = (double)rank->get(2);
  29                 }else{ doubles = 0.0;  }
  30
  31                 double chaovar = 0.0000;
  32 //cout << "singles = " << singles << " doubles = " << doubles << " sobs = " << sobs << endl;
  33                 double chao = sobs + singles*(singles-1)/(2*(doubles+1));
  34
  35                 if(singles > 0 && doubles > 0){
  36                         chaovar = singles*(singles-1)/(2*(doubles+1))
  37                                         + singles*pow(2*singles-1, 2)/(4*pow(doubles+1,2))
  38                                         + pow(singles, 2)*doubles*pow(singles-1, 2)/(4*pow(doubles+1,4));
  39                 }
  40                 else if(singles > 0 && doubles == 0){
  41                         chaovar = singles*(singles-1)/2 + singles*pow(2*singles-1, 2)/4 - pow(singles, 4)/(4*chao);
  42                 }
  43                 else if(singles == 0){
  44                         chaovar = sobs*exp(-1*rank->getNumSeqs()/sobs)*(1-exp(-1*rank->getNumSeqs()/sobs));
  45                 }
  46
  47                 double chaohci, chaolci;
  48
  49                 if(singles>0){
  50                         double denom = pow(chao-sobs,2);
  51                         double c = exp(1.96*pow((log(1+chaovar/denom)),0.5));
  52                         chaolci = sobs+(chao-sobs)/c;//chao lci
  53                         chaohci = sobs+(chao-sobs)*c;//chao hci
  54                 }
  55                 else{
  56                         double p = exp(-1*rank->getNumSeqs()/sobs);
  57                         chaolci = sobs/(1-p)-1.96*pow(sobs*p/(1-p), 0.5);
  58                         chaohci = sobs/(1-p)+1.96*pow(sobs*p/(1-p), 0.5);
  59                         if(chaolci < sobs){     chaolci = sobs; }
  60                 }
  61
  62                 data[0] = chao;
  63                 data[1] = chaolci;
  64                 data[2] = chaohci;
  65
  66             if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  67                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  68                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  69
  70                 return data;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "Chao1", "getValues");
  74                 exit(1);
  75         }
  76 }
  77
  78 /***********************************************************************/