rarecalc.cpp

   1 /*
   2  *  rarecalc.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 "rarecalc.h"
  11
  12 /***********************************************************************/
  13
  14 EstOutput RareCalc::getValues(int n){
  15         try {
  16                 EstOutput output(3,0);
  17
  18                 double richness = (double)numBins;
  19                 double varS = 0.0000;
  20
  21                 double varTerm1 = 0.0000;
  22                 double varTerm2 = 0.0000;
  23
  24                 double rSummation = 0;
  25                 for(int i=0;i<numBins;i++){
  26                         int N_ni = numSeqs - bins->get(i);
  27                         rSummation += (bMatrix[N_ni][n]);
  28
  29                         varTerm1 += (bMatrix[N_ni][n] * (1.0 - bMatrix[N_ni][n] / bMatrix[numSeqs][n]));
  30
  31                         for(int j=i+1;j<numBins;j++){
  32                                 varTerm2 += ( bMatrix[N_ni-bins->get(j)][n] - bMatrix[N_ni][n] * bMatrix[numSeqs-bins->get(j)][n] / bMatrix[numSeqs][n]);
  33                         }
  34
  35                 }
  36                 richness -= (rSummation / bMatrix[numSeqs][n]);
  37                 varS = (varTerm1 + 2 * varTerm2) / bMatrix[numSeqs][n];
  38                 float sd = pow(varS, 0.5);
  39
  40
  41                 output[0] = richness;
  42                 output[1] = richness - 1.96 * sd;
  43                 output[2] = richness + 1.96 * sd;
  44
  45                 return output;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "RareCalc", "getValues");
  49                 exit(1);
  50         }
  51 }
  52
  53 /***********************************************************************/