memchi2.cpp

   1 /*
   2  *  memchi2.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/17/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "memchi2.h"
  11
  12 /***********************************************************************/
  13 EstOutput MemChi2::getValues(vector<SharedRAbundVector*> shared) {
  14         try {
  15                 data.resize(1,0);
  16
  17                 int nonZeroA = 0;
  18                 int nonZeroB = 0;
  19                 int totalOtus = shared[0]->getNumBins();
  20                 //int totalGroups = shared.size();
  21
  22                 //for each otu
  23                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  24                         if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
  25                         if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
  26                 }
  27
  28                 double sum = 0.0;
  29                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  30                         int A = shared[0]->getAbundance(i);
  31                         int B = shared[1]->getAbundance(i);
  32
  33                         if (A > 0) { A = 1; }
  34                         if (B > 0) { B = 1; }
  35
  36                         double Aterm = A / (float) nonZeroA;
  37                         double Bterm = B / (float) nonZeroB;
  38
  39                         int incidence = 0;
  40                         for(int j=0;j<shared.size();j++){
  41                                 if(shared[j]->getAbundance(i) != 0){    incidence++;    }
  42                         }
  43
  44                         if(incidence != 0){
  45                                 sum += (((Aterm-Bterm)*(Aterm-Bterm))/incidence);
  46                         }
  47                 }
  48
  49                 data[0] = sqrt(totalOtus * sum);
  50
  51                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  52
  53                 return data;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "MemChi2", "getValues");
  57                 exit(1);
  58         }
  59 }
  60 /***********************************************************************/
  61