mempearson.cpp

   1 /*
   2  *  mempearson.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 "mempearson.h"
  11
  12 /***********************************************************************/
  13 EstOutput MemPearson::getValues(vector<SharedRAbundVector*> shared) {
  14         try {
  15                 data.resize(1,0);
  16
  17                 int nonZeroA = 0;
  18                 int nonZeroB = 0;
  19                 int numOTUS = shared[0]->getNumBins();
  20
  21                 //for each otu
  22                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  23                         if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
  24                         if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
  25                 }
  26
  27                 double numTerm1 = 0.0;
  28                 double numTerm2 = 0.0;
  29                 double denomTerm1 = 0.0;
  30                 double denomTerm2 = 0.0;
  31
  32                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  33                         int Aij =  shared[0]->getAbundance(i);
  34                         int Bij =  shared[1]->getAbundance(i);
  35
  36                         if (Aij > 0) { Aij = 1; }
  37                         if (Bij > 0) { Bij = 1; }
  38
  39                         numTerm1 += (Aij - (nonZeroA / (float) numOTUS));
  40                         numTerm2 += (Bij - (nonZeroB / (float) numOTUS));
  41
  42                         denomTerm1 += ((Aij - (nonZeroA / (float) numOTUS)) * (Aij - (nonZeroA / (float) numOTUS)));
  43                         denomTerm2 += ((Bij - (nonZeroB / (float) numOTUS)) * (Bij - (nonZeroB / (float) numOTUS)));
  44                 }
  45
  46                 denomTerm1 = sqrt(denomTerm1);
  47                 denomTerm2 = sqrt(denomTerm2);
  48
  49                 double denom = denomTerm1 * denomTerm2;
  50                 double numerator = numTerm1 * numTerm2;
  51
  52                 if (denom != 0) {
  53                         data[0] = 1.0 - (numerator / denom);
  54                 }else {
  55                         data[0] = 1.0;
  56                 }
  57
  58                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  59
  60                 return data;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "MemPearson", "getValues");
  64                 exit(1);
  65         }
  66 }
  67 /***********************************************************************/
  68