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 numTerm = 0.0;
  28                 double denomTerm1 = 0.0;
  29                 double denomTerm2 = 0.0;
  30                 double averageA = nonZeroA / (float) numOTUS;
  31                 double averageB = nonZeroB / (float) numOTUS;
  32
  33                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  34                         int Aij =  shared[0]->getAbundance(i);
  35                         int Bij =  shared[1]->getAbundance(i);
  36
  37                         if (Aij > 0) { Aij = 1; }
  38                         if (Bij > 0) { Bij = 1; }
  39
  40                         numTerm += ((Aij - averageA) * (Bij - averageB));
  41                         denomTerm1 += ((Aij - averageA) * (Aij - averageA));
  42                         denomTerm2 += ((Bij - averageB) * (Bij - averageB));
  43                 }
  44
  45                 denomTerm1 = sqrt(denomTerm1);
  46                 denomTerm2 = sqrt(denomTerm2);
  47
  48                 double denom = denomTerm1 * denomTerm2;
  49
  50                 if (denom != 0) {
  51                         data[0] = (numTerm / denom);
  52                 }else {
  53                         data[0] = 1.0;
  54                 }
  55
  56                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  57
  58                 return data;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "MemPearson", "getValues");
  62                 exit(1);
  63         }
  64 }
  65 /***********************************************************************/
  66