spearman.cpp

   1 /*
   2  *  spearman.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/15/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "spearman.h"
  11
  12 /***********************************************************************/
  13
  14 EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
  15         try {
  16                 data.resize(1,0);
  17
  18                 SAbundVector savA = shared[0]->getSAbundVector();
  19                 SAbundVector savB = shared[1]->getSAbundVector();
  20
  21                 double sumRanks = 0.0;
  22                 int numOTUS = shared[0]->getNumBins();
  23
  24                 vector<double> rankVectorA(savA.getMaxRank()+1, 0);
  25                 int currentRankA = 0;
  26                 for(int i=savA.getMaxRank();i>0;i--){
  27                         int numWithAbundanceI = savA.get(i);
  28
  29                         if(numWithAbundanceI > 1){      rankVectorA[i] = (currentRankA + 1 + currentRankA + numWithAbundanceI) / 2.0;   }
  30                         else                                    {       rankVectorA[i] = currentRankA+numWithAbundanceI;        }
  31                         currentRankA += numWithAbundanceI;
  32                 }
  33                 rankVectorA[0] = (numOTUS + currentRankA + 1) / 2.0;
  34
  35
  36                 vector<double> rankVectorB(savB.getMaxRank()+1, 0);
  37                 int currentRankB = 0;
  38                 for(int i=savB.getMaxRank();i>0;i--){
  39                         int numWithAbundanceI = savB.get(i);
  40
  41                         if(numWithAbundanceI > 1){      rankVectorB[i] = (currentRankB + 1 + currentRankB + numWithAbundanceI) / 2.0;   }
  42                         else                                    {       rankVectorB[i] = currentRankB+numWithAbundanceI;        }
  43                         currentRankB += numWithAbundanceI;
  44                 }
  45                 rankVectorB[0] = (numOTUS + currentRankB + 1) / 2.0;
  46
  47
  48
  49                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  50                         int Aij = shared[0]->getAbundance(i);
  51                         int Bij = shared[1]->getAbundance(i);
  52
  53                         float rankA = rankVectorA[Aij];
  54                         float rankB = rankVectorB[Bij];
  55
  56                         sumRanks += ((rankA - rankB) * (rankA - rankB));
  57                 }
  58                 data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * ((numOTUS*numOTUS)-1)));
  59
  60                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  61
  62                 return data;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "Spearman", "getValues");
  66                 exit(1);
  67         }
  68 }
  69
  70 /***********************************************************************/
  71