sharedbraycurtis.cpp

   1 /*
   2  *  sharedbraycurtis.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/24/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedbraycurtis.h"
  11
  12 /***********************************************************************/
  13 //This is used by SharedJAbund and SharedSorAbund
  14 EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
  15         try {
  16                 data.resize(1,0);
  17
  18                 double sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
  19                 sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0;
  20
  21                 /*Xi, Yi = abundance of the ith shared OTU in A and B
  22                 sumSharedA = the number of otus in A
  23                 sumSharedB = the sum of all shared otus in B
  24                 sumSharedAB = the sum of the minimum otus int all shared otus in AB.
  25                 */
  26
  27                 for (int i = 0; i < shared[0]->getNumBins(); i++) {
  28                         //store in temps to avoid multiple repetitive function calls
  29                         tempA = shared[0]->getAbundance(i);
  30                         tempB = shared[1]->getAbundance(i);
  31
  32                         sumSharedA += tempA;
  33                         sumSharedB += tempB;
  34
  35                         //sum the min of tempA and tempB
  36                         if (tempA < tempB) { sumSharedAB += tempA; }
  37                         else  { sumSharedAB += tempB; }
  38                 }
  39
  40                 data[0] = 1.0 - (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
  41
  42                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  43
  44                 return data;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "BrayCurtis", "getValues");
  48                 exit(1);
  49         }
  50 }
  51
  52 /***********************************************************************/