npshannon.cpp

   1 /*
   2  *  npshannon.cpp
   3  *  Dotur
   4  *
   5  *  Created by John Westcott on 1/7/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "npshannon.h"
  11
  12 /***********************************************************************/
  13
  14
  15 EstOutput NPShannon::getValues(SAbundVector* rank){
  16         try {
  17                 data.resize(1,0);
  18                 float npShannon = 0.0000;
  19
  20                 double maxRank = (double)rank->getMaxRank();
  21                 double sampled = rank->getNumSeqs();
  22
  23                 double Chat = 1.0000 - (double)rank->get(1)/(double)sampled;
  24
  25                 if(Chat>0)      {
  26                         for(int i=1;i<=maxRank;i++){
  27                                 double pi = ((double) i)/((double)sampled);
  28                                 double ChatPi = Chat*pi;
  29                                 if(ChatPi>0){
  30                                         npShannon += rank->get(i) * ChatPi*log(ChatPi)/(1-pow(1-ChatPi,(double)sampled));
  31                                 }
  32                         }
  33                         npShannon = -npShannon;
  34                 }
  35                 else{
  36                         npShannon = 0.000;
  37                 }
  38
  39                 data[0] = npShannon;
  40
  41                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  42
  43                 return data;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "NPShannon", "getValues");
  47                 exit(1);
  48         }
  49 }
  50
  51 /***********************************************************************/