geom.cpp

   1 /*
   2  *  geom.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 2/23/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "geom.h"
  11
  12 /***********************************************************************/
  13
  14 double Geom::kEq(double k, double spec){
  15         return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
  16 }
  17
  18 RAbundVector Geom::getRAbundVector(SAbundVector* rank){
  19                 vector <int> rData;
  20                 int mr = 1;
  21                 int nb = 0;
  22                 int ns = 0;
  23
  24                 for(int i = rank->size()-1; i > 0; i--)
  25                 {
  26                         int cur = rank->get(i);
  27                         if(mr == 1 && cur > 0)
  28                                 mr = i;
  29                         nb += cur;
  30                         ns += i*cur;
  31                         for(int j = 0; j < cur; j++)
  32                                 rData.push_back(i);
  33                 }
  34
  35                 RAbundVector rav = RAbundVector(rData, mr, nb, ns);
  36                 rav.setLabel(rank->getLabel());
  37                 return rav;
  38 }
  39
  40 /***********************************************************************************/
  41
  42 /***********************************************************************************/
  43 EstOutput Geom::getValues(SAbundVector* rank){
  44         try {
  45                 data.resize(3,0);
  46
  47                 rdata = getRAbundVector(rank);
  48                 int numInd = rdata.getNumSeqs();
  49                 int numSpec = rdata.getNumBins();
  50                 int min = rdata.get(rdata.size()-1);
  51                 double k = .5;
  52                 double step = .49999;
  53
  54                 while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) //This uses a binary search to find the value of k.
  55                 {
  56                         if(numInd*kEq(k, numSpec) > min)
  57                                 k += step;
  58                         else
  59                                 k -= step;
  60                         step /= 2;
  61                 }
  62
  63                 double cK = 1/(1-pow(1-k, numSpec));
  64                 double sumExp = 0;
  65                 double sumObs = 0;
  66                 double maxDiff = 0;
  67
  68                 for(int i = 0; i < numSpec; i++)
  69                 {
  70                         sumObs += rdata.get(i);
  71                         sumExp += numInd*cK*k*pow(1-k, i);
  72
  73                         double diff = fabs(sumObs-sumExp);
  74                         if(diff > maxDiff)      {       maxDiff = diff;         }
  75
  76                 }
  77
  78
  79                 /*cout << "Geom:\n";
  80                 cout << "D-Statistic = " << DStatistic << "\n";
  81                 cout << "Critical value for 95% confidence interval = ";*/
  82
  83                 data[0] = maxDiff/numInd;
  84                 data[1] = 0.886/sqrt(numSpec);
  85                 data[2] = 1.031/sqrt(numSpec);
  86
  87                 /*cout << critVal << "\n";
  88                 cout << "If D-Statistic is less than the critical value then the data fits the Geometric Series model w/ 95% confidence.\n\n";*/
  89
  90                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  91                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  92                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  93
  94                 return data;
  95         }
  96         catch(exception& e) {
  97                 cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  98                 exit(1);
  99         }
 100         catch(...) {
 101                 cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 102                 exit(1);
 103         }
 104 }
 105
 106 /***********************************************************************/
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