bstick.cpp

   1 /*
   2  *  bstick.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 3/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "bstick.h"
  11
  12
  13 /***********************************************************************/
  14 double BStick::invSum(int index, double numSpec)
  15 {
  16         double sum = 0;
  17         for(int i = index; i <= numSpec; i++)
  18                 sum += 1/(double)i;
  19         return sum;
  20 }
  21
  22 RAbundVector BStick::getRAbundVector(SAbundVector* rank){
  23                 vector <int> rData;
  24                 int mr = 1;
  25                 int nb = 0;
  26                 int ns = 0;
  27
  28                 for(int i = rank->size()-1; i > 0; i--)
  29                 {
  30                         int cur = rank->get(i);
  31                         if(mr == 1 && cur > 0)
  32                                 mr = i;
  33                         nb += cur;
  34                         ns += i*cur;
  35                         for(int j = 0; j < cur; j++)
  36                                 rData.push_back(i);
  37                 }
  38
  39                 RAbundVector rav = RAbundVector(rData, mr, nb, ns);
  40                 rav.setLabel(rank->getLabel());
  41                 return rav;
  42 }
  43
  44 /***************************************************************************/
  45
  46 /***************************************************************************/
  47 EstOutput BStick::getValues(SAbundVector* rank){
  48         try {
  49                 data.resize(2,0);
  50                 rdata = getRAbundVector(rank);
  51                 double numInd = (double)rdata.getNumSeqs();
  52                 double numSpec = (double)rdata.getNumBins();
  53
  54                 double sumExp = 0;
  55                 double sumObs = 0;
  56                 double maxDiff = 0;
  57
  58                 for(int i = 0; i < rdata.size(); i++)
  59                 {
  60                         sumObs += rdata.get(i);
  61                         sumExp += numInd/numSpec*invSum(i+1,numSpec);
  62                         double diff = fabs(sumObs-sumExp);
  63                         if(diff > maxDiff)
  64                                 maxDiff = diff;
  65                 }
  66
  67                 double DStatistic = maxDiff/numInd;
  68                 double critVal = 0;
  69                 /*cout << "BStick:\n";
  70                 cout << "D-Statistic = " << DStatistic << "\n";
  71                 cout << "Critical value for 95% confidence interval = ";*/
  72                 if(rdata.size() > 20)
  73                 {
  74                         critVal = .886/sqrt(rdata.size());
  75                 }
  76                 else
  77                 {
  78                         KOSTable table;
  79                         critVal = table.getConfLimit(numSpec);
  80                 }
  81                 /*cout << critVal << "\n";
  82                 cout << "If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n\n";*/
  83
  84                 data[0] = DStatistic;
  85                 data[1] = critVal;
  86                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  87                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  88
  89                 return data;
  90         }
  91         catch(exception& e) {
  92                 cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95         catch(...) {
  96                 cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99 }
 100
 101 /***********************************************************************/
 102
 103