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                         double cur = rank->get(i);
  30                         if(mr == 1 && cur > 0)
  31                                 mr = i;
  32                         nb += cur;
  33                         ns += i*cur;
  34                         for(int j = 0; j < cur; j++)
  35                                 rData.push_back(i);
  36                 }
  37
  38                 RAbundVector rav = RAbundVector(rData, mr, nb, ns);
  39                 rav.setLabel(rank->getLabel());
  40                 return rav;
  41 }
  42
  43 /***************************************************************************/
  44
  45 /***************************************************************************/
  46 EstOutput BStick::getValues(SAbundVector* rank){
  47         try {
  48                 data.resize(3,0);
  49                 rdata = getRAbundVector(rank);
  50                 double numInd = (double)rdata.getNumSeqs();
  51                 double numSpec = (double)rdata.getNumBins();
  52
  53                 double sumExp = 0;
  54                 double sumObs = 0;
  55                 double maxDiff = 0;
  56
  57                 for(int i = 0; i < rdata.size(); i++) {
  58                         sumObs += rdata.get(i);
  59                         sumExp += numInd/numSpec*invSum(i+1,numSpec);
  60                         double diff = fabs(sumObs-sumExp);
  61                         if(diff > maxDiff)
  62                                 maxDiff = diff;
  63                 }
  64
  65
  66                 data[0] = maxDiff/numInd;
  67                 data[1] = 0.886/sqrt(rdata.size());
  68                 data[2] = 1.031/sqrt(rdata.size());
  69
  70                 /*m->mothurOut(critVal); m->mothurOutEndLine();
  71                 m->mothurOut("If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n");*/
  72
  73
  74                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
  75                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
  76                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
  77
  78                 return data;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "BStick", "getValues");
  82                 exit(1);
  83         }
  84 }
  85
  86 /***********************************************************************/
  87
  88