sharedjackknife.cpp

   1 /*
   2  *  sharedjackknife.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 3/30/09.
   6  *  Copyright 2009 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedjackknife.h"
  11
  12 /***************************************************************************************
  13
  14 ***************************************************************************************/
  15 double SharedJackknife::simpson(int abunds[], double numInd, int numBins){
  16         double denom = numInd*(numInd-1);
  17         double sum = 0;
  18         for(int i = 0; i < numBins; i++)
  19                 sum += (double)abunds[i]*((double)abunds[i]-1)/denom;
  20
  21         return sum;
  22 }
  23
  24 /*****************************************************************************************/
  25
  26 double* SharedJackknife::jackknife(){
  27         int numBins = groups.at(0)->getNumBins()-1;
  28         int cArray[numBins];
  29         for(int i = 0; i < numBins; i++)
  30                 cArray[i] = 0;
  31
  32         double numInd = 0;
  33         for(int i = 0; i < numGroups; i++)
  34                 for(int j = 0; j < numBins; j++) {
  35                         int curAbund = groups.at(i)->get(j+1).abundance;
  36                         cArray[j] += curAbund;
  37                         numInd += (double)curAbund;
  38                 }
  39
  40         double baseD = 1/simpson(cArray, numInd, numBins);
  41
  42         double pseudoVals[numBins];
  43         double jackknifeEstimate = 0;
  44         for(int i = 0; i < numGroups; i++) {
  45                 for(int j = 0; j < numBins-1; j++) {
  46                         int abundDiff = -groups.at(i)->get(j+1).abundance;
  47                         if(i > 0)
  48                                 abundDiff += groups.at(i-1)->get(j+1).abundance;
  49
  50                         cArray[j] += abundDiff;
  51                         numInd += abundDiff;
  52                 }
  53
  54                 double curD = 1/simpson(cArray, numInd, numBins);
  55                 pseudoVals[i] = (double)numGroups*(baseD - curD) + curD;
  56                 jackknifeEstimate += pseudoVals[i];
  57         }
  58         jackknifeEstimate /= (double)numGroups;
  59
  60         double variance = 0;
  61         for(int i = 0; i < numGroups; i++)
  62                 variance += pow(pseudoVals[i]-jackknifeEstimate, 2);
  63
  64         variance /= (double)numGroups*((double)numGroups-1);
  65         double stErr = sqrt(variance);
  66         TDTable table;
  67         double confLimit = 0;
  68         if(numGroups <= 30)
  69                 confLimit = table.getConfLimit(numGroups-1, 1);
  70         else
  71                 confLimit = 1.645;
  72
  73         confLimit *= stErr;
  74
  75         double* rdata = new double[3];
  76         rdata[0] = baseD;
  77         rdata[1] = jackknifeEstimate - confLimit;
  78         rdata[2] = jackknifeEstimate + confLimit;
  79
  80         return rdata;
  81 }
  82
  83 /************************************************************************************************
  84 ************************************************************************************************/
  85
  86 EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){ //Fix this for collect, mistake was that it was made with summary in mind.
  87         try {
  88                 SharedRAbundVector* shared1 = vectorShared[0];
  89                 SharedRAbundVector* shared2 = vectorShared[1];
  90                 if(numGroups == -1) {
  91                         globaldata = GlobalData::getInstance();
  92                         numGroups = globaldata->Groups.size();
  93                 }
  94
  95                 if(callCount == numGroups*(numGroups-1)/2) {
  96                         currentCallDone = true;
  97                         callCount = 0;
  98                 }
  99                 callCount++;
 100
 101                 if(currentCallDone) {
 102                         groups.clear();
 103                         currentCallDone = false;
 104                 }
 105
 106                 if(groups.size() != numGroups) {
 107                         if(groups.size() == 0)
 108                                 groups.push_back(shared1);
 109                         groups.push_back(shared2);
 110                 }
 111
 112                 if(groups.size() == numGroups && callCount < numGroups) {
 113                         data.resize(3,0);
 114
 115                         double* rdata = jackknife();
 116                         data[0] = rdata[0];
 117                         data[1] = rdata[1];
 118                         data[2] = rdata[2];
 119
 120                         //cout << "sT = " << data[0] << "    lower confLimit = " << data[1] << "     upper confLimit = " << data[2] << "\n";
 121                         if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 122                         if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
 123                         if (isnan(data[2]) || isinf(data[0])) { data[2] = 0; }
 124
 125                         /*for(int i = 0; i < groups.size(); i++)
 126                                 cout << groups.at(i)->getGroup() << " ";
 127                         cout << "\n";
 128                         cout << groups.size() << "     " << data[0] << "    " << data[1] << "     " << data[2] << "\n\n";*/
 129
 130                         return data;
 131                 }
 132
 133                 data.resize(3,0);
 134                 data[0] = 0;
 135                 data[1] = 0;
 136                 data[2] = 0;
 137
 138                 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 139                 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
 140                 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
 141                 return data;
 142         }
 143
 144         catch(exception& e) {
 145                 cout << "Standard Error: " << e.what() << " has occurred in the SharedJackknife class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148         catch(...) {
 149                 cout << "An unknown error has occurred in the SharedJackknife class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 150                 exit(1);
 151         }
 152 }
 153
 154 /***********************************************************************/
 155