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/*
* sharedjackknife.cpp
* Mothur
*
* Created by Thomas Ryabin on 3/30/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "sharedjackknife.h"
/***************************************************************************************
***************************************************************************************/
double SharedJackknife::simpson(vector<int> abunds, double numInd, int numBins){
double denom = numInd*(numInd-1);
double sum = 0;
for(int i = 0; i < numBins; i++)
sum += (double)abunds[i]*((double)abunds[i]-1)/denom;
return sum;
}
/*****************************************************************************************/
double* SharedJackknife::jackknife(){
int numBins = groups.at(0)->getNumBins()-1;
vector<int> cArray(numBins);
for(int i = 0; i < numBins; i++)
cArray[i] = 0;
double numInd = 0;
for(int i = 0; i < numGroups; i++)
for(int j = 0; j < numBins; j++) {
int curAbund = groups.at(i)->get(j+1).abundance;
cArray[j] += curAbund;
numInd += (double)curAbund;
}
double baseD = 1/simpson(cArray, numInd, numBins);
vector<double> pseudoVals(numBins);
double jackknifeEstimate = 0;
for(int i = 0; i < numGroups; i++) {
for(int j = 0; j < numBins-1; j++) {
int abundDiff = -groups.at(i)->get(j+1).abundance;
if(i > 0)
abundDiff += groups.at(i-1)->get(j+1).abundance;
cArray[j] += abundDiff;
numInd += abundDiff;
}
double curD = 1/simpson(cArray, numInd, numBins);
pseudoVals[i] = (double)numGroups*(baseD - curD) + curD;
jackknifeEstimate += pseudoVals[i];
}
jackknifeEstimate /= (double)numGroups;
double variance = 0;
for(int i = 0; i < numGroups; i++)
variance += pow(pseudoVals[i]-jackknifeEstimate, 2);
variance /= (double)numGroups*((double)numGroups-1);
double stErr = sqrt(variance);
TDTable table;
double confLimit = 0;
if(numGroups <= 30)
confLimit = table.getConfLimit(numGroups-1, 1);
else
confLimit = 1.645;
confLimit *= stErr;
double* rdata = new double[3];
rdata[0] = baseD;
rdata[1] = jackknifeEstimate - confLimit;
rdata[2] = jackknifeEstimate + confLimit;
return rdata;
}
/************************************************************************************************
************************************************************************************************/
EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){ //Fix this for collect, mistake was that it was made with summary in mind.
try {
SharedRAbundVector* shared1 = vectorShared[0];
SharedRAbundVector* shared2 = vectorShared[1];
if(numGroups == -1) {
numGroups = m->getNumGroups();
}
if(callCount == numGroups*(numGroups-1)/2) {
currentCallDone = true;
callCount = 0;
}
callCount++;
if(currentCallDone) {
groups.clear();
currentCallDone = false;
}
if(groups.size() != numGroups) {
if(groups.size() == 0)
groups.push_back(shared1);
groups.push_back(shared2);
}
if(groups.size() == numGroups && callCount < numGroups) {
data.resize(3,0);
double* rdata = jackknife();
data[0] = rdata[0];
data[1] = rdata[1];
data[2] = rdata[2];
if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
if (isnan(data[2]) || isinf(data[0])) { data[2] = 0; }
return data;
}
data.resize(3,0);
data[0] = 0;
data[1] = 0;
data[2] = 0;
if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
return data;
}
catch(exception& e) {
m->errorOut(e, "SharedJackknife", "getValues");
exit(1);
}
}
/***********************************************************************/
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