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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);
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);
if(i > 0)
abundDiff += groups.at(i-1)->get(j+1);
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);
double confLimit = 0;
if(numGroups <= 30)
confLimit = 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;
}
/***********************************************************************/
double SharedJackknife::getConfLimit(int row, int col) //Rows are the degrees of freedom
{
//Found on http://www.vgtu.lt/leidiniai/elektroniniai/Probability.pdf/Table%203.pdf
//Confidence Level .90 .95 .975 .99 .995 .999 .9995
double values[30][7] = {{3.078, 6.314, 12.706, 31.821, 63.656, 318.289, 636.578},
{1.886, 2.920, 4.303, 6.965, 9.925, 22.328, 31.600},
{1.638, 2.353, 3.182, 4.541, 5.841, 10.214, 12.924},
{1.533, 2.132, 2.776, 3.747, 4.604, 7.173, 8.610},
{1.476, 2.015, 2.571, 3.365, 4.032, 5.894, 6.869},
{1.440, 1.943, 2.447, 3.143, 3.707, 5.208, 5.959},
{1.415, 1.895, 2.365, 2.998, 3.499, 4.785, 5.408},
{1.397, 1.860, 2.306, 2.896, 3.355, 4.501, 5.041},
{1.383, 1.833, 2.262, 2.821, 3.250, 4.297, 4.781},
{1.372, 1.812, 2.228, 2.764, 3.169, 4.144, 4.587},
{1.363, 1.796, 2.201, 2.718, 3.106, 4.025, 4.437},
{1.356, 1.782, 2.179, 2.681, 3.055, 3.930, 4.318},
{1.350, 1.771, 2.160, 2.650, 3.012, 3.852, 4.221},
{1.345, 1.761, 2.145, 2.624, 2.977, 3.787, 4.140},
{1.341, 1.753, 2.131, 2.602, 2.947, 3.733, 4.073},
{1.337, 1.746, 2.120, 2.583, 2.921, 3.686, 4.015},
{1.333, 1.740, 2.110, 2.567, 2.898, 3.646, 3.965},
{1.330, 1.734, 2.101, 2.552, 2.878, 3.610, 3.922},
{1.328, 1.729, 2.093, 2.539, 2.861, 3.579, 3.883},
{1.325, 1.725, 2.086, 2.528, 2.845, 3.552, 3.850},
{1.323, 1.721, 2.080, 2.518, 2.831, 3.527, 3.819},
{1.321, 1.717, 2.074, 2.508, 2.819, 3.505, 3.792},
{1.319, 1.714, 2.069, 2.500, 2.807, 3.485, 3.768},
{1.318, 1.711, 2.064, 2.492, 2.797, 3.467, 3.745},
{1.316, 1.708, 2.060, 2.485, 2.787, 3.450, 3.725},
{1.315, 1.706, 2.056, 2.479, 2.779, 3.435, 3.707},
{1.314, 1.703, 2.052, 2.473, 2.771, 3.421, 3.689},
{1.313, 1.701, 2.048, 2.467, 2.763, 3.408, 3.674},
{1.311, 1.699, 2.045, 2.462, 2.756, 3.396, 3.660},
{1.310, 1.697, 2.042, 2.457, 2.750, 3.385, 3.646}};
return values[row][col];
}
/***********************************************************************/
/************************************************************************************************/
EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){ //Fix this for collect, mistake was that it was made with summary in mind.
try {
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(vectorShared[0]);
groups.push_back(vectorShared[1]);
}
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];
delete[] rdata;
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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