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/*
* geom.cpp
* Mothur
*
* Created by Thomas Ryabin on 2/23/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "geom.h"
/***********************************************************************/
double Geom::kEq(double k, double spec){
return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
}
RAbundVector Geom::getRAbundVector(SAbundVector* rank){
vector <int> rData;
int mr = 1;
int nb = 0;
int ns = 0;
for(int i = rank->size()-1; i > 0; i--) {
int cur = rank->get(i);
if(mr == 1 && cur > 0)
mr = i;
nb += cur;
ns += i*cur;
for(int j = 0; j < cur; j++)
rData.push_back(i);
}
RAbundVector rav = RAbundVector(rData, mr, nb, ns);
rav.setLabel(rank->getLabel());
return rav;
}
/***********************************************************************************/
/***********************************************************************************/
EstOutput Geom::getValues(SAbundVector* rank){
try {
data.resize(3,0);
rdata = getRAbundVector(rank);
double numInd = rdata.getNumSeqs();
double numSpec = rdata.getNumBins();
double min = rdata.get(rdata.size()-1);
double k = .5;
double step = .49999;
while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) { //This uses a binary search to find the value of k.
if(numInd*kEq(k, numSpec) > min)
k += step;
else
k -= step;
step /= 2;
}
double cK = 1/(1-pow(1-k, numSpec));
double sumExp = 0;
double sumObs = 0;
double maxDiff = 0;
for(int i = 0; i < numSpec; i++)
{
sumObs += rdata.get(i);
sumExp += numInd*cK*k*pow(1-k, i);
double diff = fabs(sumObs-sumExp);
if(diff > maxDiff) { maxDiff = diff; }
}
data[0] = maxDiff/numInd;
data[1] = 0.886/sqrt(numSpec);
data[2] = 1.031/sqrt(numSpec);
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, "Geom", "getValues");
exit(1);
}
}
/***********************************************************************/
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