int nb = 0;
int ns = 0;
- for(int i = rank->size()-1; i > 0; i--)
- {
+ for(int i = rank->size()-1; i > 0; i--) {
int cur = rank->get(i);
if(mr == 1 && cur > 0)
mr = i;
/***********************************************************************************/
EstOutput Geom::getValues(SAbundVector* rank){
try {
- data.resize(2,0);
+ data.resize(3,0);
rdata = getRAbundVector(rank);
- int numInd = rdata.getNumSeqs();
- int numSpec = rdata.getNumBins();
- int min = rdata.get(rdata.size()-1);
+ 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.
- {
+ 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
double sumExp = 0;
double sumObs = 0;
double maxDiff = 0;
-
- for(int i = 0; i < rdata.size(); i++)
+
+ 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;
+ if(diff > maxDiff) { maxDiff = diff; }
+
}
- double DStatistic = maxDiff/numInd;
- double critVal = 0;
- /*cout << "Geom:\n";
- cout << "D-Statistic = " << DStatistic << "\n";
- cout << "Critical value for 95% confidence interval = ";*/
- if(rdata.size() > 20)
- {
- critVal = .886/sqrt(rdata.size());
- }
- else
- {
- KOSTable table;
- critVal = table.getConfLimit(numSpec);
- }
- /*cout << critVal << "\n";
- cout << "If D-Statistic is less than the critical value then the data fits the Geometric Series model w/ 95% confidence.\n\n";*/
-
- data[0] = DStatistic;
- data[1] = critVal;
+
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Geom", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************************/