* Mothur
*
* Created by Thomas Ryabin on 3/6/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
sum += 1/(double)i;
return sum;
}
-
+/***********************************************************************/
RAbundVector BStick::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);
+ for(int i = rank->size()-1; i > 0; i--) {
+ double cur = rank->get(i);
if(mr == 1 && cur > 0)
mr = i;
nb += cur;
/***************************************************************************/
EstOutput BStick::getValues(SAbundVector* rank){
try {
- data.resize(2,0);
+ data.resize(3,0);
rdata = getRAbundVector(rank);
double numInd = (double)rdata.getNumSeqs();
double numSpec = (double)rdata.getNumBins();
double sumObs = 0;
double maxDiff = 0;
- for(int i = 0; i < rdata.size(); i++)
- {
+ for(int i = 0; i < rdata.size(); i++) {
sumObs += rdata.get(i);
sumExp += numInd/numSpec*invSum(i+1,numSpec);
double diff = fabs(sumObs-sumExp);
maxDiff = diff;
}
- double DStatistic = maxDiff/numInd;
- double critVal = 0;
- /*cout << "BStick:\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 Broken Stick model w/ 95% confidence.\n\n";*/
+
+ data[0] = maxDiff/numInd;
+ data[1] = 0.886/sqrt(rdata.size());
+ data[2] = 1.031/sqrt(rdata.size());
+
+ /*m->mothurOut(critVal); m->mothurOutEndLine();
+ m->mothurOut("If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n\n");*/
- data[0] = DStatistic;
- data[1] = critVal;
+
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, "BStick", "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);
- }
}
/***********************************************************************/