X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=geom.cpp;h=5bd150ef7f8201254a392a52a7583b07b83e0b00;hp=31580db15b7bbb08b648cd10ff3c0bcf4cd98a10;hb=615301e57c25e241356a9c2380648d117709458d;hpb=e4827e0945cbda536064e5a345996b2a7dfcbb81

diff --git a/geom.cpp b/geom.cpp
index 31580db..5bd150e 100644
--- a/geom.cpp
+++ b/geom.cpp
@@ -21,8 +21,7 @@ RAbundVector Geom::getRAbundVector(SAbundVector* rank){
 		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;
@@ -45,14 +44,13 @@ EstOutput Geom::getValues(SAbundVector* rank){
 		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
@@ -75,25 +73,11 @@ EstOutput Geom::getValues(SAbundVector* rank){
 			
 		}
 
-		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)
-		{
-			data[1] = 1.031/sqrt(rdata.size());
-			data[2] = 0.886/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[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; }
@@ -102,13 +86,9 @@ EstOutput Geom::getValues(SAbundVector* rank){
 		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);
-	}	
 }
 
 /***********************************************************************/