X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=geom.cpp;h=5bd150ef7f8201254a392a52a7583b07b83e0b00;hp=8b484de49bcd27c772ead83f10cbf77aa14adf91;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=eb1c88346fb246e95a6b38935b103f95e38b82ca

diff --git a/geom.cpp b/geom.cpp
index 8b484de..5bd150e 100644
--- a/geom.cpp
+++ b/geom.cpp
@@ -3,12 +3,11 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 2/23/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "geom.h"
-#include "calculator.h"
 
 /***********************************************************************/
 
@@ -22,8 +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;
@@ -43,17 +41,16 @@ RAbundVector Geom::getRAbundVector(SAbundVector* rank){
 /***********************************************************************************/
 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
@@ -65,49 +62,33 @@ EstOutput Geom::getValues(SAbundVector* rank){
 		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);
-	}	
 }
 
 /***********************************************************************/