X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=logsd.cpp;h=6a795415d832f265325138422f48d77afe3315be;hp=fddee4f5e94e977bd417e0d32a82f6f37894d232;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445

diff --git a/logsd.cpp b/logsd.cpp
index fddee4f..6a79541 100644
--- a/logsd.cpp
+++ b/logsd.cpp
@@ -14,6 +14,7 @@
 double LogSD::logS(double x){
 	return -(1-x)*log(1-x)/x;
 }
+/***********************************************************************/
 EstOutput LogSD::getValues(SAbundVector* rank){
 	try {
 		
@@ -28,15 +29,14 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		SAbundVector rankw = SAbundVector(dvec, mr,nb,ns);
 		SAbundVector *rank = &rankw;*/
 		
-		data.resize(2,0);
-		int numInd = rank->getNumSeqs();
-		int numSpec = rank->getNumBins();
+		data.resize(3,0);
+		double numInd = rank->getNumSeqs();
+		double numSpec = rank->getNumBins();
 		double snRatio = (double)numSpec/numInd;
 		double x = .5;
 		double step = .4999999999;
 		
-		while(fabs(snRatio - logS(x)) > .00001) //This uses a binary search to find the value of x.
-		{
+		while(fabs(snRatio - logS(x)) > .00001) { //This uses a binary search to find the value of x.
 			if(logS(x) > snRatio)
 				x += step;
 			else
@@ -45,21 +45,18 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		}
 		double alpha = numInd*(1-x)/x;
 
-		int oct = 1;
+		double oct = 1;
 		double octSumObs = 0;
 		double sumObs = 0;
 		double octSumExp = 0;
 		double sumExp = 0;
 		double maxDiff = 0;
-		for(int y = 1; y < rank->size(); y++)
-		{
-			if(y - .5 < pow(2.0, oct))
-			{
+		for(int y = 1; y < rank->size(); y++) {
+			if(y - .5 < pow(2.0, oct)) {
 				octSumObs += rank->get(y);
 				octSumExp += alpha*pow(x,y)/(y);
 			}	
-			else
-			{
+			else {
 				sumObs += octSumObs;
 				octSumObs = rank->get(y);
 
@@ -68,8 +65,7 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 				oct++;
 			}
 	
-			if(y == rank->size()-1)
-			{
+			if(y == rank->size()-1) {
 				sumObs += octSumObs;
 				sumExp += octSumExp;
 			}
@@ -78,27 +74,21 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 			if(diff > maxDiff)
 				maxDiff = diff;
 		}
+
+		data[0] = (maxDiff + .5)/numSpec;
+		data[1] = 0.886/sqrt(numSpec);
+		data[2] = 1.031/sqrt(numSpec);
 		
-		double DStatistic = (maxDiff + .5)/numSpec;
-		/*cout << "LogSD:\n";
-		cout << "D Test Statistic = " << DStatistic << "\n";
-		cout << ".05 confidence value = " << .89196/sqrt(numSpec) << "\n";
-		cout << "If D Test Statistic is greater than the critical value then the data fits the Log Series Distribution model w/ 95% confidence.\n\n";*/
-		
-		data[0] = DStatistic;
-		data[1] = .89196/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, "LogSD", "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);
-	}	
 }
 
 /***********************************************************************/