X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=logsd.cpp;h=62faf8eab68c726f9499451ec3207fc66ae2cbd2;hb=30b3ffcd1cfd08e7144ae721bb53e27eb3f7a5d1;hp=14d2e442fa2bea0a6e153dc310b59d687b51b642;hpb=e4827e0945cbda536064e5a345996b2a7dfcbb81;p=mothur.git

diff --git a/logsd.cpp b/logsd.cpp
index 14d2e44..62faf8e 100644
--- a/logsd.cpp
+++ b/logsd.cpp
@@ -35,8 +35,7 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		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
@@ -51,15 +50,12 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		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 +64,7 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 				oct++;
 			}
 	
-			if(y == rank->size()-1)
-			{
+			if(y == rank->size()-1) {
 				sumObs += octSumObs;
 				sumExp += octSumExp;
 			}
@@ -78,27 +73,21 @@ 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";
+		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);
-	}	
 }
 
 /***********************************************************************/