X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chao1.cpp;h=d7ec7ea7015da078452562bd526d56944d590560;hp=d938eb4ab71504f66f72eec2c91f9bfbb243a212;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/chao1.cpp b/chao1.cpp
index d938eb4..d7ec7ea 100644
--- a/chao1.cpp
+++ b/chao1.cpp
@@ -15,33 +15,49 @@ EstOutput Chao1::getValues(SAbundVector* rank){
 		data.resize(3,0);
 	
 		double sobs = (double)rank->getNumBins();
-	
-		double singles = (double)rank->get(1);
-		double doubles = (double)rank->get(2);
+		
+		//this is a modification do to a vector fill error that occurs when an empty sharedRabund creates a sabund
+		//in that case there is no 1 0r 2.
+		double singles;
+		if (rank->size() > 1) {
+			singles = (double)rank->get(1);
+		}else{ singles = 0.0;  }
+
+		double doubles;
+		if (rank->size() > 2) {
+			 doubles = (double)rank->get(2);
+		}else{ doubles = 0.0;  }
+
 		double chaovar = 0.0000;
+//cout << "singles = " << singles << " doubles = " << doubles << " sobs = " << sobs << endl;
+		double chao = sobs + singles*(singles-1)/(2*(doubles+1));
 	
-		double chao = sobs + pow(singles,2)/(2*(doubles+1)) - (singles*doubles/(2*pow(doubles+1,2)));
-	
-		if(doubles==0){chaovar=0;}
-		else{
-			double g=singles/doubles;
-			chaovar = doubles*(0.25*pow(g,4)+pow(g,3)+0.5*pow(g,2));
+		if(singles > 0 && doubles > 0){
+			chaovar = singles*(singles-1)/(2*(doubles+1))
+					+ singles*pow(2*singles-1, 2)/(4*pow(doubles+1,2))
+					+ pow(singles, 2)*doubles*pow(singles-1, 2)/(4*pow(doubles+1,4));
 		}
-
-	
+		else if(singles > 0 && doubles == 0){
+			chaovar = singles*(singles-1)/2 + singles*pow(2*singles-1, 2)/4 - pow(singles, 4)/(4*chao); 
+		}
+		else if(singles == 0){
+			chaovar = sobs*exp(-1*rank->getNumSeqs()/sobs)*(1-exp(-1*rank->getNumSeqs()/sobs));
+		}
+			
 		double chaohci, chaolci;
 	
-		if(chao==sobs){
-			double ci = 1.96*pow(chaovar,0.5);
-			chaolci = chao-ci;//chao lci
-			chaohci = chao+ci;//chao hci
-		}
-		else{
+		if(singles>0){
 			double denom = pow(chao-sobs,2);
 			double c = exp(1.96*pow((log(1+chaovar/denom)),0.5));
 			chaolci = sobs+(chao-sobs)/c;//chao lci
 			chaohci = sobs+(chao-sobs)*c;//chao hci
 		}
+		else{
+			double p = exp(-1*rank->getNumSeqs()/sobs);
+			chaolci = sobs/(1-p)-1.96*pow(sobs*p/(1-p), 0.5);
+			chaohci = sobs/(1-p)+1.96*pow(sobs*p/(1-p), 0.5);
+			if(chaolci < sobs){	chaolci = sobs;	}
+		}
 		
 		data[0] = chao;
 		data[1] = chaolci;
@@ -54,13 +70,9 @@ EstOutput Chao1::getValues(SAbundVector* rank){
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Chao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Chao1", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Chao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-};
+}
 
 /***********************************************************************/