X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chao1.cpp;fp=chao1.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=ad1faa242b81c1520d29fb6395fa5f5825d179ec;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/chao1.cpp b/chao1.cpp
deleted file mode 100644
index ad1faa2..0000000
--- a/chao1.cpp
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- *  chao1.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "chao1.h"
-
-/***********************************************************************/
-EstOutput Chao1::getValues(SAbundVector* rank){
-	try {
-		data.resize(3,0);
-	
-		double sobs = (double)rank->getNumBins();
-		
-		//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));
-	
-		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(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;
-		data[2] = chaohci;
-
-	    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) {
-		m->errorOut(e, "Chao1", "getValues");
-		exit(1);
-	}
-}
-
-/***********************************************************************/