X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarecalc.cpp;fp=rarecalc.cpp;h=9145061255d415eb7a48749bdbaaa405b78425fd;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/rarecalc.cpp b/rarecalc.cpp
new file mode 100644
index 0000000..9145061
--- /dev/null
+++ b/rarecalc.cpp
@@ -0,0 +1,53 @@
+/*
+ *  rarecalc.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "rarecalc.h"
+
+/***********************************************************************/
+
+EstOutput RareCalc::getValues(int n){
+	try {
+		EstOutput output(3,0);
+
+		double richness = (double)numBins;
+		double varS = 0.0000;
+	
+		double varTerm1 = 0.0000;
+		double varTerm2 = 0.0000;
+	
+		double rSummation = 0;
+		for(int i=0;i<numBins;i++){
+			int N_ni = numSeqs - bins->get(i);
+			rSummation += (bMatrix[N_ni][n]);
+		
+			varTerm1 += (bMatrix[N_ni][n] * (1.0 - bMatrix[N_ni][n] / bMatrix[numSeqs][n]));
+
+			for(int j=i+1;j<numBins;j++){
+				varTerm2 += ( bMatrix[N_ni-bins->get(j)][n] - bMatrix[N_ni][n] * bMatrix[numSeqs-bins->get(j)][n] / bMatrix[numSeqs][n]);
+			}
+		
+		}
+		richness -= (rSummation / bMatrix[numSeqs][n]);
+		varS = (varTerm1 + 2 * varTerm2) / bMatrix[numSeqs][n];
+		float sd = pow(varS, 0.5);
+	
+
+		output[0] = richness;
+		output[1] = richness - 1.96 * sd;	
+		output[2] = richness + 1.96 * sd;
+	
+		return output;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareCalc", "getValues");
+		exit(1);
+	}
+}
+
+/***********************************************************************/