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[mothur.git] / rarecalc.cpp

diff --git a/rarecalc.cpp b/rarecalc.cpp
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+/*
+ *  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);
+       }
+}
+
+/***********************************************************************/