moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / simpson.cpp

diff --git a/simpson.cpp b/simpson.cpp
deleted file mode 100644 (file)
index edc35bd..0000000
--- a/simpson.cpp
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- *  simpson.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "simpson.h"
-
-/***********************************************************************/
-
-EstOutput Simpson::getValues(SAbundVector* rank){
-       try {
-               //vector<double> simpsonData(3,0);
-               data.resize(3,0);
-               double simpson = 0.0000;
-               double ci = 0;
-       
-               double maxRank = (double)rank->getMaxRank();
-               double sampled = (double)rank->getNumSeqs();
-               double sobs = (double)rank->getNumBins();
-       
-               double firstTerm = 0;
-               double secondTerm = 0;
-       
-               if(sobs != 0){
-                       double simnum=0.0000;
-               
-                       for(unsigned long long i=1;i<=maxRank;i++){
-                               simnum += (double)(rank->get(i)*i*(i-1));
-                       }
-                       
-                       simpson = simnum / (sampled*(sampled-1));
-               
-                       for(unsigned long long i=1;i<=maxRank;i++){
-                               double piI = (double) i / (double)sampled;
-                               firstTerm += rank->get(i) * pow(piI, 3);
-                               secondTerm += rank->get(i) * pow(piI, 2);
-                       }
-               
-                       double var = (4.0 / sampled) * (firstTerm - secondTerm*secondTerm);
-                       ci = 1.95 * pow(var, 0.5);
-               }
-       
-               double simpsonlci = simpson - ci;
-               double simpsonhci = simpson + ci;
-               
-               data[0] = simpson;
-               data[1] = simpsonlci;
-               data[2] = simpsonhci;
-               
-               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, "Simpson", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/