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

[mothur.git] / chao1.cpp

diff --git a/chao1.cpp b/chao1.cpp
deleted file mode 100644 (file)
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);
-       }
-}
-
-/***********************************************************************/