modified some calculators and other stuff - pds

[mothur.git] / chao1.cpp

diff --git a/chao1.cpp b/chao1.cpp
index d938eb4ab71504f66f72eec2c91f9bfbb243a212..c05bdef2b7179a01f722cf497ab67f5b72ed7e3c 100644 (file)
--- a/chao1.cpp
+++ b/chao1.cpp
@@ -20,28 +20,34 @@ EstOutput Chao1::getValues(SAbundVector* rank){
                double doubles = (double)rank->get(2);
                double chaovar = 0.0000;
        
-               double chao = sobs + pow(singles,2)/(2*(doubles+1)) - (singles*doubles/(2*pow(doubles+1,2)));
+               double chao = sobs + singles*(singles-1)/(2*(doubles+1));
        
-               if(doubles==0){chaovar=0;}
-               else{
-                       double g=singles/doubles;
-                       chaovar = doubles*(0.25*pow(g,4)+pow(g,3)+0.5*pow(g,2));
+               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(chao==sobs){
-                       double ci = 1.96*pow(chaovar,0.5);
-                       chaolci = chao-ci;//chao lci
-                       chaohci = chao+ci;//chao hci
-               }
-               else{
+               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;