R/Gst.est.r

In DEMEtics: Evaluating the genetic differentiation between populations based on Gst and D values.

Gst.est<-function(Hs,Ht,values){

#Variables
#------------------------------------------------------------------------------------------------------------------------------
# Input:
#           Hs,Ht,values <- Gst.est.calc();
#------------------------------------------------------------------------------------------------------------------------------  

          # A function that calculates the Gst.est value.
          # The arguments are the Hs-value, the Ht-value and the vector 'values'
          # (a vector that contains the number of individuals that have been 
          # sampled from each population - the sample sizes).
          
          # The Hs- and Ht-values can be calculated by the functions 'Hs()' and 'Ht()'.
           
          # See: Jost L. (2008). Gst and its relatives do not measure differentiation. 
          # Molecular Ecology 17,4015-4026.

          n<-length(values)

                    # n is the number of populations that have been sampled.
                    

                                  
                    # The harmonic mean is calculated from the sample sizes...

          N<-harmonic(values,n)
                                  
                    # ... and ascribed to the variable N.

          
          Hs.est<-Hs.est(Hs,N)
          
                    # The Hs.est values are calculated and ascribed to the variable 'Hs.est'.
                    # See: Jost L. (2008). Gst and its relatives do not measure differentiation. 
                    # Molecular Ecology 17,4015-4026.  


                                    
          Ht.est<-Ht.est(Ht,Hs.est,N,n)
          
                    # The Ht.est values are calculated and ascribed to the variable 'Ht.est'.
                    # See: Jost L. (2008). Gst and its relatives do not measure differentiation. 
                    # Molecular Ecology 17,4015-4026. 

          (Ht.est-Hs.est)/Ht.est
          
                    # Out of Ht.est, Hs.est and n, the Gst value is calculated.                                      
                       
          }