biodyn: Biomass Dynamic Model

# as.mcmc.rjags <- function (x) {
#   x <- x$BUGSoutput
#   if (x$n.chains > 1) {
#     z <- list()
#     for (i in 1:x$n.chains) {
#       z[[i]] <- mcmc(x$sims.array[, i, ], start = 1, thin = x$n.thin)
#     }
#     class(z) <- 'mcmc.list'
#   }
#   else {
#     z <- mcmc(x$sims.matrix, start = 1, thin = x$n.thin)
#   }
#   return(z)
# }
# 
# setGeneric('k'                    ,function(object, ...)  standardGeneric('k'))            
# # setGeneric('r'                    ,function(object, ...)  standardGeneric('r'))            
# setGeneric('x'                    ,function(object, ...)  standardGeneric('x'))            
# setGeneric('q'                    ,function(object, ...)  standardGeneric('q'))            
# setGeneric('sigmaosq'             ,function(object, ...)  standardGeneric('sigmaosq'))            
# setGeneric('sigmapsq'             ,function(object, ...)  standardGeneric('sigmapsq'))            
# setGeneric('h'                    ,function(object, ...)  standardGeneric('h'))            
# # setGeneric('m'                    ,function(object, ...)  standardGeneric('m'))            
# setGeneric('g'                    ,function(object, ...)  standardGeneric('g'))             
# # setGeneric('stock'                ,function(object, ...)  standardGeneric('stock'))            
# setGeneric('depletion'            ,function(object, ...)  standardGeneric('depletion'))           
# # setGeneric('harvest'              ,function(object, ...)  standardGeneric('harvest_rate'))       
# setGeneric('sp'                   ,function(object, ...)  standardGeneric('sp')) 
# setGeneric('epsilonO'             ,function(object, ...)  standardGeneric('epsilon_o'))   
# setGeneric('epsilonP'             ,function(object, ...)  standardGeneric('epsilon_p'))  
# setGeneric('current_biomass'      ,function(object, ...)  standardGeneric('current_biomass'))    
# setGeneric('current_depletion'    ,function(object, ...)  standardGeneric('current_depletion'))  
# setGeneric('current_harvest_rate' ,function(object, ...)  standardGeneric('current_harvest_rate'))
# # setGeneric('bmsy'                 ,function(object, ...)  standardGeneric('bmsy'))
# # setGeneric('fmsy'                 ,function(object, ...)  standardGeneric('fmsy'))
# # setGeneric('msy'                  ,function(object, ...)  standardGeneric('msy'))
# # setGeneric('dmsy'                 ,function(object, ...)  standardGeneric('dmsy'))            
# # setGeneric('index'                ,function(object, ...)  standardGeneric('index'))
# # setGeneric('indexHat'             ,function(object, ...)  standardGeneric('indexHat'))
# # setGeneric('lp'                   ,function(object, ...)  standardGeneric('lp'))
#           
# setMethod('k'                    ,signature=c('bdm'), function(object) exp(object@trace$logK))             
# setMethod('r'                    ,signature=c('bdm','missing'), function(m) m@trace$r)             
# setMethod('x'                    ,signature=c('bdm'), function(object) object@trace$x)             
# setMethod('q'                    ,signature=c('bdm'), function(object) object@trace$q)            
# setMethod('sigmaosq'             ,signature=c('bdm'), function(object) object@trace$sigmaosq)             
# setMethod('sigmapsq'             ,signature=c('bdm'), function(object) object@trace$sigmaosq)            
# setMethod('h'                    ,signature=c('bdm'), function(object) object@trace$h)            
# setMethod('m'                    ,signature=c('bdm'), function(object) object@trace$m)             
# setMethod('g'                    ,signature=c('bdm'), function(object) object@trace$g)             
# setMethod('stock'                ,signature=c('bdm'), function(object) object@trace$biomass)             
# setMethod('depletion'            ,signature=c('bdm'), function(object) object@trace$depletion)           
# setMethod('harvest'              ,signature=c('bdm'), function(object) object@trace$harvest_rate)        
# setMethod('sp'                   ,signature=c('bdm'), function(object) object@trace$surplus_production)  
# setMethod('epsilonO'             ,signature=c('bdm'), function(object) object@trace$epsilon_o)    
# setMethod('epsilonP'             ,signature=c('bdm'), function(object) object@trace$epsilon_p)   
# setMethod('current_biomass'      ,signature=c('bdm'), function(object) object@trace$current_biomass)    
# setMethod('current_depletion'    ,signature=c('bdm'), function(object) object@trace$current_depletion)   
# setMethod('current_harvest_rate' ,signature=c('bdm'), function(object) object@trace$current_harvest_rate)
# setMethod('bmsy'                 ,signature=c('bdm'), function(object) object@trace$biomass_at_msy)
# setMethod('fmsy'                 ,signature=c('bdm'), function(object) object@trace$harvest_rate_at_msy)
# setMethod('msy'                  ,signature=c('bdm'), function(object) fmsy(object)/bmsy(object))
# setMethod('dmsy'                 ,signature=c('bdm'), function(object) object@trace$dmsy)            
# 
# setMethod('index'                ,signature=c('bdm'), function(object) object@trace$observed_index)
# setMethod('indexHat'             ,signature=c('bdm'), function(object) object@trace$predicted_index)
# setMethod('lp'                   ,signature=c('bdm'), function(object) object@trace$lp__)