biodyn: Biomass Dynamic Model

# #' plot(biodyn)
# #'
# #' Basic plot for biodyn.
# #' 
# #' @param probs numeric vector of probabilities with values in [0,1]. (Values up to 2e-14 outside that range are accepted and moved to the nearby endpoint.)
# #' @param na.rm logical; if true, any NA and NaN's are removed from x before the quantiles are computed.
# #' @param type an integer between 1 and 9 selecting one of the nine quantile algorithms detailed below to be used.
# #' @param worm iters
# #' @param fn list of functions
# #' @param facet facet for plots
# #'
# #' @aliases plot,biodyn,missing-method
# #' @rdname plot
# #' 
# #' @examples
# #' \dontrun{
# #'   bd=sim()
# #'   bd=fwd(bd,harvest=rlnorm(100,harvest(bd)[,-1]))
# #'   plot(bd)
# #'   }
# 
# setMethod("plot", signature(x="biodyn", y="missing"),
#       function(x, xlab="Year", ylab="", 
#                fn=list(Stock  =stock,
#                        Catch  =catch,
#                        Harvest=harvest),
#                probs=c(0.25,0.5,0.75),na.rm=TRUE,type=7,
#                rel=FALSE,...) {
#             
#           # extract info to plot
#           fqs = FLQuants(mlply(fn, function(fn) fn(x)))
#           
#           p <- plot(fqs,na.rm=na.rm,probs=probs,type=type)+
#             xlab(xlab)+ylab(ylab)
#             
#           return(p)})
# 
# #' plot(biodyns) 
# #' 
# #' plot() method for biodyns
# #'
# #' @param probs numeric vector of probabilities with values in [0,1]. (Values up to 2e-14 outside that range are accepted and moved to the nearby endpoint.)
# #' @param na.rm logical; if true, any NA and NaN's are removed from x before the quantiles are computed.
# #' @param type an integer between 1 and 9 selecting one of the nine quantile algorithms detailed below to be used.
# #' @param fn list of functions
# #' @param facet facet for plots
# #' 
# #' @aliases plot,biodyns,missing-method
# #' @rdname plot2
# #' 
# #' @examples
# #' \dontrun{
# #'   data(bd)
# #'   bds <- biodyns(runA=bd, runB=bd)
# #'   plot(bds)
# #'   }
# 
# setMethod("plot", signature(x="biodyns", y="missing"),
#           function(x, xlab="Year", ylab="", 
#                    fn=list(Stock  =stock,
#                            Catch  =catch,
#                            Harvest=harvest),
#                    probs=c(0.25,0.5,0.75),na.rm=TRUE,type=7,
#                    rel=FALSE,...) {
#             
#             cos <- c('red', 'blue')
#             
#             # extract slots by stock
#             fqs <- lapply(x, function(y) FLQuants(Stock=stock(y),
#                                                   Catch=catch(y), Harvest=fbar(y)))
#             
#             # get median & 85% quantiles if iters
#             its <- unlist(lapply(x, function(x) dims(x)$iter))
#             if(any(its > 1))
#             {
#               # quantiles
#               fqs <- lapply(fqs, function(y) as.data.frame(lapply(y, quantile,
#                                                                   c(0.10, 0.50, 0.90))))
#             } else {
#               fqs <- lapply(fqs, as.data.frame)
#               fqs <- lapply(fqs, function(x) {x$iter <- "50%"; return(x)})
#             }
#             
#             # stock names
#             stk <- rep.int(names(fqs), unlist(lapply(fqs, nrow)))
#             # rbind dfs
#             fqs <- do.call(rbind, fqs)
#             rownames(fqs) <- NULL
#             # add stock names
#             fqs <- transform(fqs, stock=stk)
#             
#             # cast with quantiles in columns
#             df <- dcast(fqs, age+year+unit+season+area+qname+stock~iter, value.var="data")
#             
#             # plot data vs. year + facet on qname +
#             p <- ggplot(data=df, aes(x=year, y=`50%`, group=stock)) +
#               facet_grid(qname~., scales="free") +
#               # line + xlab + ylab + limits to include 0 +
#               geom_line(aes(colour=stock)) + xlab(xlab) + ylab(ylab) + expand_limits(y=0) +
#               # no legend
#               theme(legend.title = element_blank())
#             
#             # object w/ iters?
#             if(any(unlist(lapply(x, function(y) dims(y)$iter)) > 1)) {
#               p <- p +
#                 # 75% quantile ribbon in red, alpha=0.25
#                 geom_ribbon(aes(x=year, ymin = `10%`, ymax = `90%`, group=stock,
#                                 colour=stock, fill=stock), alpha = .20, linetype = 0)
#               # 90% quantile ribbon in red, aplha=0.10
#             }
#             return(p)})