R/kobe-jabba.R

In laurieKell/kobe: Tools for Scientific Fisheries Management Advice

# library(FLCore)
# library(ggplotFL)
# library(kobe)
# 
# require(plyr)
# require(dplyr)
# require(reshape2)
# 
# 
# kobeJabba<-function(x,minyear=1){
#   
#   res=cbind(melt(x[,,2]),c(x[,,3]))
#   names(res)=c("iter","year","stock","harvest")
#   res$year=res$year+minyear-1
#   
#   res}
# 
# if (FALSE){
#   
#   kb=kobeJabba(trajectories,1950)
#   kobe:::kobePhaseMar3(subset(kb,year==2015))
# 
#   }
# 
# kobeJabbaProj<-function(x,minyear=1,tac=NULL){
#   
#   res=cbind(melt(x[,,,2]),c(x[,,,3]))
#   names(res)=c("iter","year","tac","stock","harvest")
#   res$year=res$year+minyear-1
#   
#   res}
# 
# if (FALSE){
#   
#   kbPrj=kobeJabbaProj(projections,2015)
#   kbPrj=transform(kbPrj,tac=seq(4000,16000,1000)[tac])
#   
#   stk=FLQuants(dlply(kbPrj,.(tac), with, as.FLQuant(data.frame(year=year,iter=iter,data=stock))))
#   p=plot(stk)$data
#   ggplot(p)+
#     geom_hline(aes(yintercept=1))+
#     geom_line(aes(year,`50%`,col=qname))+
#     xlab("Year")+ylab(expression(B/B[MSY]))+ 
#     labs(colour = "TAC")+
#     theme_bw()
#   
#   hvt=FLQuants(dlply(kbPrj,.(tac), with, as.FLQuant(data.frame(year=year,iter=iter,data=harvest))))
#   p=plot(hvt)$data
#   ggplot(p)+
#     geom_hline(aes(yintercept=1))+
#     geom_line(aes(year,`50%`,col=qname))+
#     xlab("Year")+ylab(expression(F/F[MSY]))+ 
#     labs(colour = "TAC")+
#     theme_bw()
#   
#   t.=ddply(kbPrj,.(year,tac), with, kobe:::smry(stock,harvest))
#   
#   k2smTab=list()
#   k2smTab[[1]]=cast(t.,tac~year,value="underFishing")
#   k2smTab[[2]]=cast(t.,tac~year,value="underFished")
#   k2smTab[[3]]=cast(t.,tac~year,value="green")
#   
# }
#   
#