to_add_to_pkg/SSB and r quantiles.r

In CCSBT/sbtr: sbtr

#####################################################
#Boxplots for spawning biomass
#Note: these are not revisited from the 2000 grid, these are the 
#values from the 320 scenarios
#There will be  switch to go from one to the other using the .lev
#file
#####################################################

plot.SSB.r.quantplots <- function(objects, label="", type=c("obj","grid")) {
   #type="obj" just do this for the 320 cells with no resampling
   #type="grid" resample from the grid to get the 2000 cells
   
   type <- type[1]  
   par(mfrow=c(2,1),oma=c(5,0,3,1),mar=c(0,5,1,0))
   nobjects <- length(objects) 
   
   nssb <- length(objects[[1]]$Sbio)
   #print(nssb)
   years <- c(objects[[1]]$years[1]:(objects[[1]]$years[2]+1))
   #print(length(years))
   depl <- matrix(nrow=nobjects, ncol=nssb)
   for (i in 1:nobjects) {
      x <- objects[[i]]
      depl[i,] <- x$Sbio/x$Sbio[1]   #since first element is SSB0
   }
   quants <- apply(depl,MARGIN=2,quantile,c(0.05,0.5,0.95))
   #print(dim(quants))
   plot(x=years,y=quants[2,],type="l", ylim=c(0,1.1*max(quants)), col="black",
        lwd=2,xaxt="n",lty=1, yaxs="i", xaxs="i", las=1, ylab="Spawning biomass / unexpl", xlab="Years")
   lines(x=years,y=quants[1,],ylim=c(0,1.2*max(quants)), col="black",
         lwd=1,lty=2)
   lines(x=years,y=quants[3,],ylim=c(0,1.2*max(quants)), col="black",
         lwd=1,lty=2)
   mtext(side=3,line=1,label,cex=1.2, outer=F)
   
   #=========now plot the recruitment
   nssb <- length(objects[[1]]$Recruitment)
   #print(nssb)
   years <- c(objects[[1]]$years[1]:(objects[[1]]$years[2]+1))
   #print(length(years))
   depl <- matrix(nrow=nobjects, ncol=nssb)
   for (i in 1:nobjects) {
      x <- objects[[i]]
      depl[i,] <- x$Recruitment/x$Recruitment[1]   #since first element is SSB0
   }
   Rquants <- apply(depl,MARGIN=2,quantile,c(0.05,0.5,0.95))
   #print(dim(Rquants))
   plot(x=years,y=Rquants[2,],type="l", ylim=c(0,1.1*max(Rquants)), col="black",
        lwd=2,lty=1, yaxs="i", xaxs="i", las=1, ylab="Recruitment / unexpl", xlab="Years")
   lines(x=years,y=Rquants[1,],ylim=c(0,1.2*max(Rquants)), col="black",
         lwd=1,lty=2)
   lines(x=years,y=Rquants[3,],ylim=c(0,1.2*max(Rquants)), col="black",
         lwd=1,lty=2)
   
   invisible(list(SSBquants=quants, Rquants=Rquants))
}
#source("get.all.files.r")
#data.base.NS <- get.all.files("arc\\base2010sqrtns")