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06_figures.r
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06_figures.r
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#-------------------------------------------------------------------------------
# WKHERMPII
#
# Author: Niels Hintzen
# IMARES, The Netherland
#
# Performs an MSE of North Sea Herring under different TAC scenario's
#
# Date: 03-Oct-2011
#
# Build for R2.8.1
#-------------------------------------------------------------------------------
rm(list=ls())
library(FLCore)
library(FLAssess)
library(FLSAM)
library(MASS)
library(msm)
wine <- F
path <- "W:/IMARES/Data/ICES-WG/WKMACLTMP/"
inPath <- "W:/IMARES/Data/ICES-WG/WKMACLTMP/Data/"
codePath <- "W:/IMARES/Data/ICES-WG/WKMACLTMP/R code/"
outPath <- "W:/IMARES/Data/ICES-WG/WKMACLTMP/Results/"
plotPath <- "W:/IMARES/Data/ICES-WG/WKMACLTMP/Results/Plots input/"
if(substr(R.Version()$os,1,3)== "lin"){
path <- sub("W:/","/media/n/",path)
inPath <- sub("W:/","/media/n/",inPath)
codePath <- sub("W:/","/media/n/",codePath)
outPath <- sub("W:/","/media/n/",outPath)
}
home<-F
if(home)
{
path <- "D://MSE/"
inPath <- "D://MSE/Data/"
codePath <- "D://MSE/R code/"
outPath <- "D://MSE/Results/"
}
perm<-T
if (perm)cat("!!! scenario with permanent changes")
if (perm) outPathp <- paste(outPath,"perm",sep="")
#- Load objects
load(file=paste(outPath,"Mac.RData", sep=""))
load(file=paste(outPath,"Macctrl.RData", sep=""))
load(file=paste(outPathp,"biol.RData", sep=""))
load(file=paste(outPathp,"fishery.RData", sep=""))
load(file=paste(outPath,"propN.RData", sep=""))
load(file=paste(outPath,"propWt.RData", sep=""))
load(file=paste(outPath,"ctch.RData", sep=""))
load(file=paste(outPath,"surveys.RData", sep=""))
load(file=paste(outPathp,"stocks.RData", sep=""))
load(file=paste(outPath,"settings.RData", sep=""))
#load(file=paste(outPath,"resNFinal_1000.RData", sep=""))
#load(file=paste(outPath,"resFFinal_1000.RData", sep=""))
load(file=paste(outPath,"SRmod.RData", sep=""))
for(i in 1:length(settings)) assign(x=names(settings)[i],value=settings[[i]])
source(paste(codePath,"functions.r", sep=""))
source(paste(codePath,"04_forecastScenarios.r", sep=""))
RecType<-settings$RecType
projPeriod<-ac(2014:2042)
scen <- c("LTMP2.4mt") #
opt <- 7 # for multiple scenario combinations a counter
TACvarlim <- T # whether or not to apply the 20% limit on TAC change
Fvarlim <- T # whether or not to apply the 10% limit on Fbar change
BBscen <- "noBB" # banking borrowing options :
# "Banking" : always bank
# "Borrowing" : always borrow
# "AlternateBank" : bank first and then alternate
# "AlternateBorrow" : borrow first and then alternate
# "MinVar" : use BB to minise TAC variability
LastRecOp <- "geom" # option to replace the last estimated recruitment : "SAM", "geom", "RCT3"
# "SAM" = don't overwrite the SAM estimmate
# "SAM" = don't overwrite the SAM estimmate
# "geom" = replace by geomean 1990/(TaY-1)
# "RCT3" = replace by RCT3 output
mpOptions<-list(opt=opt,TACvarlim=TACvarlim,Fvarlim=Fvarlim,BBscen=BBscen)
sc.name<-paste(scen,opt,"_TACvarlim",TACvarlim,"_Fvarlim",Fvarlim,"_",BBscen,"_LastRec",LastRecOp,sep="")
outPath<-paste(outPath,"HCR base case/",sc.name,"/",sep="")
test<-F
if(test)
{
outPath<-paste(path,"Results/test/",sep="")
scen<-"LTMP2.2mt15"
}
load(file=paste(outPath,"/",scen,opt,"_Finalf.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_Finalbiol.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_Finalstocks.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_Finalpercievedstocks.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_FinalTAC.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_FinalfSTF.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_Finalfishery.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_FinalmpPoints.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_Finalsettings.RData", sep=""))
load(file=paste(outPath,"/",scen,opt,"_FinalSSB.RData", sep=""))
source(paste(codePath,"functions.r", sep=""))
source(paste(codePath,"04_forecastScenarios.r", sep=""))
RecType<-settings$RecType
nits<- dim(stocks@stock.n)[6]
projPeriod<-settings$projPeriod
projPeriod<-projPeriod[-length(projPeriod)]
##-------------------------------------------------------------------------------
## Figures on stochastic variables
##-------------------------------------------------------------------------------
ca <- 1.1
cl <- 1.3
fonts <- 2
#-------------------------------------------------------------------------------
# 0): Figure of biol future weights and recruitment
#-------------------------------------------------------------------------------
plotPathsc<-paste( "W:/IMARES/Data/ICES-WG/WKMACLTMP/Results/figures input output/",scen,opt,sep="")
dir.create(plotPathsc)
plotPath<-paste(plotPathsc,"/Plots input/",sep="")
dir.create(plotPath)
#- Recruitment lognormal default fit
hist(biol@n[1,projPeriod],breaks=100,xlab="Recruitment",ylab="Simulated frequency",main="",cex.lab=cl,cex.axis=ca,font=fonts)
abline(v=exp(mean(log(biol@n[1,recrPeriod]))),col="red",lty=3,lwd=3)
legend("topright",legend=c("Simulated recruitment","Geometric mean recruitment"),lty=c(0,2),pch=c(22,0),
pt.bg="white",pt.cex=c(1,0),box.lty=0,col=c("black","red"),lwd=c(0,3))
legend("bottomright",lty=c(0,0),c(paste("Btrigger=",mpPoints$Btrigger),paste("Ftarget=",mpPoints$Ftarget)))
savePlot(file=paste(plotPath,"input_recruitment.png",sep=""),type="png")
#- Recruitment cummulative distribution
plot(x=sort(c(rec(Mac[,ac(recrPeriod)]))),y=seq(0,1,length.out=length(c(rec(Mac[,ac(recrPeriod)])))+2)[-c(1,length(c(rec(Mac[,ac(recrPeriod)])))+2)],
ylim=c(0,1),col=2,pch=15,xlab="Recruitment",ylab="Probability",las=1,xlim=range(c(biol[1,projPeriod]@n)),yaxs="i")
points(x=sort(c(biol@n[1,ac(projPeriod)])),y=seq(0,1,length.out=length(sort(c(biol@n[1,ac(projPeriod)])))+2)[c(-1,-length(sort(c(biol@n[1,ac(projPeriod)]))))],pch=19,cex=0.3)
legend("topleft",legend=c("Simulated recruitment","Observed recruitment"),lty=c(0,0),pch=c(16,15),
pt.cex=c(0.5,1),box.lty=0,col=c("black","red"),lwd=c(0,0))
legend("bottomright",lty=c(0,0),c(paste("Btrigger=",mpPoints$Btrigger),paste("Ftarget=",mpPoints$Ftarget)))
savePlot(file=paste(plotPath,"input_recruitmentDistri.png",sep=""),type="png")
#- SR plot with simulated data
Recs<-c(biol@n[1,ac(projPeriod)]@.Data)
SSBs<-c(ssbb(biol,f,stocks)[,ac(projPeriod)]@.Data)/1e6
RecO<-c(rec(Mac[,ac(recrPeriod)]))
SSBO<-c(ssb(Mac[,ac(recrPeriod)]))/1e6
png(file=paste(plotPath,"input_simulated recruitments.png",sep=""),width=8,height=6,units="in",res=300)
plot(SSBs,Recs,xlim=c(0,8),xlab="SSB (10^6t)",ylab="Rec (thousands)",cex=0.4,pch=19,main=paste("RecType=",RecType,"Ftarget=",mpPoints$Ftarget))
seqMin <- 0.5
seqStep <- 0.5
Xmax <-8
up=seq(seqMin,Xmax,seqStep)
lw=seq(seqMin,Xmax,seqStep)
md=seq(seqMin,Xmax,seqStep)
ssb=seq(seqMin,Xmax,seqStep)
loopNum <- length(ssb)
for (j in 1:loopNum){
up[j]=quantile(Recs[((SSBs>up[j])*(SSBs<up[j+1]))>0],probs=.95,na.rm=TRUE)
lw[j]=quantile(Recs[((SSBs>lw[j])&(SSBs<lw[j+1]))>0],probs=.05,na.rm=TRUE)
md[j]=quantile(Recs[((SSBs>md[j])&(SSBs<md[j+1]))>0],probs=.5,na.rm=TRUE)
}
lines(ssb,md[1:loopNum],col="green",lwd=3)
lines(ssb,up[1:loopNum],col=4,lwd=3)
lines(ssb,lw[1:loopNum],col=4,lwd=3)
points(SSBO,RecO,col="red",cex=1,pch=19)
legend("topleft",lty=c(0,0),c(paste("Btrigger=",mpPoints$Btrigger),paste("Ftarget=",mpPoints$Ftarget)))
dev.off()
Recs<-biol@n[1,]
SSBs<-ssbb(biol,f,stocks)/1e6
png(file=paste(plotPath,"input_simulated recruitments_iterations.png",sep=""),width=12,height=8,units="in",res=300)
par(mfrow=c(3,4))
for (its in 1:12)
{
plot(SSBs[,ac(projPeriod),,,,its],Recs[,ac(projPeriod),,,,its],xlim=c(0,6)
,ylim=c(0,2e7) ,pch=19,
xlab="SSB (in mt)",ylab="Rct (thousands)",
main=paste("iteration",its))
points(SSBs[,ac(recrPeriod),,,,its],Recs[,ac(recrPeriod),,,,its],col="red",pch=19 )
bs<-seq(0,6e6,length.out=1000)
mod<-B2Rsimple(bs,SRmod[its,])
lines(bs/1e6,mod)
legend("topleft",lty=c(0,0),c(paste("Btrigger=",mpPoints$Btrigger),paste("Ftarget=",mpPoints$Ftarget)))
}
dev.off()
#
#
#RecO<-c(rec(Mac[,ac(recrPeriod)]))
#SSBO<-c(ssb(Mac[,ac(recrPeriod)]))/1e6
#Rec<-c(rec(Mac))
#SSB<-c(ssb(Mac))/1e6
#
#plot(SSB,Rec,xlim=c(0,6),ylim=c(0,1.2e7),xlab="SSB (10^6t)",ylab="Rec (thousands)",cex=0.4,pch=19,main="")
#points(SSBO,RecO,col="red",cex=1,pch=19)
#
#- Numbers-at-age
par(mfrow=c(4,6),mar=c(0.3,0.1,0.3,0.1),oma=c(6,6,2,2),las=1)
for(iYr in 1990:2013){
if(iYr %in% seq(1990,2007,6)) boxplot(data ~ as.factor(age),data=as.data.frame(biol@n[,ac(iYr)]),xaxt="n",xlab="",ylab="",ylim=c(0,rev(pretty(max(as.data.frame(biol@n[,ac(1990:2013)])$data,na.rm=T)))[1]))
if(iYr %in% 2009:2013) boxplot(data ~ as.factor(age),data=as.data.frame(biol@n[,ac(iYr)]),yaxt="n",xlab="",ylab="",ylim=c(0,rev(pretty(max(as.data.frame(biol@n[,ac(1990:2013)])$data,na.rm=T)))[1]))
if(iYr == 2008) boxplot(data ~ as.factor(age),data=as.data.frame(biol@n[,ac(iYr)]),xlab="",ylab="",ylim=c(0,rev(pretty(max(as.data.frame(biol@n[,ac(1990:2013)])$data,na.rm=T)))[1]))
if(!iYr %in% c(seq(1990,2007,6),2008:2013)) boxplot(data ~ as.factor(age),data=as.data.frame(biol@n[,ac(iYr)]),xlab="",ylab="",xaxt="n",yaxt="n",ylim=c(0,rev(pretty(max(as.data.frame(biol@n[,ac(1990:2013)])$data,na.rm=T)))[1]))
text(x=9,y=rev(pretty(max(as.data.frame(biol@n[,ac(1990:2013)])$data,na.rm=T)))[1],pos=1,labels=iYr,font=2,cex=1)
}
savePlot(file=paste(plotPath,"input_natage.png",sep=""),type="png"); dev.off()
#- Weight at age
boxplot(as.data.frame(biol@wt[,projPeriod])$data~as.factor(as.data.frame(biol@wt[,projPeriod])$age),
boxwex=0.5,col="grey90",medlty=0,medlwd=1,medpch=19,medcol="black",boxlty=1,outlty=0,outcex=0.5,outpch=1,staplelty=1,
xlab="Age",ylab="Weight in the stock(kg)",cex.axis=ca,cex.lab=cl,font=fonts)
points(as.data.frame(iter(Mac@stock.wt[,ac(2001:2012)],1))$data~as.factor(as.data.frame(iter(Mac@stock.wt[,ac(2001:2012)],1))$age),pch=19,cex=0.5,col="red")
legend("bottomright",legend=c("Simulated weights","Observed weights"),col=c("black","red"),
pch=c(22,19),
pt.bg="grey90",pt.cex=c(1,1),box.lty=0)
savePlot(file=paste(plotPath,"input_wtatage.png",sep=""),type="png"); dev.off()
xyplot(data ~ year | as.factor(age),data=subset(subset(as.data.frame(biol@wt[ac(1:6)]),year %in% 2001:futureMaxYr),iter %in% 1:5),type="l",group=iter,
prepanel=function(...) {list(ylim=range(pretty(c(0,list(...)$y))))},
scales=list(alternating=1,y=list(relation="free",rot=0)))
savePlot(file=paste(plotPath,"input_wtscenarios.png",sep=""),type="png"); dev.off()
#- Maturity at age
boxplot(as.data.frame(biol@fec[,projPeriod])$data~as.factor(as.data.frame(biol@fec[,projPeriod])$age),
boxwex=0.5,col="grey90",medlty=0,medlwd=1,medpch=19,medcol="black",boxlty=1,outlty=0,outcex=0.5,outpch=1,staplelty=1,
xlab="Age",ylab="Proportion mature",cex.axis=ca,cex.lab=cl,font=fonts)
points(as.data.frame(iter(Mac@mat[,ac(2001:2010)],1))$data~as.factor(as.data.frame(iter(Mac@mat[,ac(2001:2010)],1))$age),pch=19,cex=0.5,col="red")
legend("bottomright",legend=c("Simulated maturity","Observed maturity"),col=c("black","red"),
pch=c(22,19),
pt.bg="grey90",pt.cex=c(1,1),box.lty=0)
savePlot(file=paste(plotPath,"input_matatage.png",sep=""),type="png"); dev.off()
xyplot(data ~ year | as.factor(age),data=subset(subset(as.data.frame(biol@fec),year %in% 2001:2022),iter %in% 1:5),type="l",group=iter,
prepanel=function(...) {list(ylim=range(pretty(list(...)$y)))},
scales=list(alternating=1,y=list(relation="free",rot=0)))
savePlot(file=paste(plotPath,"input_matscenarios.png",sep=""),type="png"); dev.off()
#-------------------------------------------------------------------------------
# 1): Figure of fisheries future landing weights and selectivity
#-------------------------------------------------------------------------------
#- Landings weight
for(iFsh in dimnames(fishery@landings.wt)$unit){
boxplot(as.data.frame(fishery@landings.wt[,projPeriod,iFsh])$data~as.factor(as.data.frame(fishery@landings.wt[,projPeriod,iFsh])$age),
boxwex=0.5,col="grey90",medlty=0,medlwd=1,medpch=19,medcol="black",boxlty=1,outlty=0,outcex=0.5,outpch=1,staplelty=1,
xlab="Age",ylab="Weight (kg)",cex.lab=cl,cex.axis=ca,font=fonts,main=paste("Fleet",iFsh))
points(as.data.frame(iter(fishery@landings.wt[,ac(2001:2010),iFsh],1))$data~as.factor(as.data.frame(iter(fishery@landings.wt[,ac(2001:2010),iFsh],1))$age),pch=19,cex=0.5,col="red")
legend("bottomright",legend=c("Simulated weights","Observed weights"),col=c("black","red"),
pch=c(22,19),
pt.bg="grey90",pt.cex=c(1,1),box.lty=0)
}
savePlot(file=paste(plotPath,"input_fish_wtatage.png",sep=""),type="png"); dev.off()
#- Selectivity
boxplot(as.data.frame(landings.sel(fishery)[,projPeriod])$data~as.factor(as.data.frame(landings.sel(fishery)[,projPeriod])$age),
boxwex=0.5,col="grey90",medlty=0,medlwd=1,medpch=19,medcol="black",boxlty=1,outlty=0,outcex=0.5,outpch=1,staplelty=1,
xlab="Age",ylab="Selectivity",cex.lab=cl,cex.axis=ca,font=fonts,main=paste("Fleet",iFsh))
lines(as.data.frame(apply(landings.sel(fishery)[,projPeriod],1,median))$data~as.factor(as.data.frame(apply(landings.sel(fishery)[,projPeriod],1,median))$age),
lwd=2,lty=2)
lines(as.data.frame(iter(landings.sel(fishery)[,ac(histMaxYr)],1))$data~as.factor(as.data.frame(iter(landings.sel(fishery)[,ac(histMaxYr)],1))$age),
col="red",lty=1,lwd=2)
savePlot(file=paste(plotPath,"input_fish_selatage.png",sep=""),type="png"); dev.off()
xyplot(data ~ age | as.factor(year),data=subset(subset(as.data.frame(landings.sel(fishery)[,,1]),year %in% 2001:futureMaxYr),iter %in% 1:5),type="l",group=iter,
prepanel=function(...) {list(ylim=range(pretty(c(0,list(...)$y))))},
scales=list(alternating=1,y=list(relation="free",rot=0)))
savePlot(file=paste(plotPath,"input_selAscenarios.png",sep=""),type="png"); dev.off()
sel<-sweep(landings.sel(fishery)[ac(0:7),,,,,2:5],c(2:6),landings.sel(fishery)[ac(7),,,,,2:5],"/")
xyplot(data ~ year | iter,group= as.factor(age),data=sel[,ac(2000:2032)],type="l",auto.key=list(columns = 2))
savePlot(file=paste(plotPath,"input_selAscenarios2.png",sep=""),type="png"); dev.off()
#-------------------------------------------------------------------------------
# 2): Figure of survey residual pattern
#-------------------------------------------------------------------------------
xyplot(data ~ year,subset(subset(as.data.frame(Rindex[1,]),year %in% 1998:2012),iter %in% 1:5),type="l",group=iter,
prepanel=function(...) {list(ylim=range(pretty(c(0,list(...)$y))))},
scales=list(alternating=1,y=list(relation="free",rot=0)))
savePlot(file=paste(plotPath,"input_Rindex_errors.png",sep=""),type="png"); dev.off()
#-------------------------------------------------------------------------------
# 3): Figures of the stock
#-------------------------------------------------------------------------------
units(stocks)$harvest<-"f"
units(stockstore)$harvest<-"f"
plot(trim(stocks,year=an(1990:histMaxYr)))
savePlot(file=paste(plotPath,"input_stocks.png",sep=""),type="png"); dev.off()
#
##- Assessment stock.n error
#xyplot(data ~ year|as.factor(age),data=as.data.frame(devN),pch=19,col="black",cex=0.4,xlab="Years",ylab="Error (log ratio)",main="Assessment numbers-at-age error")
#savePlot(file=paste(plotPath,"input_stock_errornatage.png",sep=""),type="png"); dev.off()
#
##- Assessment harvest error
#xyplot(data ~ year|as.factor(age),data=as.data.frame(devF),pch=19,col="black",cex=0.4,xlab="Years",ylab="Error (log ratio)",main="Assessment f-at-age error")
#savePlot(file=paste(plotPath,"input_stock_errorfatage.png",sep=""),type="png"); dev.off()
#
##- Catch number residuals
#xyplot(data ~ year|as.factor(age),data=as.data.frame(catchResids),pch=19,col="black",cex=0.4,xlab="Years",ylab="Error multiplier",main="Catch numbers-at-age error")
#savePlot(file=paste(plotPath,"input_stock_errorcatchatage.png",sep=""),type="png"); dev.off()
#
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
# Figures on results
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
#-------------------------------------------------------------------------------
plotPath2<-paste(plotPathsc,"/Plots results/",sep="")
dir.create(plotPath2)
#-------------------------------------------------------------------------------
# assessment errors figures
#-------------------------------------------------------------------------------
# error on real scale
devSSB<-(ssb(stockstore)[,projPeriod]-ssbb(biol,f,stocks)[,projPeriod])
devSSB<-devSSB[,ac(projPeriod)]
histogram(1~data, data=(devSSB),col="grey",main="assess errors SSB(TaY)")
savePlot(file=paste(plotPath2,"1.SSBinTaY_error.png",sep=""),type="png"); dev.off()
par(mfrow=c(3,3),mar=c(3,3,3,3),oma=c(3.1,3.1,1,1))
for (i in 1:9)
{xrange <- range(an(projPeriod))
yrange <- range(c(-1.5e6,1.5e6))
plot(c(iter(devSSB,i))~an(projPeriod),type="l",xlab="Years",ylab="",
xlim=xrange,ylim=yrange,lwd=2,font=fonts,cex.lab=cl,cex.axis=ca,las=1,col=i)
mtext(side=2,at=yrange[2]/2,text="error on SSB (TaY)",outer=F,line=4,font=fonts,cex=ca)
abline(h=0,lwd=2)
grid(); box()
}
savePlot(file=paste(plotPath2,"1.2.SSBinTaY_error_iters.png",sep=""),type="png"); dev.off()
# error on log scale
devSSB<-log(ssb(stockstore)[,projPeriod]/ssbb(biol,f,stocks)[,projPeriod])
devSSB<-devSSB[,1:(dim(devSSB[,projPeriod])[2]-1)]
cvSSBTaY<-apply(devSSB,c(1,3:6),sd)
histogram(1~data, data=(devSSB),col="grey",main="assess errors logSSB(TaY)")
savePlot(file=paste(plotPath2,"2.logSSBinTaY_error_CVis",round(mean(cvSSBTaY),2),".png",sep=""),type="png"); dev.off()
# autocor error on log scale
rhoSSBdev<-rep(NA,nits)
for (i in 1:nits) rhoSSBdev[i]<- an(unlist(acf(iter(devSSB,i),plot=F)[1])[1])
histogram(1~rhoSSBdev,col="grey",main="RHO errors logSSB(TaY)")
savePlot(file=paste(plotPath2,"3.RHO_logSSBinTaYerrors_mean.is",round(mean(rhoSSBdev),2),".png",sep=""),type="png"); dev.off()
# error on the advisory year
ys<-dimnames(SSB)$year[which(!is.na(iter(SSB,1)))]
devSSB<-log(SSB[,ys]/ssbb(biol,f,stocks)[,ys])
devSSB<-devSSB[,1:(dim(devSSB)[2]-1)]
cvSSBAdY<-apply(devSSB,c(1,3:6),sd)
histogram(1~data, data=(devSSB),col="grey",main="assess errors logSSB(AdY)")
savePlot(file=paste(plotPath2,"4.logSSBinAdY_error_CVis",round(mean(cvSSBAdY),2),".png",sep=""),type="png"); dev.off()
# autocor error in advice year on log scale
rhoSSBdev<-rep(NA,nits)
for (i in 1:nits) rhoSSBdev[i]<- an(unlist(acf(iter(devSSB,i),plot=F)[1])[1])
histogram(1~rhoSSBdev,col="grey",main="RHO errors logSSB(AdY)")
savePlot(file=paste(plotPath2,"5.RHO_logSSBinAdYerrors_mean.is",round(mean(rhoSSBdev),2),".png",sep=""),type="png"); dev.off()
devFbar<-log(quantMeans(harvest(stockstore)[ac(4:8),])/quantMeans(f[ac(4:8),]))
devFbar<-devFbar[,1:(dim(devFbar)[2]-1)]
devFbar<-devFbar[,ac(projPeriod)]
cvFbarTaY<-apply(devFbar,c(1,3:6),sd)
rhoFdev<-rep(NA,nits)
for (i in 1:nits) rhoFdev[i]<- an(unlist(acf(iter(devFbar,i),plot=F)[1])[1])
#
#xyplot(data ~ year ,data=subset(subset(as.data.frame(devFbar),year %in% 2012:2032),iter %in% 1:5),type="l",group=iter,
# prepanel=function(...) {list(ylim=range(pretty(c(0,list(...)$y))))},
# scales=list(alternating=1,y=list(relation="free",rot=0)))
##savePlot(file=paste(plotPath,"input_Fbar_errorscenario.png",sep=""),type="png"); dev.off()
histogram(1~data, data=(devFbar),col="grey",main="assess errors logFbar(TaY)")
savePlot(file=paste(plotPath2,"6.logFbarinTaY_error_CVis",round(mean(cvFbarTaY),2),".png",sep=""),type="png"); dev.off()
histogram(1~rhoFdev,col="grey",main="RHO errors logFbar(TaY)")
savePlot(file=paste(plotPath2,"7.RHO_logFbarinTaYerrors_mean.is",round(mean(rhoFdev),2),".png",sep=""),type="png"); dev.off()
#-------------------------------------------------------------------------------
# stock trajectories figures
#-------------------------------------------------------------------------------
###############
rSSBp <- apply(ssbb(biol,unitSums(f),stocks)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rSSBs <- apply(ssb(stockstore)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rFp <- apply(apply(unitSums(f)[ac(4:8),],2:6,mean,na.rm=T)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rFs <- apply(fbar(stockstore)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rFstf <- apply(apply(unitSums(fSTF)[ac(4:8),],2:6,mean,na.rm=T)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rLandf<- apply(computeLandings(fishery)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rLands<- apply(computeLandings(stockstore)@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rTAC <- apply(TAC@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
#- Plot settings
yrs <- 2001:max(an(projPeriod))
cl <- 1.2
ca <- 1.1
fonts <- 2
#-------------------------------------------------------------------------------
# 3): Plot results of SSB stock and SSB pop
#-------------------------------------------------------------------------------
par(mar=c(5.1,5.1,4.1,2.1))
xrange <- range(yrs)
yrange <- c(0,range(pretty(c(rSSBp[,,ac(yrs),,,],rSSBs[,,ac(yrs),,,])),na.rm=T)[2])
#---------
#- Biology
#---------
plot(rSSBp["50%",,ac(yrs),,,]~yrs,xlim=xrange,ylim=yrange,xlab="Years",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange)/1000,cex=ca,font=fonts)
mtext(text="SSB (thousand tonnes)",side=2,at=0.5,outer=T,cex=cl,line=-1)
grid(); box()
#-Reference level Blim & Bpa
abline(h=1.84e6,col="blue",lwd=2,lty=2);
abline(h=2.36e6,col="darkgreen",lwd=2,lty=2);
mtext(text="Blim",side=4,at=1.84e6,las=1,cex=0.8,col="blue",line=0.5,font=fonts)
mtext(text="Bpa",side=4,at=2.36e6,las=1,cex=0.8,col="darkgreen",line=0.5,font=fonts)
lines(rSSBp["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2)
lines(rSSBp["5%",,ac(yrs),,,]~yrs,lty=3)
lines(rSSBp["95%",,ac(yrs),,,]~yrs,lty=3)
#---------
#- Stock
#---------
lines(rSSBs["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2,col="red")
lines(rSSBs["5%",,ac(yrs),,,]~yrs,lty=3,col="red")
lines(rSSBs["95%",,ac(yrs),,,]~yrs,lty=3,col="red")
#---------
#- Legend
#---------
legend("bottomright",legend=c("SSB assessed stock","SSB true population"),
col=c("red","black"),lwd=3,lty=1,box.lty=0)
savePlot(file=paste(plotPath2,"8.SSB.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 4): Plot results of F stock and true F
#-------------------------------------------------------------------------------
par(mar=c(5.1,5.1,4.1,2.1))
xrange <- range(yrs)
yrange <- c(0,range(pretty(c(rFp[,,ac(yrs),,,],rFs[,,ac(yrs),,,],rFstf[,,ac(yrs),,,])),na.rm=T)[2])
#---------
#- Biology
#---------
plot(rFp["50%",,ac(yrs),,,]~yrs,xlim=xrange,ylim=yrange,xlab="Years",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange),cex=ca,font=fonts)
mtext(text="Fishing mortality (ages 4-8)",side=2,at=0.5,outer=T,cex=cl,line=-1)
grid(); box()
#-Reference level Fpa
abline(h=0.26,col="darkgreen",lwd=2,lty=2);
mtext(text="Fpa",side=4,at=0.26,las=1,cex=0.8,col="darkgreen",line=0.5,font=fonts)
lines(rFp["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2)
lines(rFp["5%",,ac(yrs),,,]~yrs,lty=3)
lines(rFp["95%",,ac(yrs),,,]~yrs,lty=3)
#---------
#- Stock
#---------
lines(rFs["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2,col="red")
lines(rFs["5%",,ac(yrs),,,]~yrs,lty=3,col="red")
lines(rFs["95%",,ac(yrs),,,]~yrs,lty=3,col="red")
#---------
#- STF
#---------
lines(rFstf["50%",,ac(2014:rev(projPeriod)[2]),,,]~ac(2014:rev(projPeriod)[2]),lty=1,lwd=2,col="blue")
lines(rFstf["5%",,ac(2014:rev(projPeriod)[2]),,,]~ac(2014:rev(projPeriod)[2]),lty=3,col="blue")
lines(rFstf["95%",,ac(2014:rev(projPeriod)[2]),,,]~ac(2014:rev(projPeriod)[2]),lty=3,col="blue")
#---------
#- Legend
#---------
legend("bottomright",legend=c("F assessed stock","F true population","F short term forecast"),
col=c("red","black","blue"),lwd=3,lty=1,box.lty=0)
savePlot(file=paste(plotPath2,"9.F.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 5): Plot results of landings by fleet & TAC on top
#-------------------------------------------------------------------------------
#---------
#- Fishery
#---------
par(mar=c(5.1,5.1,4.1,2.1))
iFsh<-1
xrange <- range(yrs)
yrange <- c(0,range(pretty(c(rLandf[,,ac(yrs),iFsh,,],rTAC[,,ac(yrs),iFsh,,])),na.rm=T)[2])
#- Landings
plot(rLandf["50%",,ac(yrs),iFsh,,]~yrs,xlim=xrange,ylim=yrange,xlab="Year",ylab="Landings (thousand tonnes)",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange)/1000,cex=ca,font=fonts)
grid(); box()
lines(rLandf["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2)
lines(rLandf["5%",,ac(yrs),iFsh,,]~yrs,lty=3)
lines(rLandf["95%",,ac(yrs),iFsh,,]~yrs,lty=3)
#- TAC
lines(rTAC["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2,col="red")
lines(rTAC["5%",,ac(yrs),iFsh,,]~yrs,lty=3,col="red")
lines(rTAC["95%",,ac(yrs),iFsh,,]~yrs,lty=3,col="red")
legend("bottomright",legend=c("Landings","Advice TAC"),
col=c("black","red"),lwd=3,lty=1,box.lty=0)
savePlot(file=paste(plotPath2,"10.CatchTAC.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 6): Plot results total landings fishery and stock
#-------------------------------------------------------------------------------
par(mar=c(5.1,5.1,4.1,2.1))
xrange <- range(yrs)
yrange <- c(0,range(pretty(c(rLandf[,,ac(yrs),,,],rLands[,,ac(yrs),,,])),na.rm=T)[2])
#---------
#- Biology
#---------
plot((rLandf["50%",,ac(yrs),,,])~yrs,xlim=xrange,ylim=yrange,xlab="Years",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange),cex=ca,font=fonts)
mtext(text="Landings (tonnes)",side=2,at=0.5,outer=T,cex=cl,line=-1)
grid(); box()
lines((rLandf["50%",,ac(yrs),,,])~yrs,lty=1,lwd=2)
lines((rLandf["5%",,ac(yrs),,,])~yrs,lty=3)
lines((rLandf["95%",,ac(yrs),,,])~yrs,lty=3)
#---------
#- Stock
#---------
lines(rLands["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2,col="red")
lines(rLands["5%",,ac(yrs),,,]~yrs,lty=3,col="red")
lines(rLands["95%",,ac(yrs),,,]~yrs,lty=3,col="red")
#---------
#- Legend
#---------
legend("bottomright",legend=c("Catch assessed stock","Catch true population"),
col=c("red","black"),lwd=3,lty=1,box.lty=0)
savePlot(file=paste(plotPath2,"11.Catch.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 7): Plot results of TAC
#-------------------------------------------------------------------------------
par(mar=c(2.1,2.1,2.1,2.1),oma=c(3,3,2,0))
#---------
#- Fishery
#---------
iFsh<-1
xrange <- range(yrs)
yrange <- c(0,range(pretty(rTAC[,,ac(yrs),iFsh,,]),na.rm=T)[2])
plot(rTAC["50%",,ac(yrs),iFsh,,]~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange)/1000,cex=ca,font=fonts)
mtext(text="TAC (thousand tonnes)",side=2,at=0.5,outer=T,cex=cl,line=1.5)
mtext(text="Years",side=1,at=0.5,outer=T,cex=cl,line=1.5)
grid(); box()
lines(rTAC["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2)
lines(rTAC["5%",,ac(yrs),iFsh,,]~yrs,lty=3)
lines(rTAC["95%",,ac(yrs),iFsh,,]~yrs,lty=3)
savePlot(file=paste(plotPath2,"12.TAC.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 8): Plot results of TAC
#-------------------------------------------------------------------------------
par(mar=c(2.1,2.1,2.1,2.1),oma=c(3,3,2,0))
B <- ssbb(biol,unitSums(f),stocks)
ys <- dimnames(B)$year[which((iter(B,1))>0)]
B <- B[,ys]
risk<- apply(B<mpPoints$Blim,c(1:5),sum)/nits
xrange <- range(yrs)
yrange <- c(0,1)
plot(c(risk[1,ac(yrs)]@.Data)~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange),cex=ca,font=fonts)
mtext(text="Risk B<Blim",side=2,at=0.5,outer=T,cex=cl,line=1.5)
mtext(text="Years",side=1,at=0.5,outer=T,cex=cl,line=1.5)
grid(); box()
abline(h=0.05,lty="dotted",col="red")
ShortT <- ac(2014:2018)
MidT <- ac(2019:2028)
LongT <- ac(2029:2052)
lines(an(ShortT),rep(max(c(risk[1,ShortT]@.Data)),length(ShortT)),col="blue")
points(range(an(ShortT)),rep(max(c(risk[1,ShortT]@.Data)),2),col="blue",cex=1.2,pch="S")
lines(an(MidT),rep(max(c(risk[1,MidT]@.Data)),length(MidT)),col="blue")
points(range(an(MidT)),rep(max(c(risk[1,MidT]@.Data)),2),col="blue",cex=1.2,pch="M")
lines(an(LongT),rep(max(c(risk[1,LongT]@.Data)),length(LongT)),col="blue")
points(range(an(LongT)),rep(max(c(risk[1,LongT]@.Data)),2),col="blue",cex=1.2,pch="L")
savePlot(file=paste(plotPath2,"13.Risk.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 8): Plot age and weights indicators
#-------------------------------------------------------------------------------
# mean weight in the spawning stock and in the catches
smw<-quantSums((biol@n*biol@wt*biol@fec)) / quantSums((biol@n*biol@fec))
ymw<-quantSums((fishery@landings.n*fishery@landings.wt))/quantSums((fishery@landings.n))
rsmw <- apply(smw@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
rymw <- apply(ymw@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
par(mar=c(2.1,2.1,2.1,2.1),oma=c(3,3,2,0))
iFsh<-1
xrange <- range(yrs)
yrange <- c(range(pretty(rsmw[,,ac(yrs),iFsh,,]),na.rm=T)[1],range(pretty(rymw[,,ac(yrs),iFsh,,]),na.rm=T)[2])
plot(rsmw["50%",,ac(yrs),iFsh,,]~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange),cex=ca,font=fonts)
mtext(text="mean weight (in kg)",side=2,at=0.5,outer=T,cex=cl,line=1.5)
mtext(text="Years",side=1,at=0.5,outer=T,cex=cl,line=1.5)
grid(); box()
lines(rsmw["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2)
lines(rsmw["5%",,ac(yrs),iFsh,,]~yrs,lty=3)
lines(rsmw["95%",,ac(yrs),iFsh,,]~yrs,lty=3)
lines(rymw["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2,col="red")
lines(rymw["5%",,ac(yrs),iFsh,,]~yrs,lty=3,col="red")
lines(rymw["95%",,ac(yrs),iFsh,,]~yrs,lty=3,col="red")
legend(x="topright", col=c("black","red"),lty= c(1,1), c("in the spawning stock","in the catches"),bg="white")
savePlot(file=paste(plotPath2,"14.meanW.png",sep=""),type="png");dev.off()
# mean age in the spawning stock and in the catches
sma<-quantSums(sweep((biol@n*biol@fec),c(1:6) ,c(0:12),"*"))/quantSums((biol@n*biol@fec))
yma<-quantSums(sweep((fishery@landings.n),c(1:6) ,c(0:12),"*"))/quantSums((fishery@landings.n))
rsma <- apply(sma@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
ryma <- apply(yma@.Data,1:5,quantile,probs=c(0.05,0.5,0.95),na.rm=T)
par(mar=c(2.1,2.1,2.1,2.1),oma=c(3,3,2,0))
iFsh<-1
xrange <- range(yrs)
yrange <- c(range(pretty(rsma[,,ac(yrs),iFsh,,]),na.rm=T)[1],range(pretty(ryma[,,ac(yrs),iFsh,,]),na.rm=T)[2])
plot(rsma["50%",,ac(yrs),iFsh,,]~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=2,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange),cex=ca,font=fonts)
mtext(text="mean Age",side=2,at=0.5,outer=T,cex=cl,line=1.5)
mtext(text="Years",side=1,at=0.5,outer=T,cex=cl,line=1.5)
grid(); box()
lines(rsma["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2)
lines(rsma["5%",,ac(yrs),iFsh,,]~yrs,lty=3)
lines(rsma["95%",,ac(yrs),iFsh,,]~yrs,lty=3)
lines(ryma["50%",,ac(yrs),iFsh,,]~yrs,lty=1,lwd=2,col="red")
lines(ryma["5%",,ac(yrs),iFsh,,]~yrs,lty=3,col="red")
lines(ryma["95%",,ac(yrs),iFsh,,]~yrs,lty=3,col="red")
legend(x="topright", col=c("black","red"),lty= c(1,1), c("in the spawning stock","in the catches"),bg="white")
savePlot(file=paste(plotPath2,"15.meanAge.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 9): Plot trajectories of ssb(biol), rec(biol), f(biol), TAC(A)
#-------------------------------------------------------------------------------
par(mfrow=c(2,2),mar=c(3,3,3,3),oma=c(3.1,3.1,1,1))
its<-sample(1:nits,10,replace=F)
#- Plot ssb based on biol
xrange <- range(yrs)
yrange <- range(0,pretty(range(c(iter(ssbb(biol[,ac(yrs)],unitSums(f[,ac(yrs)]),stocks[,ac(yrs)]),1:10))/1000),1))
plot(c(iter(ssbb(biol[,ac(yrs)],unitSums(f[,ac(yrs)]),stocks[,ac(yrs)]),1))/1000~yrs,type="l",xlab="Years",ylab="",
xlim=xrange,ylim=yrange,lwd=2,font=fonts,cex.lab=cl,cex.axis=ca,las=1)
mtext(side=2,at=yrange[2]/2,text="Spawning Stock Biomass (kt)",outer=F,line=4,font=fonts,cex=ca)
grid(); box()
for(i in its) lines(c(iter(ssbb(biol[,ac(yrs)],unitSums(f[,ac(yrs)]),stocks[,ac(yrs)]),i))/1000~yrs,col=i,lwd=2)
#- Plot rec based on biol
xrange <- range(yrs)
yrange <- c(0,rev(pretty(range(c(iter(biol@n[1,ac(yrs)],1:10))/1e6),1))[1])
plot(c(iter(biol@n[1,ac(yrs)],1))/1e6~yrs,type="l",xlab="Years",ylab="",
xlim=xrange,ylim=yrange,lwd=2,font=fonts,cex.lab=cl,cex.axis=ca,las=1)
mtext(side=2,at=yrange[2]/2,text="Recruitment (millions)",outer=F,line=4,font=fonts,cex=ca)
grid();box()
for(i in its) lines(c(iter(biol@n[1,ac(yrs)],i))/1e6~yrs,col=i,lwd=2)
#- f-ages 2-6
xrange <- range(yrs)
yrange <- c(0,pretty(range(c(iter(quantMeans(unitSums(f[ac(4:8),ac(yrs)])),1:10))),1)[3])
plot(c(iter(quantMeans(unitSums(f[ac(4:8),ac(yrs)])),1))~yrs,type="l",xlab="Years",ylab="",
xlim=xrange,ylim=yrange,lwd=2,font=fonts,cex.lab=cl,cex.axis=ca,las=1)
mtext(side=2,at=yrange[2]/2,text="Fishing mortality",outer=F,line=4,font=fonts,cex=ca)
grid();box()
for(i in its) lines(c(iter(quantMeans(unitSums(f[ac(4:8),ac(yrs)])),i))~yrs,col=i,lwd=2)
#- TAC of fleet A
xrange <- range(yrs)
yrange <- c(0,pretty(range(c(iter(TAC[,ac(yrs),"A"]/1000,1:10))),1)[3])
plot(c(iter(TAC[,ac(yrs),"A"]/1000,1))~yrs,type="l",xlab="Years",ylab="",
xlim=xrange,ylim=yrange,lwd=2,font=fonts,cex.lab=cl,cex.axis=ca,las=1)
mtext(side=2,at=yrange[2]/2,text="TAC (kt)",outer=F,line=4,font=fonts,cex=ca)
grid();box()
for(i in its) lines(c(iter(TAC[,ac(yrs),"A"]/1000,i))~yrs,col=i,lwd=2)
savePlot(file=paste(plotPath2,"16.iterations.png",sep=""),type="png");dev.off()
#-------------------------------------------------------------------------------
# 9): Report figures
#-------------------------------------------------------------------------------
yrs <- 2005:an(rev(projPeriod)[2])
cl <- 1.1
ca <- 1
fonts <- 1
yrangeSSB <- c(0,6e6)
yrangeLan <- c(0,2e6)
#yrangeLan2<- c(0,2.5e4)
yrangeF <- c(0,0.5)
par(mfrow=c(3,1),oma=c(6,6,2,3),mar=c(1,0,0,0))
#---------
#- Landings
#---------
xrange <- range(yrs)
yrange <- yrangeLan
plot(rLandf["50%",,ac(yrs),1,,]~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=1,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n",xaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange)/1000,cex=ca,font=fonts)
mtext(text=expression(paste("Landings (",10^3," tonnes)",sep="")),side=2,at=(yrange[2]-yrange[1])/2+yrange[1],outer=F,cex=cl,line=4,font=fonts)
grid(); box()
lines(rLandf["50%",,ac(yrs),1,,]~yrs,lty=1,lwd=2)
lines(rLandf["5%",,ac(yrs),1,,]~yrs,lty=3,lwd=1)
lines(rLandf["95%",,ac(yrs),1,,]~yrs,lty=3,lwd=1)
#------------------
# True F
#------------------
xrange <- range(yrs)
yrange <- yrangeF
plot(rFp["50%",,ac(yrs),,,]~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=1,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n",xaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange),cex=ca,font=fonts)
mtext(text=expression(paste(F[2-6]," (",year^-1,")",sep="")),side=2,at=(yrange[2]-yrange[1])/2+yrange[1],outer=F,cex=cl,line=4,font=fonts)
grid(); box()
lines(rFp["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2)
lines(rFp["5%",,ac(yrs),,,]~yrs,lty=3,lwd=1)
lines(rFp["95%",,ac(yrs),,,]~yrs,lty=3,lwd=1)
#-Reference level Fpa
abline(h=0.26,col="darkgreen",lwd=1,lty=2);
mtext(text="Fpa",side=4,at=0.26,las=1,cex=0.65,col="darkgreen",line=0.5,font=fonts)
text(x=xrange[1],y=yrange[2],pos=1,labels="(B)",font=fonts,cex=cl)
#------------------
# True SSB
#------------------
xrange <- range(yrs)
yrange <- yrangeSSB
plot(rSSBp["50%",,ac(yrs),,,]~yrs,xlim=xrange,ylim=yrange,xlab="",ylab="",
type="l",lwd=1,cex.lab=cl,cex.axis=ca,font=fonts,yaxs="i",yaxt="n",xaxt="n")
axis(2,las=1,at=pretty(yrange),labels=pretty(yrange)/1000,cex=ca,font=fonts)
axis(1,las=1,at=pretty(xrange),labels=pretty(xrange),cex=ca,font=fonts)
mtext(text=expression(paste("SSB (",10^3," tonnes)",sep="")),side=2,at=(yrange[2]-yrange[1])/2+yrange[1],outer=F,cex=cl,line=4,font=fonts)
grid(); box()
lines(rSSBp["50%",,ac(yrs),,,]~yrs,lty=1,lwd=2)
lines(rSSBp["5%",,ac(yrs),,,]~yrs,lty=3,lwd=1)
lines(rSSBp["95%",,ac(yrs),,,]~yrs,lty=3,lwd=1)
#-Reference level Blim & Bpa
abline(h=1.84e6,col="blue",lwd=1,lty=2);
abline(h=2.36e6,col="darkgreen",lwd=1,lty=2);
mtext(text="Blim",side=4,at=1.84e6,las=1,cex=0.65,col="blue",line=0.5,font=fonts)
mtext(text="Bpa",side=4,at=2.36e6,las=1,cex=0.65,col="darkgreen",line=0.5,font=fonts)
text(x=xrange[1],y=yrange[2],pos=1,labels="(C)",font=fonts,cex=cl)
#- Labels x-axis
mtext(text=expression(Years),side=1,at=(xrange[2]-xrange[1])/2+xrange[1],outer=F,cex=cl,line=4,font=fonts)
savePlot(paste(plotPath2,"17.Truth.png",sep=""),type="png") ; dev.off()