plotAR: plotAR Plots the new proposed ICES advice rule

In Henning-Winker/FLRef: Reference point computation for advice rules

plotAR Plots the new proposed ICES advice rule

Description

plotAR Plots the new proposed ICES advice rule

Usage

plotAR(
  pars,
  ftgt = 1,
  btrigger = "missing",
  bpa = "missing",
  bthresh = "missing",
  fpa = "missing",
  fthresh = "missing",
  bclose = 0,
  fmin = 0,
  obs = "missing",
  kobe = TRUE,
  alpha = 1,
  xmax = 1.2,
  ymax = 1.5,
  ylab = "missing",
  xlab = "missing",
  rel = FALSE,
  expand = TRUE,
  labels = TRUE,
  label.cex = 3.5,
  critical = TRUE
)

Arguments

pars	FLPar object or computeFbrp() ouput 1: "Fbrp" # "F.." must first 2: "Btgt" 3: "Blim" 4: "B0"
ftgt	factor to adjust Fmsy or its proxy e.g. 0.8Fmsy
btrigger	biomass trigger below which F is linearly reduced, if > 10 value, else factor*Btgt
bpa	precautionary biomass threshold, if > 10 value, else factor*Blim
fpa	option to input Fpa value
bclose	biomass that invokes fishing closure
fmin	minimum allowable (bycatch) fishing mortality under closure
obs	obtion to show observation with input class 'FLStock'
kobe	add kobe colour-coding
alpha	transparency of shading
xmax	multiplier for upper default xlim
ymax	multiplier for upper default ylim
ylab	option customize ylab
xlab	option customize xlab
rel	option to denote x,y labs as relative B/Btgt and F/Ftgt
expand	option to expand the plot area to border - default TRUE
labels	annotate reference point labels
critical	option to highlight critical zone below blim
labelslabel.cex=3.5	set size of labels

Value

ggplot

Examples

data(ple4)
srr = srrTMB(as.FLSR(ple4,model=segreg),spr0=spr0y(ple4))
blim = params(srr)[[2]]
brp = computeFbrp(stock=ple4,sr=srr,proxy="f0.1",blim=blim)
rpt = Fbrp(brp)
plotAR(rpt,btrigger=an(0.8*rpt["Btgt"]))
# Use Bpa as trigger (ICES style)
plotAR(rpt,obs=ple4,bpa=1.4)
# Change kobe to greyscale
plotAR(rpt,obs=ple4,bpa=1.4,kobe=FALSE)
# add fishing closure with minimum unavoidable F and Btrigger
plotAR(rpt,obs=ple4,bpa=1.4,btrigger=0.7,kobe=TRUE,bclose=1,fmin=0.01)
# show a relative
plotAR(rpt,obs=ple4,rel=TRUE,bpa=1.4,btrigger=0.7,kobe=TRUE,bclose=1,fmin=0.02)

Henning-Winker/FLRef documentation built on Dec. 16, 2024, 7:23 p.m.