In DLMtool/DLMtool: Data-Limited Methods Toolkit

if (params$tabs) {
  cat('### Historical MPA & Spatial Targeting {.tabset .tabset-fade .tabset-pills}' )
} else {
  cat('### Historical MPA & Spatial Targeting')
}

dd <- dim(params$Pars$M_ageArray)
nsim <- dd[1]
maxage <- dd[2]

nsamp <- length(params$its)

Existing Spatial Closures

Plot of the fraction of each area open to fishing in each historical year. Spatial closures remain fixed in all projection years unless modified by an MP.

if (all(is.na(Pars$MPA)) | sum(Pars$MPA) == 0) {
  Pars$MPA <- matrix(NA, nrow=2, ncol=3)
  Pars$MPA[,1] <- c(1, nyears)
  Pars$MPA[,2:3] <- 1
}

# historical spatial closures have been specified
sim <- params$its[1]
nareas <- dim(Pars$mov)[3] # ncol(Pars$MPA)-1
MPA <- matrix(1, nyears+proyears, ncol=nareas)
yrindex <- Pars$MPA[,1]
if (max(yrindex)>nyears) stop("Invalid year index for spatial closures: must be <= nyears")
if (min(yrindex)<1) stop("Invalid year index for spatial closures: must be > 1")
for (xx in seq_along(yrindex)) {
  MPA[yrindex[xx]:nrow(MPA),] <- matrix(Pars$MPA[xx, 2:ncol(Pars$MPA)], 
                                        nrow=length(yrindex[xx]:nrow(MPA)),ncol=nareas, byrow = TRUE)
}
x <- 1:(nyears+proyears)
nyrs <- length(x)
op <- par(mfrow=c(1,1), mar=c(3,3,0,0), oma=c(0,0,0,0), no.readonly = TRUE)
on.exit(par(op))

area_sizes <- Pars$Asize[sim,]
names(area_sizes) <- NULL
plot(c(1, nyears+proyears), c(0,sum(area_sizes)), type="n", bty="n", xlab="", ylab="", axes=FALSE)
origin <- cumsum(c(0, area_sizes)) #  seq(0, by=1, length.out = nareas)

for (aa in 1:nareas) {
  if (aa ==1) {
    df <- data.frame(Years=x, y1=0, y2=area_sizes[aa] * MPA[,aa])
  } else {
    df <- data.frame(Years=x, y1=sum(area_sizes[1:(aa-1)]), y2=sum(area_sizes[1:(aa-1)])+(area_sizes[aa] * MPA[,aa]))
  }
  polygon(x=c(df$Years, rev(df$Years)), y=c(df$y1, rev(df$y2)),
          col='lightgray', border = TRUE)
}

if (Pars$CurrentYr < 1000) years <- (Pars$CurrentYr - nyears+1) : (Pars$CurrentYr+proyears) -Pars$CurrentYr
if (Pars$CurrentYr > 1000) years <- (Pars$CurrentYr - nyears+1) : (Pars$CurrentYr+proyears) 

xp <- seq(from=min(x), to=max(x), by=5)
ind <- match(xp, x)

axis(side=1, at=x[ind], labels=years[ind])
mtext(side=1, "Years", line=2, xpd=NA, cex=1.25)

axis(side=2, at=origin[1:(length(origin)-1)] + 0.5 * area_sizes, labels=1:nareas, las=1, col = "white", tcl = 0)

mtext(side=2, "Areas", line=2, xpd=NA, cex=1.25, las=3)
abline(v=nyears, lty=2, col="darkgray")

mtext('Fraction open to fishing (grey)', side=3, line=2)

Spatial Targeting

Histograms of r nsim simulations of spatial targeting parameter (Spat_targ), with vertical colored lines indicating r nsamp randomly drawn values:

par(mfrow=c(1,1))

hist2(Pars$Spat_targ, col=params$plotPars$col, axes=params$plotPars$axes, main="Spat_targ", breaks=params$plotPars$breaks)
abline(v=Pars$Spat_targ[params$its], col=1:nsamp, lwd=params$plotPars$lwd)
axis(side=1)