`r params$title`"

In MSEtool: Management Strategy Evaluation Toolkit

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

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

nsamp <- length(params$its)

Existing Spatial Closures

CURRENTLY NOT IMPLEMENTED !

# 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:

MSEtool:::plot.MPA(params$Pars, nsamp=nsamp, plotPars=params$plotPars, plot.num=1)

MSEtool documentation built on July 26, 2023, 5:21 p.m.