Nothing
setMethod('kobeShade', signature(object='numeric'),
function(object,breaks=c(-0.1,50,60,70,80,90,100),
kobeShades=c("","\\cellcolor{gray90}","\\cellcolor{gray80}","\\cellcolor{gray70}","\\cellcolor{gray60}","\\cellcolor{gray50}"),
pct="\\%",...){
#Kobe II strategy matrices to be prepared by the SCRS should highlight in a similar format as
#shown in Annex Table 2 a progression of probabilities over 50 % and in the range of 50-59 %, 60-
#69 %, 70-79 %, 80-89 % and ??? 90 %.
object=pmin(pmax(object,0),1)*100
res =data.frame("order"=seq(length(object)),object=round(object),"level"=cut(object,breaks))
gry =data.frame(level=attributes(unique(res$level))$levels,kobeShades)
res =merge(res,gry,all.x=TRUE)
res =res[order(res$order),]
res$object=paste(ac(round(res$object)),pct,sep="")
res=with(res,paste(kobeShades,object,sep=" "))
return(res)})
setMethod('kobeShade', signature(object='data.frame'),
function(object,breaks =c(-0.1,50,60,70,80,90,100),
kobeShades=c("","\\cellcolor{gray90}","\\cellcolor{gray80}","\\cellcolor{gray70}","\\cellcolor{gray60}","\\cellcolor{gray50}"),
pct="\\%",...){
as.data.frame(apply(object,2,kobeShade,breaks=breaks,kobeShades=kobeShades,pct=pct))
})
# setMethod('kobeShade', signature(object='cast_df'),
# function(object,breaks =c(-0.1,50,60,70,80,90,100),
# kobeShades=c("","\\cellcolor{gray90}","\\cellcolor{gray80}","\\cellcolor{gray70}","\\cellcolor{gray60}","\\cellcolor{gray50}"),
# pct="\\%",...){
#
# as.data.frame(apply(object,2,kobeShade,breaks=breaks,kobeShades=kobeShades,pct=pct))})
setMethod('kobeShade', signature(object='matrix'),
function(object,breaks =c(-0.1,50,60,70,80,90,100),
kobeShades=c("","\\cellcolor{gray90}","\\cellcolor{gray80}","\\cellcolor{gray70}","\\cellcolor{gray60}","\\cellcolor{gray50}"),
pct="\\%",...){
apply(object,2,kobeShade,breaks=breaks,kobeShades=kobeShades,pct=pct)})
setMethod('kobe2sm', signature(object='data.frame'),
function(object,cex =1.0,
image =list(levels=seq(0.0,1.0,0.05),
col =c(colorRampPalette(c("red4","red"))(12),colorRampPalette(c("yellowgreen","darkgreen"))(8))),
contour=list(levels=c(.6,.7,1.0,.9),
col =c("black"))){
nms =dimnames(object)[[2]]
nPlots=length(nms[nms %in% c("overFishing","overFished","green")])
ops<-par(mfrow=c(nPlots,1), mex=.5,mai=c( 0.5, 0.75 ,.750, 0.1),cex=par()$cex)
res=list()
if ("overFishing" %in% nms){
x=transform(object, NotOverFishing=as.numeric(1-object[,"overFishing"]))[,c(nms[1:2],"NotOverFishing")]
res[["F"]] =kobe2smFn(x, image=image,contour=contour)
mtext(expression(plain(P) (F<=F[MSY])),line=3, cex=cex)
}
if ("overFished" %in% nms){
x=transform(object, NotOverFished=as.numeric(1-object[,"overFished"]))[,c(nms[1:2],"NotOverFished")]
res[["SSB"]] =kobe2smFn(x, image=image,contour=contour)
mtext(expression(plain(P) (SSB>=SSB[MSY])),line=3, cex=cex)
}
if ("green" %in% nms){
res[["Joint"]]=kobe2smFn(cbind(object[,c(1:2)],object[,"green"]), image=image,contour=contour)
mtext(expression(plain(P) (F<=F[MSY]) %*% plain(P)(SSB>=SSB[MSY])),line=3, cex=cex)
}
par(mfrow=ops$mfrow,mex=ops$mex,mai=ops$mai,cex=ops$cex)
invisible(res)})
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