utils::globalVariables(c("ggplot","geom_line","aes","yield",
"geom_point","cast","xlab","ylab"))
utils::globalVariables(c("scale_alpha_manual"))
utils::globalVariables('data')
setMethod('plot', signature(x='aspics',y='missing'),
function(x, y, probs=c(0.95,0.75,0.50,0.25,0.05),type=7,na.rm=FALSE,
facet=facet_wrap(~qname,scales='free',ncol=1),
fn=list('Stock' =function(x) stock(x),
'Harvest'=function(x) harvest(x),
'Yield' =function(x) catch(x)),...)
{
res=ldply(x,function(x) plot(x,probs=probs,type=type,na.rm=na.rm)$data)
mdn=ldply(x,function(x) whooow(x,fn,probs=.5))
if (length(unique(res$CI))>=1){
p=ggplot(res)+
geom_ribbon(aes(year,ymax=ymax,ymin=ymin,alpha=CI,group=paste(.id,CI),fill=.id))+
geom_line( aes(year,data,col=.id,group=.id),data=mdn)+
scale_alpha_manual(values=seq(.1,.75,length.out=length(unique(res$CI))))
}else{
p=ggplot(res)+
geom_line(aes(year,data,col=.id,group=.id),data=mdn)
}
p = p + facet +
expand_limits(y = 0) +
xlab('Year') + ylab('')
p})
#' plot aspics,missing
#' plotIndex aspic
#' plotIndex aspics
# @param \code{fn}, a list of functions that estimate the quantities for plotting
# @param \code{probs}, a vector specifying the percentiles for plotting, these are c(0.95,0.50,0.05) by default.
# @param \code{size}, thinkness of percentile lines
# @param \code{lty}, line type for percentiles
# @param \code{facet}, a layer that determines the facetting of the plot
plotProduction=function(object,biomass=FLQuant(seq(0,max(params(object)["k"]),length.out=101))) {
object=as(object,"biodyn")
if ((dims(object)$iter>1 | dims(params(object))$iter>1) & dims(biomass)$iter==1)
biomass=propagate(biomass,max(dims(object)$iter,dims(params(object))$iter))
p=model.frame(FLQuants(stock=biomass, yield=FLQuant(production(object,biomass))))
p=ggplot(p)+
geom_line(aes(stock, yield, group=iter, col=iter)) +
geom_point(aes(bmsy,msy,col=iter),size=4,
data=model.frame(refpts(object))) +
geom_path(aes(stock, yield, group=iter, col=iter),
data=model.frame(mcf(FLQuants(
stock=stock(object),
yield=catch(object))))) +
xlab("Stock") + ylab("Surplus Production")
p}
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