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make_plots.R
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make_plots.R
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# file including functions for various plots
plot_other<-function(sp,firsty,lasty,chOther,firstYear=stq_year, finalYear){
x<-firstYear:finalYear
y<-rep(1.0,length(x))
names(y)<-as.character(x)
if (firstYear==firsty) y[as.character(firsty)]<-chOther
for (year in firsty:lasty) if (year>firstYear) {y[as.character(year)]<-y[as.character(year-1)]*chOther }
if (finalYear>lasty) for (year in ((lasty+1):finalYear)) y[as.character(year)]<-y[as.character(lasty)]
plot(x,y,ylab='stock abundance index',xlab='Year',main=sp,type='b')
}
plot_summary_new<-function(res,ptype=c('Yield','Fbar','SSB','Recruits','Dead','M2'),years=c(0,5000),species='Cod',splitLine=FALSE,incl.reference.points=FALSE,nox=2,noy=3) {
a<-as_tibble(subset(res$out$detail_sum,Year>=years[1] & Year<=years[2] & Species %in% species))
a2<-subset(histCondensed,Year>=years[1] & Year<=years[2] & Species %in% species)
a<-bind_rows(a,a2)%>% mutate(Year=as.integer(Year)) %>% arrange(Year)
b<-subset(res$out$detail_M2,Year>=years[1] & Year<=years[2] & Species %in% species)
b2<-subset(histAnnoM,Year>=years[1] & Year<=years[2] & Species %in% species)
b<-bind_rows(b,b2) %>% arrange(Year,Age)
if ("SSB" %in% ptype) {
pSSB<-ggplot(a,aes(x=Year,y=SSB))+
geom_line(lwd=1.5)+
geom_point(shape = 21, colour = "black", fill = "white", size = 2, stroke = 1.5)+
labs(x='',y=plotLabels['SSB'],title=paste(species,'SSB',sep=', '))+
ylim(0,max(a$SSB))+
theme(plot.title = element_text(size = 16, face = "bold",hjust=0))
if (splitLine) pSSB<- pSSB+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
if (incl.reference.points) {
if (refPoints[species,'Blim']>0) pSSB<- pSSB+geom_hline(yintercept=refPoints[species,'Blim'],lty=2,lwd=1,col='red',,na.rm = TRUE)
if (refPoints[species,'Bpa']>0) pSSB<- pSSB+geom_hline(yintercept=refPoints[species,'Bpa'],lty=3,lwd=1,col='green',na.rm = TRUE)
}
}
if ("Recruits" %in% ptype) {
y <-aggregate(Recruits~Year,data=a,sum)
pRec<-ggplot(y,aes(x=Year,y=Recruits)) +
geom_bar(stat = "identity")+
labs(x='',y=plotLabels['Recruits'],title='Recruitment')+
theme(plot.title = element_text(size = 16, face = "bold"))
if (splitLine) pRec<- pRec+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
}
if ("Fbar" %in% ptype) {
pF<-ggplot(a,aes(x=Year,y=Fbar))+
geom_line(lwd=1.5)+
geom_point(shape = 21, colour = "black", fill = "white", size = 2, stroke = 1.5)+
labs(x='',y=plotLabels['Fbar'],title='Fishing mortality, F')+
ylim(0,max(a$Fbar))+
theme(plot.title = element_text(size = 16, face = "bold"))
if (splitLine) pF<- pF+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
if (incl.reference.points) {
if ( refPoints[species,'Flim']>0) pF<- pF+geom_hline(yintercept=refPoints[species,'Flim'],lty=2,lwd=1,col='red',na.rm = TRUE)
if (refPoints[species,'Fpa']>0) pF<- pF+geom_hline(yintercept=refPoints[species,'Fpa'],lty=3,lwd=1,col='green',na.rm = TRUE)
}
}
if ("Yield_old" %in% ptype) {
y <-aggregate(Yield~Year,data=a,sum)
pY<-ggplot(y,aes(x=Year,y=Yield)) +
geom_bar(stat = "identity")+
labs(x='',y=plotLabels['Yield'],title='Catch')+
theme(plot.title = element_text(size = 16, face = "bold"))
if (splitLine) pY<- pY+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
}
if ("Yield" %in% ptype) {
y<-select(a,Year,Yield,yield.core) %>% mutate(yield.outside=Yield-yield.core,Yield=NULL) %>% select(Year,yield.outside,yield.core)
y<-as.data.frame(y)
if (any(y$yield.outside>0)) titl<-'Catch inside and outside the North Sea' else titl<-'Catch'
y<-reshape(y,direction='long',varying = list(2:3))
pY<-ggplot(y, aes(x = Year, y = yield.outside, fill = as.factor(time)) )+
geom_bar(stat = "identity")+
labs(x='',y=plotLabels['Yield'],title=titl)+
theme(plot.title = element_text(size = 16, face = "bold"),legend.position="none")
if (splitLine) pY<- pY+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
}
if ("Dead" %in% ptype) {
y<-select(a,Year,Yield,DeadM1,DeadM2)
y<-as.data.frame(y)
if (any(y$DeadM2>0)) titl<-'Biomass removed\ndue to F, M1 and M2' else titl<-'Biomass removed\ndue to F and M1'
y<-reshape(y,direction='long',varying = list(2:4))
pD<-ggplot(y, aes(x = Year, y = Yield, fill = as.factor(time)) )+
geom_bar(stat = "identity")+
labs(x='',y=plotLabels['DeadM'],title=titl)+
theme(plot.title = element_text(size = 16, face = "bold"),legend.position="none")
if (splitLine) pD<- pD+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
}
if ("M2" %in% ptype) if (any(b$M2>0)) {
b$Age<-as.factor(b$Age)
m2<-aggregate(M2~Year+Age,data=b,sum)
m2max<-aggregate(cbind(maxM2=M2)~Age,data=b,max)
m2<-droplevels(subset(merge(m2,m2max),maxM2>0.01 & as.character(Age)<"6"))
pM<-ggplot(m2,aes(x=Year,y=M2,color=Age, shape=Age)) +
geom_line(lwd=1)+
geom_point()+
labs(x='',y=plotLabels['Fbar'],title='M2 at age')+
ylim(0,max(m2max$maxM2))+
theme(plot.title = element_text(size = 16, face = "bold"),legend.position="none")
if (splitLine) pM<- pM+geom_vline(xintercept=stq_year,col='blue',lty=3,lwd=1)
}
if (any(b$M2>0)) out<-plot_grid(pSSB,pD,pF,pRec,pY,pM,ncol=3, nrow=2) else out<-plot_grid(pSSB,pD,pF,pRec,pY,ncol=3, nrow=2)
return(out)
}
plot_who_eats<-function(x,pred,prey,predPrey='by prey',years=c(0,5000),exclHumans=TRUE,exclResidM1=TRUE){
x<-bind_rows(histEaten,x)
pp<-setNames(my.colors,predPreyFormat)
x<-filter(x,Year>=years[1] & Year<=years[2])
if (exclHumans) x<-filter(x,Predator !=predPreyFormat[2])
if (exclResidM1) x<-filter(x,Predator !=predPreyFormat[1])
if (prey != 'all preys') {
tit<-paste(prey, "eaten by");
x<-filter(x,Prey==prey)
} else tit<-'All preys eaten by'
p<-unique(x$Prey)
prey_pp<-pp[predPreyFormat %in% p]
if (pred !='all predators') {
x<-filter(x,Predator==pred);
tit<-paste(tit,pred)
} else tit<-paste(tit,'all predators')
p<-unique(x$Predator)
pred_pp<-pp[predPreyFormat %in% p]
if (dim(x)[[1]]==0) return(NULL)
xxcel<<-x
if (predPrey=='by prey') {
pp<-prey_pp
x <-droplevels(aggregate(eatenW~Year+Prey,data=x,sum))
p<-ggplot(x, aes(x = Year, y = eatenW, fill = Prey))
} else if (predPrey=='by predator') {
pp<-pred_pp
x <-droplevels(aggregate(eatenW~Year+Predator,data=x,sum))
p<-ggplot(x, aes(x = Year, y = eatenW, fill = Predator))
}
p<-p + geom_bar(stat = "identity") +
scale_fill_manual(values= pp[!is.na(names(pp))])+
labs(x="", y = paste("Biomass eaten",plotLabels['DeadM'])) +
ggtitle(tit) +
theme_minimal() +
theme(plot.title = element_text(size = 18, face = "bold"))
return(p)
}
FoodWeb_plot <-function(x,pred,prey,predPrey='by prey',year=2000,width=NULL,height=NULL,margin=NULL,MyPalette=c('red','blue'),incl_sp='Cod') {
x<-bind_rows(histEaten,x)
x<-filter(x,Year==year & Predator %in% incl_sp & Prey %in% incl_sp)
#save(x,file=paste0('x2',year,'.data'))
x<-mutate(x,target=as.character(Predator),source=as.character(Prey)) %>% as.data.frame
# From these flows we need to create a node data frame: it lists every entities involved in the flow
nodes<-rbind(unique(data.frame(no=x$Predator.no, name=x$target)),
unique(data.frame(no=x$Prey.no, name=x$source))) %>% unique() %>% arrange(no) %>% select(name)
# need to reformat it.
x$IDsource=match(x$source, nodes$name)-1
x$IDtarget=match(x$target, nodes$name)-1
# prepare colour scale
#ColourScal ='d3.scaleOrdinal() .range(["#FDE725FF","#B4DE2CFF","#6DCD59FF","#35B779FF","#1F9E89FF","#26828EFF","#31688EFF","#3E4A89FF","#482878FF","#440154FF"])'
col2hex<-function (cname) {
colMat <- col2rgb(cname)
rgb(red = colMat[1, ]/255, green = colMat[2, ]/255, blue = colMat[3,
]/255)
}
ii<-NULL
for (i in col2hex(MyPalette)) ii<-paste(ii,paste0('"',i,'"'),sep=',')
ColourScal <- paste0('d3.scaleOrdinal() .range([', ii,'])')
# Make the Network
p<-sankeyNetwork(Links = x, Nodes = nodes,
Source = "IDsource", Target = "IDtarget",
Value = "eatenW", NodeID = "name",
sinksRight=FALSE,
units='kt',width=width,height=height,margin=margin,
# iterations = 0, # this will give the same layout (as defined by order of the nodes) for all years,
#colourScale=ColourScal,
nodeWidth=35, fontSize=12, nodePadding=10)
#saveWidget(p, file=file.path( paste0("sankey_",year,".html")))
return(p)
}
# Radar plot function
plot_one<-function(x,type='Yield',plot.legend = TRUE) {
a1 <- filter(x$out$b,variable==type)
a1[,2:(n.fleet+1)]<- a1[,2:(n.fleet+1)]/x$baseLine[,type]
a2<- a1
a2[,2:(n.fleet+1)]<- 1
a<-bind_rows(a1,a2)
tit<-ifelse(type=='Fbar'," F",paste0(' ',type))
a[1,'variable']<-tit
a[2,'variable']<-'Baseline'
gmax<-max( a[,2:(n.fleet+1)])
DTU.col<-c("#990000", # red
"#F6D04D") # yellow
ggradar(a,grid.max=gmax,grid.min=0,plot.title='',plot.legend=plot.legend,legend.position='top',
group.colours =DTU.col,legend.text.size = 18)
}
plot_radar_all<-function(res){
pF<-plot_one(res,type='Fbar',plot.legend = TRUE)
pYield<-plot_one(res,type='Yield')
pRec<-plot_one(res,type='Recruits')
pSSB<-plot_one(res,type='SSB')
plot_grid(pF, pYield, pRec,pSSB,
ncol = 2, nrow = 2)
}