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hcr_op_batch_optimize_compare_species.R
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opt.table<-function(out.file,dirs,labels,first.y=2051,last.y=2051,stochastic=F,test=F,addFbar=F,tableIndicators=T,relativ=F){
#####################
for (dir in dirs) {
if ( file.access(file.path(data.path,dir,"op.dat"), mode = 0)!=0) stop(paste('Directory',dir,'does not exist'))
}
Init.function() # get SMS.contol object including sp.names
ref<-Read.reference.points.OP(dir=data.path)
Blim<-as.vector(c(rep(-1, first.VPA-1),ref[,'Blim']))
Bpa<-as.vector(c(rep(-1, first.VPA-1),ref[,'Bpa']))
Fpa<-as.vector(c(rep(-1, first.VPA-1),ref[,'Fpa']))
bb<-NULL
for (dir in dirs) {
a<-Read.OP.rep(dir=file.path(data.path,dir))
a<-data.frame(scen=dir,objFunc=a$objFunc,npar=a$npar,maxGrad=a$maxGrad,Penalty=a$Penalty)
bb<-rbind(bb,a)
}
bb<-data.frame(labels=labels,bb)
print(bb)
write.table(bb,file=file.path(paste(out.file,"_perform",'.out',sep='')),quote=F,row.names=F)
b<-NULL
for (dir in dirs) {
a<-Read.OP.condensed(dir=file.path(data.path,dir))
a<-droplevels(subset(a,Year>=first.y & Year<=last.y & Species !='Plaice' & Species !='Sole'))
a<-data.frame(scen=dir,a)
b<-rbind(b,a)
}
b$belowBlim<-ifelse(b$SSB<Blim[b$Species.n],1,0)
b$belowBpa<-ifelse(b$SSB<Bpa[b$Species.n],1,0)
b$aboveFpa<-ifelse(b$Fbar>Fpa[b$Species.n],1,0)
minY<-min(b$Year)
maxY<-max(b$Year)
ny<-maxY-minY+1
a<-aggregate(cbind(Fbar,yield,CWsum,value,SSB)~scen+Species.n+Species,mean,data=b)
asd<-aggregate(cbind(yield,value,SSB)~scen+Species.n+Species,sd,data=b)
hh<-dimnames(asd)[[2]]
hh<-sub('yield', 'yieldSD',hh)
hh<-sub('value', 'valueSD',hh)
hh<-sub('SSB', 'SSBSD',hh)
dimnames(asd)[[2]]<-hh
a2<-aggregate(list(Fbarmax=b$Fbar),list(scen=b$scen,Species.n=b$Species.n,Species=b$Species),max)
risk<-aggregate(cbind(belowBlim,belowBpa,aboveFpa)~scen+Species.n+Species,sum,data=b)
risk$belowBlim<-risk$belowBlim*100/ny
risk$belowBpa<-risk$belowBpa*100/ny
risk$aboveFpa<-risk$aboveFpa*100/ny
aa<-merge(a,a2)
aa<-merge(aa,asd)
aa<-merge(aa,risk)
label<-data.frame(scen=dirs,labels)
aa<-merge(aa,label)
aa$lab1<-substr(aa$labels,1,1)
aa$Species<-paste(aa$Species.n-first.VPA+1,'. ',aa$Species,sep='')
a<-tapply(aa$Fbarmax,list(aa$Species,aa$labels),sum)
if (addFbar) {
a2<-tapply(aa$Fbar,list(aa$Species,aa$labels),sum)
a<-cbind(a,a2)
}
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_F",'.html',sep='')),
dec=rep(2,dim(a)[[2]]), width='"100%"',units=ifelse (addFbar, c(rep('FMSY',length(dirs)),rep('Fbar',length(dirs))), rep('FMSY',length(dirs))))
if (relativ) {
for (i in (2:dim(a)[[2]])) a[,i]<-a[,i]/a[,1]*100
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_F_relativ",'.html',sep='')),
dec=c(2,rep(0,dim(a)[[2]]-1)), width='"100%"',units=c(' ',rep('(% of default.)',length(dirs)-1)))
}
a<-tapply(aa$belowBlim ,list(aa$Species,aa$labels),sum)
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_blim",'.html',sep='')),
dec=rep(1,dim(a)[[2]]), width='"100%"',units=' ')
a<-tapply(aa$yield ,list(aa$Species,aa$labels),sum) /1000
All<-tapply(aa$yield ,list(aa$labels),sum) /1000
a<-rbind(a,All)
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_yield",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=' ')
if (relativ) {
for (i in (2:dim(a)[[2]])) a[,i]<-a[,i]/a[,1]*100
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_yield_relativ",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=c('(kt) ',rep('(% of default.)',length(dirs)-1)))
}
a<-tapply(aa$CWsum-aa$yield ,list(aa$Species,aa$labels),sum) /1000
All<-tapply(aa$CWsum-aa$yield ,list(aa$labels),sum) /1000
a<-rbind(a,All)
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_discard",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=' ')
a<-tapply(aa$yield ,list(aa$Species,aa$labels),sum)
a2<-tapply(aa$yieldSD ,list(aa$Species,aa$labels),sum)
a<-a2/a*100
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_yield_CV",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=' ')
a<-tapply(aa$value ,list(aa$Species,aa$labels),sum) /1000
All<-tapply(aa$value ,list(aa$labels),sum) /1000
a<-rbind(a,All)
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_value",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=' ')
a<-tapply(aa$SSB ,list(aa$Species,aa$labels),sum) /1000
All<-tapply(aa$SSB ,list(aa$labels),sum) /1000
a<-rbind(a,All)
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_SSB",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=' ')
if (relativ) {
for (i in (2:dim(a)[[2]])) a[,i]<-a[,i]/a[,1]*100
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_SSB_relativ",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=c('(kt) ',rep('(% of default.)',length(dirs)-1)))
}
a<-tapply(aa$SSB ,list(aa$Species,aa$labels),sum)
a2<-tapply(aa$SSBSD ,list(aa$Species,aa$labels),sum)
a<-a2/a*100
xtab(a, caption='', cornername=' ',
file=file.path(paste(out.file,"_SSB_CV",'.html',sep='')),
dec=rep(0,dim(a)[[2]]), width='"100%"',units=' ')
if (tableIndicators) {
b<-NULL
for (dir in dirs) {
a<-Read.OP.community.indicator(dir=file.path(data.path,dir))
a<-droplevels(subset(a,Year>=first.y & Year<=last.y ))
a<-data.frame(scen=dir,a)
b<-rbind(b,a)
}
label<-data.frame(scen=dirs,labels)
aa<-merge(b,label)
aaa<-aggregate(cbind(bio.demer,bio.small,bio.pelag,bio.forage,comm.Fland,comm.Fall,comm.M,comm.M2,community.life.expect,LFI) ~ labels,data=aa,mean)
b<-cbind(aaa$comm.M2*100,aaa$comm.Fall*100,aaa$LFI*100,aaa$community.life.expect,aaa$bio.forage/1000,aaa$bio.pelag/aaa$bio.demer)
b<-t(b)
dimnames(b)[[1]]<-c("Community M2 (%)","Community F (%)","LFI (%)","life expectancy (years)","Biomass forage (kt)","Biomass ratio pelagic:demersal")
dimnames(b)[[2]]<-aaa$labels
xtab3(b, caption='', cornername=' ',
file=file.path(paste(out.file,"_sys_Indicators",'.html',sep='')),
dec=c(0,0,0,2,0,2), width='"100%"',units=' ')
}
}
#################
#dirs<-paste("D1f_HCR_1_1_Rec0_penBpa____CVadj_limF_110_Oth",1:10,sep='')
#dirs<-paste("D2f_HCR_2_0_Rec0_penBpa____CVadj_limF_110_Oth",1:10,sep='')
#dirs<-paste("D1f_HCR_1_1_Rec0_penBpa____CVadj_limF_110_Oth",1:10,sep='')
dirs<-paste("D1c_HCR_1_1_Rec0_penBpa_atAgeW___CVadj_limF_110_Oth",1:10,sep='')
#dirs<-paste("D1e_HCR_1_1_Rec0_penBlim____CVadj_limF_110_Oth",1:10,sep='')
#dirs<-paste("D1b_HCR_1_1_Rec0_penBlim_atAgeW___CVadj_limF_110_Oth",1:10,sep='')
labels<-c('01. Default','02. Birds','03. R. radiata','04. Gurnards','05. Mackerel','06. Horse Mackerel','07. Grey seal','08. Porpoise','09. Hake','10. All')
opt.table(out.file=file.path(data.path,'opti_compare_determ_HCR1_species_1c'),first.y=2043,last.y=2043,stochastic=F, test=T,
dirs=dirs,relativ=T,
labels=labels )
##############
dirs<-c(
"D1a_HCR_1_1_Rec0__atAgeW___CVadj_limF_110_",
"D1d_HCR_1_1_Rec0_____CVadj_limF_110_",
"D1b_HCR_1_1_Rec0_penBlim_atAgeW___CVadj_limF_110_",
"D1e_HCR_1_1_Rec0_penBlim____CVadj_limF_110_",
"D1c_HCR_1_1_Rec0_penBpa_atAgeW___CVadj_limF_110_",
"D1f_HCR_1_1_Rec0_penBpa____CVadj_limF_110_"
)
labels<-c(
"Value",
"Yield",
"Value, penalize SSB < Blim",
"Yield, penalize SSB < Blim",
"Value, penalize SSB < Bpa",
"Yield, penalize SSB < Bpa"
)
opt.table(out.file=file.path(data.path,'opti_compare_determ_Species_HCR1_all'),first.y=2034,last.y=2043,stochastic=F, test=T,
dirs=dirs,
labels=labels )
dirs<-c(
"D2a_HCR_2_0_Rec0__atAgeW___CVadj_limF_110_",
"D2d_HCR_2_0_Rec0_____CVadj_limF_110_",
"D2b_HCR_2_0_Rec0_penBlim_atAgeW___CVadj_limF_110_",
"D2e_HCR_2_0_Rec0_penBlim____CVadj_limF_110_",
"D2c_HCR_2_0_Rec0_penBpa_atAgeW___CVadj_limF_110_",
"D2f_HCR_2_0_Rec0_penBpa____CVadj_limF_110_"
)
labels<-c(
"Value",
"Yield",
"Value, penalize SSB < Blim",
"Yield, penalize SSB < Blim",
"Value, penalize SSB < Bpa",
"Yield, penalize SSB < Bpa"
)
opt.table(out.file=file.path(data.path,'opti_compare_determ_Species_HCR2'),first.y=2034,last.y=2043,stochastic=F, test=T,
dirs=dirs,
labels=labels )