inst/Frameworks/LFA3438Framework/LFA35-38Assessment/lobster.sim.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
# Lobster population simulation
p = bio.lobster::load.environment()
require(fields)
la()
SoMplot(Areas='34',graphic='png',fp=file.path(project.datadirectory('bio.lobster'),'figures','LFA3438Framework2019'),LS=82.5,legend=F)
TempModelling = TempModel(areas = 'subarea')
#TempModelPlot(TempModelling,xlim=c(1980,2017),depths=c(5,25,50),Area=c("27N","27S", "29", "30","31A","31B", "32", "33E", "33W"),graphic='R')
p$TempModel = TempModelling$Model
TempModelling = TempModel(areas = 'subarea',annual.by.area=T)
tempModel=TempModelPlot(TempModelling,xlim=c(1980,2018),depths=c(5,25,50),Area=p$subareas,graphic='png',type=1:3)
MoltModelling = moltModel(p,redo.dd=F)
p$moltModel = MoltModelling
#moltModelPlot(p$moltModel,graphic='png')
p$lfas = c("34") # specify lfa
p$season = c("1999-11-28","2000-05-31")
e= 0.6789005
t = as.numeric(as.Date(p$season[2])-as.Date(p$season[1]))/365
p$F = -log(1-e)/t
####### Base
plist = getSimList(p,sex=1)
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2)
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
simBubPlot(rlist,graphic='R',cex.lab=2,cex.axis=1.5)
round(rlist$mlist$'27N'$moltProb[,,1,1],2)
##### Legal Size
LegalSize = c(85,87.5,90)
names(LegalSize) = paste0("LS",LegalSize)
for(i in 1:length(LegalSize)){
plist = getSimList(p,sex=1,LS=LegalSize[i])
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,LS=LegalSize[i])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(LegalSize)[i],".rdata")))
}
############ Season reduction
ShorterSeason = c(0.9,0.8,0.7,0.6,0.5)
names(ShorterSeason) = paste0("SS",9:5)
for(i in 1:length(ShorterSeason)){
plist = getSimList(p,sex=1,Sadj=ShorterSeason[i], Sclose='start')
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,Sadj=ShorterSeason[i])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(ShorterSeason)[i],".rdata")))
}
##### Window size
WindowSize = list(c(115,125),c(105,125))
names(WindowSize) = c("SmallWin","BigWin")
for(i in 1:length(WindowSize)){
plist = getSimList(p,sex=1,window=WindowSize[[i]])
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,window=WindowSize[[i]])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(WindowSize)[i],".rdata")))
}
##### Max size
MaxSize = list(c(135,210),c(130,210),c(125,210))
names(MaxSize) = paste0("Max",lapply(MaxSize,min))
for(i in 1:length(MaxSize)){
plist = getSimList(p,sex=1,window=MaxSize[[i]])
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,window=MaxSize[[i]])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(MaxSize)[i],".rdata")))
}
for(i in 1:length(WindowSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
rlistb = rlist
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(WindowSize)[i],".rdata")))
rlist1 = rlist
#females only
rlist = list(plist=rlist1$plist,mlist=rlistb$mlist,flist=rlist1$flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(WindowSize)[i],".rdata")))
}
for(i in 1:length(MaxSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
rlistb = rlist
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(MaxSize)[i],".rdata")))
rlist1 = rlist
#females only
rlist = list(plist=rlist1$plist,mlist=rlistb$mlist,flist=rlist1$flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(MaxSize)[i],".rdata")))
}
############# Plots
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
simBubPlot(rlist,graphic='R',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn='Base',cex.lab=2,cex.axis=1.5)
for(i in 1:length(ShorterSeason)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(ShorterSeason)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(ShorterSeason)[i],cex.lab=2,cex.axis=1.5)
}
for(i in 1:length(LegalSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(LegalSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(LegalSize)[i],cex.lab=2,cex.axis=1.5)
}
for(i in 1:length(WindowSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(WindowSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(WindowSize)[i],cex.lab=2,cex.axis=1.5)
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(WindowSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=paste0("F",names(WindowSize)[i]),cex.lab=2,cex.axis=1.5)
}
for(i in 1:length(MaxSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(MaxSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(MaxSize)[i],cex.lab=2,cex.axis=1.5)
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(MaxSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=paste0("F",names(MaxSize)[i]),cex.lab=2,cex.axis=1.5)
}
LFAs = c("34")
simSumLegalSize = simSummary(runs=c("Base","LS85","LS87.5","LS90"),lfas=LFAs,lab=34)
simSumSeason = simSummary(runs=c("Base","SS9","SS8","SS7","SS6","SS5"),lfas=LFAs,lab=34)
simSumWindow = simSummary(runs=c("Base","FSmallWin","FBigWin","SmallWin","BigWin"),lfas=LFAs,lab=34)
simSumMaxSize = simSummary(runs=c("Base","FMax125","FMax130","FMax135","Max125","Max130","Max135"),lfas=LFAs,lab=34)
LStabRP = data.frame(rbind(
round(100*(simSumLegalSize[[1]][4,]/simSumLegalSize[[1]][1,]-1)),
round(100*(simSumLegalSize[[1]][3,]/simSumLegalSize[[1]][1,]-1)),
round(100*(simSumLegalSize[[1]][2,]/simSumLegalSize[[1]][1,]-1))
))
names(LStabRP) = LFAs
rownames(LStabRP) = c("LS82.5", "LS80", "LS78.5")
write.csv(LStabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","LStab34RP70.csv"),row.names=T)
LStabNo = data.frame(rbind(
round(100*(simSumLegalSize[[2]][4,]/simSumLegalSize[[2]][1,]-1)),
round(100*(simSumLegalSize[[2]][3,]/simSumLegalSize[[2]][1,]-1)),
round(100*(simSumLegalSize[[2]][2,]/simSumLegalSize[[2]][1,]-1))
))
names(LStabNo) = LFAs
rownames(LStabNo) = c("LS82.5", "LS80", "LS78.5")
write.csv(LStabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","LStab34No70.csv"),row.names=T)
LStabKg = data.frame(rbind(
round(100*(simSumLegalSize[[3]][4,]/simSumLegalSize[[3]][1,]-1)),
round(100*(simSumLegalSize[[3]][3,]/simSumLegalSize[[3]][1,]-1)),
round(100*(simSumLegalSize[[3]][2,]/simSumLegalSize[[3]][1,]-1))
))
names(LStabKg) = LFAs
rownames(LStabKg) = c("LS82.5", "LS80", "LS78.5")
write.csv(LStabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","LStab34Kg70.csv"),row.names=T)
OStabRP = data.frame(rbind(
round(100*(simSumSeason[[1]][6,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][5,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][4,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][3,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][2,]/simSumSeason[[1]][1,]-1))
))
names(OStabRP) = LFAs
rownames(OStabRP) = c("SS5", "SS6", "SS7", "SS8", "SS9")
write.csv(OStabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","OStab34RP.csv"),row.names=T)
OStabNo = data.frame(rbind(
round(100*(simSumSeason[[2]][6,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][5,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][4,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][3,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][2,]/simSumSeason[[2]][1,]-1))
))
names(OStabNo) = LFAs
rownames(OStabNo) = c("SS5", "SS6", "SS7", "SS8", "SS9")
write.csv(OStabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","OStab34No.csv"),row.names=T)
OStabKg = data.frame(rbind(
round(100*(simSumSeason[[3]][6,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][5,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][4,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][3,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][2,]/simSumSeason[[3]][1,]-1))
))
names(OStabKg) = LFAs
rownames(OStabNo) = c("SS5", "SS6", "SS7", "SS8", "SS9")
write.csv(OStabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","OStab34Kg.csv"),row.names=T)
WintabRP = data.frame(rbind(
round(100*(simSumWindow[[1]][5,]/simSumWindow[[1]][1,]-1)),
round(100*(simSumWindow[[1]][4,]/simSumWindow[[1]][1,]-1)),
round(100*(simSumWindow[[1]][3,]/simSumWindow[[1]][1,]-1)),
round(100*(simSumWindow[[1]][2,]/simSumWindow[[1]][1,]-1))
))
names(WintabRP) = LFAs
rownames(WintabRP) = c("BigWin", "SmallWin","FBigWin", "FSmallWin")
write.csv(WintabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Wintab34RP.csv"),row.names=T)
WintabNo = data.frame(rbind(
round(100*(simSumWindow[[2]][5,]/simSumWindow[[2]][1,]-1)),
round(100*(simSumWindow[[2]][4,]/simSumWindow[[2]][1,]-1)),
round(100*(simSumWindow[[2]][3,]/simSumWindow[[2]][1,]-1)),
round(100*(simSumWindow[[2]][2,]/simSumWindow[[2]][1,]-1))
))
names(WintabNo) = LFAs
rownames(WintabNo) = c("BigWin", "SmallWin","FBigWin", "FSmallWin")
write.csv(WintabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Wintab34No.csv"),row.names=T)
WintabKg = data.frame(rbind(
round(100*(simSumWindow[[3]][5,]/simSumWindow[[3]][1,]-1)),
round(100*(simSumWindow[[3]][4,]/simSumWindow[[3]][1,]-1)),
round(100*(simSumWindow[[3]][3,]/simSumWindow[[3]][1,]-1)),
round(100*(simSumWindow[[3]][2,]/simSumWindow[[3]][1,]-1))
))
names(WintabKg) = LFAs
rownames(WintabKg) = c("BigWin", "SmallWin","FBigWin", "FSmallWin")
write.csv(WintabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Wintab34Kg.csv"),row.names=T)
MaxtabRP = data.frame(rbind(
round(100*(simSumMaxSize[[1]][7,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][6,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][5,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][4,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][3,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][2,]/simSumMaxSize[[1]][1,]-1))
))
names(MaxtabRP) = LFAs
rownames(MaxtabRP) = c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125")
write.csv(MaxtabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Maxtab34RP.csv"),row.names=T)
MaxtabNo = data.frame(rbind(
round(100*(simSumMaxSize[[2]][7,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][6,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][5,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][4,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][3,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][2,]/simSumMaxSize[[2]][1,]-1))
))
names(MaxtabNo) = LFAs
rownames(MaxtabNo) = c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125")
write.csv(MaxtabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Maxtab34No.csv"),row.names=T)
MaxtabKg = data.frame(rbind(
round(100*(simSumMaxSize[[3]][7,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][6,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][5,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][4,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][3,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][2,]/simSumMaxSize[[3]][1,]-1))
))
names(MaxtabKg) = LFAs
rownames(MaxtabKg) = c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125")
write.csv(MaxtabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Maxtab34Kg.csv"),row.names=T)
for(i in 1){
LS=data.frame(Eggs=LStabRP[,i],Numbers=LStabNo[,i],Weight=LStabKg[,i],row.names= c("LS90", "LS87.5", "LS85"))
OS=data.frame(Eggs=OStabRP[,i],Numbers=OStabNo[,i],Weight=OStabKg[,i],row.names= c("SS5", "SS6", "SS7", "SS8", "SS9"))
Win=data.frame(Eggs=WintabRP[,i],Numbers=WintabNo[,i],Weight=WintabKg[,i],row.names= c("BigWin", "SmallWin","FBigWin", "FSmallWin"))
Max=data.frame(Eggs=MaxtabRP[,i],Numbers=MaxtabNo[,i],Weight=MaxtabKg[,i],row.names= c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125"))
write.csv(rbind(LS,OS,Win,Max),file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("LFA",LFAs[i],".csv")),row.names=T)
}
cols=tim.colors(9)
ltys=1:9
pchs=c(1:6,15:17)
#x11()
png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumLegalSize.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(70,90,2.5),simSumLegalSize$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
axis(4)
abline(v=82.5,lty=3,col='grey')
legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(70,90,2.5),simSumLegalSize$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
axis(4)
abline(v=82.5,lty=3,col='grey')
matplot(x=seq(70,90,2.5),simSumLegalSize$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
axis(4)
abline(v=82.5,lty=3,col='grey')
mtext("Minimum Legal Size (mm)",1,3)
dev.off()
#x11()
png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumSeason.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(0,50,10),simSumSeason$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
axis(4)
#abline(v=0,lty=3,col='grey')
legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(0,50,10),simSumSeason$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
axis(4)
#abline(v=0,lty=3,col='grey')
matplot(x=seq(0,50,10),simSumSeason$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
axis(4)
#abline(v=0,lty=3,col='grey')
mtext("Season reduction (%)",1,3)
dev.off()
#####
x11()
#png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumLegalSize.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(82.5,90,2.5),simSumLegalSize$landnum[6:9,],type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
par(new=T)
matplot(x=seq(0,50,10),simSumSeason$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
#abline(v=82.5,lty=3,col='grey')
#legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(82.5,90,2.5),simSumLegalSize$landkg[6:9,],type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
par(new=T)
matplot(x=seq(0,50,10),simSumSeason$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
#abline(v=82.5,lty=3,col='grey')
matplot(x=seq(82.5,90,2.5),simSumLegalSize$eggs[6:9,]/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
par(new=T)
matplot(x=seq(0,50,10),simSumSeason$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
#abline(v=82.5,lty=3,col='grey')
mtext("Minimum Legal Size (mm)",1,3)
#dev.off()
par(new=T)
#x11()
#png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumSeason.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(0,50,10),simSumSeason$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
#abline(v=0,lty=3,col='grey')
legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(0,50,10),simSumSeason$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
#abline(v=0,lty=3,col='grey')
matplot(x=seq(0,50,10),simSumSeason$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
#abline(v=0,lty=3,col='grey')
mtext("Season reduction (%)",1,3)
dev.off()
# from 1.IndicatorEstimation.CohortAnalysis.r
ad
outS
bins=seq(80,150,5)
### LFA 33
is=which(ad$LFA==33&ad$YEAR>2001)
CLF.lst=list()
lens=NULL
for(i in is) lens = c(lens,outS[[i]])
CLF.lst[[1]]=hist(lens[lens>82.5&lens<max(bins)],breaks=bins,plot=F)$counts
#load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
CLF.lst[[2]]=
colSums(rlist$mlist$'33W'$totalRemovals[,7:31])+
colSums(rlist$mlist$'33E'$totalRemovals[,7:31])+
colSums(rlist$flist$'33W'$totalRemovals[,7:31])+
colSums(rlist$flist$'33E'$totalRemovals[,7:31])
compareCLF(CLF.lst,bins=bins,col='grey',rel=T,graphic='pdf',filen=file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018',"CLFcompareLFA33.pdf"),LS=c(82.5,82.5),xl=c(0,length(bins)),title="LFA 33",labels=c("At Sea Sampling","Simulation"))
##############
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
transMat = getTransMatrix(rlist)
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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# Lobster population simulation
p = bio.lobster::load.environment()
require(fields)
la()
SoMplot(Areas='34',graphic='png',fp=file.path(project.datadirectory('bio.lobster'),'figures','LFA3438Framework2019'),LS=82.5,legend=F)
TempModelling = TempModel(areas = 'subarea')
#TempModelPlot(TempModelling,xlim=c(1980,2017),depths=c(5,25,50),Area=c("27N","27S", "29", "30","31A","31B", "32", "33E", "33W"),graphic='R')
p$TempModel = TempModelling$Model
TempModelling = TempModel(areas = 'subarea',annual.by.area=T)
tempModel=TempModelPlot(TempModelling,xlim=c(1980,2018),depths=c(5,25,50),Area=p$subareas,graphic='png',type=1:3)
MoltModelling = moltModel(p,redo.dd=F)
p$moltModel = MoltModelling
#moltModelPlot(p$moltModel,graphic='png')
p$lfas = c("34") # specify lfa
p$season = c("1999-11-28","2000-05-31")
e= 0.6789005
t = as.numeric(as.Date(p$season[2])-as.Date(p$season[1]))/365
p$F = -log(1-e)/t
####### Base
plist = getSimList(p,sex=1)
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2)
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
simBubPlot(rlist,graphic='R',cex.lab=2,cex.axis=1.5)
round(rlist$mlist$'27N'$moltProb[,,1,1],2)
##### Legal Size
LegalSize = c(85,87.5,90)
names(LegalSize) = paste0("LS",LegalSize)
for(i in 1:length(LegalSize)){
plist = getSimList(p,sex=1,LS=LegalSize[i])
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,LS=LegalSize[i])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(LegalSize)[i],".rdata")))
}
############ Season reduction
ShorterSeason = c(0.9,0.8,0.7,0.6,0.5)
names(ShorterSeason) = paste0("SS",9:5)
for(i in 1:length(ShorterSeason)){
plist = getSimList(p,sex=1,Sadj=ShorterSeason[i], Sclose='start')
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,Sadj=ShorterSeason[i])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(ShorterSeason)[i],".rdata")))
}
##### Window size
WindowSize = list(c(115,125),c(105,125))
names(WindowSize) = c("SmallWin","BigWin")
for(i in 1:length(WindowSize)){
plist = getSimList(p,sex=1,window=WindowSize[[i]])
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,window=WindowSize[[i]])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(WindowSize)[i],".rdata")))
}
##### Max size
MaxSize = list(c(135,210),c(130,210),c(125,210))
names(MaxSize) = paste0("Max",lapply(MaxSize,min))
for(i in 1:length(MaxSize)){
plist = getSimList(p,sex=1,window=MaxSize[[i]])
names(plist) = p$lfas
mlist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(mlist) = p$lfas
plist = getSimList(p,sex=2,window=MaxSize[[i]])
names(plist) = p$lfas
flist = mclapply(X = plist, FUN = simMolt, mc.cores=length(p$lfas))
names(flist) = p$lfas
rlist = list(plist=plist,mlist=mlist,flist=flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(MaxSize)[i],".rdata")))
}
for(i in 1:length(WindowSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
rlistb = rlist
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(WindowSize)[i],".rdata")))
rlist1 = rlist
#females only
rlist = list(plist=rlist1$plist,mlist=rlistb$mlist,flist=rlist1$flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(WindowSize)[i],".rdata")))
}
for(i in 1:length(MaxSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
rlistb = rlist
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(MaxSize)[i],".rdata")))
rlist1 = rlist
#females only
rlist = list(plist=rlist1$plist,mlist=rlistb$mlist,flist=rlist1$flist)
save("rlist",file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(MaxSize)[i],".rdata")))
}
############# Plots
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
simBubPlot(rlist,graphic='R',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn='Base',cex.lab=2,cex.axis=1.5)
for(i in 1:length(ShorterSeason)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(ShorterSeason)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(ShorterSeason)[i],cex.lab=2,cex.axis=1.5)
}
for(i in 1:length(LegalSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(LegalSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(LegalSize)[i],cex.lab=2,cex.axis=1.5)
}
for(i in 1:length(WindowSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(WindowSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(WindowSize)[i],cex.lab=2,cex.axis=1.5)
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(WindowSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=paste0("F",names(WindowSize)[i]),cex.lab=2,cex.axis=1.5)
}
for(i in 1:length(MaxSize)){
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34Results",names(MaxSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=names(MaxSize)[i],cex.lab=2,cex.axis=1.5)
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("sim34ResultsF",names(MaxSize)[i],".rdata")))
simBubPlot(rlist,graphic='png',path=file.path(project.datadirectory("bio.lobster"),"figures","LFA3438Framework2019","sim"),fn=paste0("F",names(MaxSize)[i]),cex.lab=2,cex.axis=1.5)
}
LFAs = c("34")
simSumLegalSize = simSummary(runs=c("Base","LS85","LS87.5","LS90"),lfas=LFAs,lab=34)
simSumSeason = simSummary(runs=c("Base","SS9","SS8","SS7","SS6","SS5"),lfas=LFAs,lab=34)
simSumWindow = simSummary(runs=c("Base","FSmallWin","FBigWin","SmallWin","BigWin"),lfas=LFAs,lab=34)
simSumMaxSize = simSummary(runs=c("Base","FMax125","FMax130","FMax135","Max125","Max130","Max135"),lfas=LFAs,lab=34)
LStabRP = data.frame(rbind(
round(100*(simSumLegalSize[[1]][4,]/simSumLegalSize[[1]][1,]-1)),
round(100*(simSumLegalSize[[1]][3,]/simSumLegalSize[[1]][1,]-1)),
round(100*(simSumLegalSize[[1]][2,]/simSumLegalSize[[1]][1,]-1))
))
names(LStabRP) = LFAs
rownames(LStabRP) = c("LS82.5", "LS80", "LS78.5")
write.csv(LStabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","LStab34RP70.csv"),row.names=T)
LStabNo = data.frame(rbind(
round(100*(simSumLegalSize[[2]][4,]/simSumLegalSize[[2]][1,]-1)),
round(100*(simSumLegalSize[[2]][3,]/simSumLegalSize[[2]][1,]-1)),
round(100*(simSumLegalSize[[2]][2,]/simSumLegalSize[[2]][1,]-1))
))
names(LStabNo) = LFAs
rownames(LStabNo) = c("LS82.5", "LS80", "LS78.5")
write.csv(LStabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","LStab34No70.csv"),row.names=T)
LStabKg = data.frame(rbind(
round(100*(simSumLegalSize[[3]][4,]/simSumLegalSize[[3]][1,]-1)),
round(100*(simSumLegalSize[[3]][3,]/simSumLegalSize[[3]][1,]-1)),
round(100*(simSumLegalSize[[3]][2,]/simSumLegalSize[[3]][1,]-1))
))
names(LStabKg) = LFAs
rownames(LStabKg) = c("LS82.5", "LS80", "LS78.5")
write.csv(LStabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","LStab34Kg70.csv"),row.names=T)
OStabRP = data.frame(rbind(
round(100*(simSumSeason[[1]][6,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][5,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][4,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][3,]/simSumSeason[[1]][1,]-1)),
round(100*(simSumSeason[[1]][2,]/simSumSeason[[1]][1,]-1))
))
names(OStabRP) = LFAs
rownames(OStabRP) = c("SS5", "SS6", "SS7", "SS8", "SS9")
write.csv(OStabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","OStab34RP.csv"),row.names=T)
OStabNo = data.frame(rbind(
round(100*(simSumSeason[[2]][6,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][5,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][4,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][3,]/simSumSeason[[2]][1,]-1)),
round(100*(simSumSeason[[2]][2,]/simSumSeason[[2]][1,]-1))
))
names(OStabNo) = LFAs
rownames(OStabNo) = c("SS5", "SS6", "SS7", "SS8", "SS9")
write.csv(OStabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","OStab34No.csv"),row.names=T)
OStabKg = data.frame(rbind(
round(100*(simSumSeason[[3]][6,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][5,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][4,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][3,]/simSumSeason[[3]][1,]-1)),
round(100*(simSumSeason[[3]][2,]/simSumSeason[[3]][1,]-1))
))
names(OStabKg) = LFAs
rownames(OStabNo) = c("SS5", "SS6", "SS7", "SS8", "SS9")
write.csv(OStabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","OStab34Kg.csv"),row.names=T)
WintabRP = data.frame(rbind(
round(100*(simSumWindow[[1]][5,]/simSumWindow[[1]][1,]-1)),
round(100*(simSumWindow[[1]][4,]/simSumWindow[[1]][1,]-1)),
round(100*(simSumWindow[[1]][3,]/simSumWindow[[1]][1,]-1)),
round(100*(simSumWindow[[1]][2,]/simSumWindow[[1]][1,]-1))
))
names(WintabRP) = LFAs
rownames(WintabRP) = c("BigWin", "SmallWin","FBigWin", "FSmallWin")
write.csv(WintabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Wintab34RP.csv"),row.names=T)
WintabNo = data.frame(rbind(
round(100*(simSumWindow[[2]][5,]/simSumWindow[[2]][1,]-1)),
round(100*(simSumWindow[[2]][4,]/simSumWindow[[2]][1,]-1)),
round(100*(simSumWindow[[2]][3,]/simSumWindow[[2]][1,]-1)),
round(100*(simSumWindow[[2]][2,]/simSumWindow[[2]][1,]-1))
))
names(WintabNo) = LFAs
rownames(WintabNo) = c("BigWin", "SmallWin","FBigWin", "FSmallWin")
write.csv(WintabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Wintab34No.csv"),row.names=T)
WintabKg = data.frame(rbind(
round(100*(simSumWindow[[3]][5,]/simSumWindow[[3]][1,]-1)),
round(100*(simSumWindow[[3]][4,]/simSumWindow[[3]][1,]-1)),
round(100*(simSumWindow[[3]][3,]/simSumWindow[[3]][1,]-1)),
round(100*(simSumWindow[[3]][2,]/simSumWindow[[3]][1,]-1))
))
names(WintabKg) = LFAs
rownames(WintabKg) = c("BigWin", "SmallWin","FBigWin", "FSmallWin")
write.csv(WintabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Wintab34Kg.csv"),row.names=T)
MaxtabRP = data.frame(rbind(
round(100*(simSumMaxSize[[1]][7,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][6,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][5,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][4,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][3,]/simSumMaxSize[[1]][1,]-1)),
round(100*(simSumMaxSize[[1]][2,]/simSumMaxSize[[1]][1,]-1))
))
names(MaxtabRP) = LFAs
rownames(MaxtabRP) = c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125")
write.csv(MaxtabRP,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Maxtab34RP.csv"),row.names=T)
MaxtabNo = data.frame(rbind(
round(100*(simSumMaxSize[[2]][7,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][6,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][5,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][4,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][3,]/simSumMaxSize[[2]][1,]-1)),
round(100*(simSumMaxSize[[2]][2,]/simSumMaxSize[[2]][1,]-1))
))
names(MaxtabNo) = LFAs
rownames(MaxtabNo) = c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125")
write.csv(MaxtabNo,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Maxtab34No.csv"),row.names=T)
MaxtabKg = data.frame(rbind(
round(100*(simSumMaxSize[[3]][7,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][6,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][5,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][4,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][3,]/simSumMaxSize[[3]][1,]-1)),
round(100*(simSumMaxSize[[3]][2,]/simSumMaxSize[[3]][1,]-1))
))
names(MaxtabKg) = LFAs
rownames(MaxtabKg) = c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125")
write.csv(MaxtabKg,file.path(project.datadirectory("bio.lobster"),"outputs","sim","Maxtab34Kg.csv"),row.names=T)
for(i in 1){
LS=data.frame(Eggs=LStabRP[,i],Numbers=LStabNo[,i],Weight=LStabKg[,i],row.names= c("LS90", "LS87.5", "LS85"))
OS=data.frame(Eggs=OStabRP[,i],Numbers=OStabNo[,i],Weight=OStabKg[,i],row.names= c("SS5", "SS6", "SS7", "SS8", "SS9"))
Win=data.frame(Eggs=WintabRP[,i],Numbers=WintabNo[,i],Weight=WintabKg[,i],row.names= c("BigWin", "SmallWin","FBigWin", "FSmallWin"))
Max=data.frame(Eggs=MaxtabRP[,i],Numbers=MaxtabNo[,i],Weight=MaxtabKg[,i],row.names= c("Max135", "Max130", "Max125", "FMax135", "FMax130", "FMax125"))
write.csv(rbind(LS,OS,Win,Max),file.path(project.datadirectory("bio.lobster"),"outputs","sim",paste0("LFA",LFAs[i],".csv")),row.names=T)
}
cols=tim.colors(9)
ltys=1:9
pchs=c(1:6,15:17)
#x11()
png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumLegalSize.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(70,90,2.5),simSumLegalSize$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
axis(4)
abline(v=82.5,lty=3,col='grey')
legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(70,90,2.5),simSumLegalSize$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
axis(4)
abline(v=82.5,lty=3,col='grey')
matplot(x=seq(70,90,2.5),simSumLegalSize$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
axis(4)
abline(v=82.5,lty=3,col='grey')
mtext("Minimum Legal Size (mm)",1,3)
dev.off()
#x11()
png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumSeason.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(0,50,10),simSumSeason$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
axis(4)
#abline(v=0,lty=3,col='grey')
legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(0,50,10),simSumSeason$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
axis(4)
#abline(v=0,lty=3,col='grey')
matplot(x=seq(0,50,10),simSumSeason$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
axis(4)
#abline(v=0,lty=3,col='grey')
mtext("Season reduction (%)",1,3)
dev.off()
#####
x11()
#png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumLegalSize.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(82.5,90,2.5),simSumLegalSize$landnum[6:9,],type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
par(new=T)
matplot(x=seq(0,50,10),simSumSeason$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
#abline(v=82.5,lty=3,col='grey')
#legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(82.5,90,2.5),simSumLegalSize$landkg[6:9,],type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
par(new=T)
matplot(x=seq(0,50,10),simSumSeason$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
#abline(v=82.5,lty=3,col='grey')
matplot(x=seq(82.5,90,2.5),simSumLegalSize$eggs[6:9,]/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
par(new=T)
matplot(x=seq(0,50,10),simSumSeason$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
#abline(v=82.5,lty=3,col='grey')
mtext("Minimum Legal Size (mm)",1,3)
#dev.off()
par(new=T)
#x11()
#png(file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018','simSumSeason.png'),width=8,height=8,units='in',res=200)
par(mfrow=c(3,1),mar=c(0,5,0,0),omi=c(0.75,0,0.5,0.5),las=1)
matplot(x=seq(0,50,10),simSumSeason$landnum,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (#s)',ylim=c(0,2000))
#abline(v=0,lty=3,col='grey')
legend('bottomleft',LFAs,col=cols,lty=ltys,inset=0.03,bty='n', pch=pchs)
matplot(x=seq(0,50,10),simSumSeason$landkg,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Catch (kg)',ylim=c(0,2000))
#abline(v=0,lty=3,col='grey')
matplot(x=seq(0,50,10),simSumSeason$eggs/10^6,type = 'b', pch=pchs,col=cols,lty=ltys,ylab='Eggs (millions)',ylim=c(0,25))
#abline(v=0,lty=3,col='grey')
mtext("Season reduction (%)",1,3)
dev.off()
# from 1.IndicatorEstimation.CohortAnalysis.r
ad
outS
bins=seq(80,150,5)
### LFA 33
is=which(ad$LFA==33&ad$YEAR>2001)
CLF.lst=list()
lens=NULL
for(i in is) lens = c(lens,outS[[i]])
CLF.lst[[1]]=hist(lens[lens>82.5&lens<max(bins)],breaks=bins,plot=F)$counts
#load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
CLF.lst[[2]]=
colSums(rlist$mlist$'33W'$totalRemovals[,7:31])+
colSums(rlist$mlist$'33E'$totalRemovals[,7:31])+
colSums(rlist$flist$'33W'$totalRemovals[,7:31])+
colSums(rlist$flist$'33E'$totalRemovals[,7:31])
compareCLF(CLF.lst,bins=bins,col='grey',rel=T,graphic='pdf',filen=file.path(project.datadirectory('bio.lobster'),'figures','LFA2733Framework2018',"CLFcompareLFA33.pdf"),LS=c(82.5,82.5),xl=c(0,length(bins)),title="LFA 33",labels=c("At Sea Sampling","Simulation"))
##############
load(file=file.path(project.datadirectory("bio.lobster"),"outputs","sim","sim34ResultsBase.rdata"))
transMat = getTransMatrix(rlist)
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