inst/Frameworks/LFA2733Framework/LFA2733Framework2017vic.R
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
p = bio.lobster::load.environment()
p$syr = 2005
p$yrs = p$syr:p$current.assessment.year
figdir = file.path(project.datadirectory("bio.lobster"),"figures","LFA2733Framework2018")
p$lfas = c("27", "28", "29", "30", "31A", "31B", "32", "33") # specify lfas for data summary
## Carapace Length Frequency Plots
# at Sea Sampling
CarapaceLengthFrequencies(LFAs= '27', DS='atSea', by='SEX', fn='27',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '29', DS='atSea', by='SEX', fn='29',Yrs = c(2013, 2015, 2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '30', DS='atSea', by='SEX', fn='30',Yrs = c(2012),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '31A', DS='atSea', by='SEX', fn='31A',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '31B', DS='atSea', by='SEX', fn='31B',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '32', DS='atSea', by='SEX', fn='32',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '33', DS='atSea', by='SEX', fn='33',Yrs = c(2012:2014),vers=2,rootdir=figdir)
p$lfas = c("27", "28", "29", "30", "31.1", "31.2", "32", "33") # specify lfas for data summary
# FSRS recruitment traps
CarapaceLengthFrequencies(LFAs= p$lfas, DS='fsrs', by="LFA", bins=seq(0,140,10),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '27', fn= '27', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '29', fn= '29', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '30', fn= '30', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= 31.1, fn= '31A', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= 31.2, fn= '31B', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '32', fn= '32', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '33', fn= '33', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '27', fn= '27', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '29', fn= '29', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '30', fn= '30', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= 31.1, fn= '31A', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= 31.2, fn= '31B', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '32', fn= '32', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '33', fn= '33', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
## CPUE
p$lfas = c("27", "28", "29", "30", "31A", "31B", "32", "33") # specify lfas for data summary
p$subareas = c("27N","27S", "28", "29", "30", "31A", "31B", "32", "33E", "33W") # specify lfas for data summary
logsInSeason<-lobster.db('process.logs')
cpueLFA.dat = CPUEplot(logsInSeason,lfa= p$lfas,yrs=2006:2016,graphic='pdf',path=figdir)
cpueSubArea.dat = CPUEplot(logsInSeason,subarea= p$subareas,yrs=2006:2016,graphic='R')
## Fishery Footprint - Landings
catchLevels = c(0,100000,200000,300000,400000,500000,600000,700000,800000)
yrs = 2011:2016
for(i in 1:length(yrs)){
catchgrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR==yrs[i],c("LFA","GRID_NUM","TOTAL_WEIGHT_KG")),FUN=sum,lvls=catchLevels)
saveRDS(catchgrids,file=file.path(fd,paste('Figure3',yrs[i],'.rds')))
# pdf(file.path(figdir,paste0("FisheryFootprint",yrs[i],".pdf")))
LobsterMap('27-33',poly.lst=catchgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=catchgrids$lvls/1000,Cont.data=catchgrids,title="Catch (tons)",inset=0.02,cex=0.8,bg='white')
# dev.off()
}
## Fishery Footprint - CPUE
cpueLevels = c(0,0.2,0.4,0.6,0.8,0.9,1,2,3)
yrs = 2011:2016
#logsInSeason$logCPUE = log(logsInSeason$CPUE+1)
for(i in 1:length(yrs)){
cpuegrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR == yrs[i],c("LFA","GRID_NUM","CPUE")),FUN=median,lvls=cpueLevels)
# pdf(file.path(figdir,paste0("FishFootcpue", yrs[i],".pdf")))
saveRDS(cpuegrids,file=file.path(fd,paste('Figure5',yrs[i],'.rds')))
#
LobsterMap('27-33',poly.lst=cpuegrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=cpuegrids$lvls,Cont.data=cpuegrids,title="CPUE (kg/TH)",inset=0.02,cex=0.8,bg='white')
# dev.off()
}
## Fishery Footprint - Mean Pots Hauled
potLevels = c (0,1000,100000,200000,300000,400000,500000,600000)
yrs = 2011:2016
for(i in 1:length(yrs)){
potgrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR == yrs[i],c("LFA","GRID_NUM","NUM_OF_TRAPS")),FUN=sum,lvls=potLevels)
saveRDS(potgrids,file=file.path(fd,paste('Figure4',yrs[i],'.rds')))
#pdf(file.path(figdir,paste0("FishFootpot", yrs[i],".pdf")))
LobsterMap('27-33',poly.lst=potgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=potgrids$lvls/1000,Cont.data=potgrids,title="Pots Hauled (000s)",inset=0.02,cex=0.8,bg='white')
#dev.off()
}
## Fishery Footprint - Days Fished
daysLevels = c(0,500,1000,1500,2000,2500,3000)
daysFished<-aggregate(DATE_FISHED ~ SYEAR + LFA + GRID_NUM + LICENCE_ID, data=logsInSeason,FUN= function(x) length(unique(x)))
yrs = 2011:2016
for (i in 1: length(yrs)){
daysgrids = lobGridPlot(subset(daysFished, LFA%in%p$lfas&SYEAR == yrs[i],c("LFA", "GRID_NUM", "DATE_FISHED")),FUN=sum, lvls= daysLevels)
saveRDS(daysgrids,file=file.path(fd,paste('Figure6',yrs[i],'.rds')))
# pdf(file.path(figdir,paste0("FishFootDaysFished", yrs[i],".pdf")))
LobsterMap('27-33',poly.lst=daysgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=daysgrids$lvls,Cont.data=daysgrids,title="Total Days Fished",inset=0.02,cex=0.8,bg='white')
# dev.off()
}
## Fishery Footprint - Licences Fished
licenceLevels = c(0,15,30,45,60,75,90,105,120)
yrs=2011:2016
daysFished$LICENCE<-1
for(i in 1: length(yrs)){
licencegrids = lobGridPlot(subset(daysFished, LFA%in%p$lfas&SYEAR==yrs[i], c("LFA", "GRID_NUM", "LICENCE")), FUN=sum, lvls= licenceLevels)
saveRDS(licencegrids,file=file.path(fd,paste('Figure7',yrs[i],'.rds')))
#pdf(file.path(figdir,paste0("FishFootLicenceFished", yrs[i],".pdf")))
LobsterMap('27-33', poly.lst=licencegrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright', lvls=licencegrids$lvls, Cont.data=licencegrids, title= "Number of Licence Fished", inset =0.02,cex=0.8,bg='white')
dev.off()
}
###Models need to be fixed for following
## FSRS MOdels
FSRSvesday<-FSRSModelData()
FSRSModelResultsShort = list()
FSRSModelResultsLegal = list()
for(i in 1:length( p$subareas)){
mdata = subset(FSRSvesday,subarea==p$subareas[i])
FSRSModelResultsShort[[i]]=FSRSmodel(LFA27north, response="SHORTS")
FSRSModelResultsLegal[[i]]=FSRSmodel(LFA27north, response="LEGALS")
}
## Commercial CPUE MOdels
CPUE.data<-CPUEModelData()
CPUEModelResults = list()
for(i in 1:length( p$subareas)){
mdata = subset(CPUE.data,subarea==p$subareas[i])
CPUEModelResults[[i]]=CPUEmodel(LFA27north)
}
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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p = bio.lobster::load.environment()
p$syr = 2005
p$yrs = p$syr:p$current.assessment.year
figdir = file.path(project.datadirectory("bio.lobster"),"figures","LFA2733Framework2018")
p$lfas = c("27", "28", "29", "30", "31A", "31B", "32", "33") # specify lfas for data summary
## Carapace Length Frequency Plots
# at Sea Sampling
CarapaceLengthFrequencies(LFAs= '27', DS='atSea', by='SEX', fn='27',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '29', DS='atSea', by='SEX', fn='29',Yrs = c(2013, 2015, 2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '30', DS='atSea', by='SEX', fn='30',Yrs = c(2012),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '31A', DS='atSea', by='SEX', fn='31A',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '31B', DS='atSea', by='SEX', fn='31B',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '32', DS='atSea', by='SEX', fn='32',Yrs = c(2011:2016),vers=2,rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '33', DS='atSea', by='SEX', fn='33',Yrs = c(2012:2014),vers=2,rootdir=figdir)
p$lfas = c("27", "28", "29", "30", "31.1", "31.2", "32", "33") # specify lfas for data summary
# FSRS recruitment traps
CarapaceLengthFrequencies(LFAs= p$lfas, DS='fsrs', by="LFA", bins=seq(0,140,10),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '27', fn= '27', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '29', fn= '29', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '30', fn= '30', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= 31.1, fn= '31A', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= 31.2, fn= '31B', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '32', fn= '32', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '33', fn= '33', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir,ss=NULL)
CarapaceLengthFrequencies(LFAs= '27', fn= '27', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '29', fn= '29', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '30', fn= '30', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= 31.1, fn= '31A', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= 31.2, fn= '31B', DS='fsrs', by="SEX", bins=seq(0,140,10),vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '32', fn= '32', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
CarapaceLengthFrequencies(LFAs= '33', fn= '33', DS='fsrs', by="SEX", bins=seq(0,140,10), vers=2,Yrs = c(2011:2016),rootdir=figdir)
## CPUE
p$lfas = c("27", "28", "29", "30", "31A", "31B", "32", "33") # specify lfas for data summary
p$subareas = c("27N","27S", "28", "29", "30", "31A", "31B", "32", "33E", "33W") # specify lfas for data summary
logsInSeason<-lobster.db('process.logs')
cpueLFA.dat = CPUEplot(logsInSeason,lfa= p$lfas,yrs=2006:2016,graphic='pdf',path=figdir)
cpueSubArea.dat = CPUEplot(logsInSeason,subarea= p$subareas,yrs=2006:2016,graphic='R')
## Fishery Footprint - Landings
catchLevels = c(0,100000,200000,300000,400000,500000,600000,700000,800000)
yrs = 2011:2016
for(i in 1:length(yrs)){
catchgrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR==yrs[i],c("LFA","GRID_NUM","TOTAL_WEIGHT_KG")),FUN=sum,lvls=catchLevels)
saveRDS(catchgrids,file=file.path(fd,paste('Figure3',yrs[i],'.rds')))
# pdf(file.path(figdir,paste0("FisheryFootprint",yrs[i],".pdf")))
LobsterMap('27-33',poly.lst=catchgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=catchgrids$lvls/1000,Cont.data=catchgrids,title="Catch (tons)",inset=0.02,cex=0.8,bg='white')
# dev.off()
}
## Fishery Footprint - CPUE
cpueLevels = c(0,0.2,0.4,0.6,0.8,0.9,1,2,3)
yrs = 2011:2016
#logsInSeason$logCPUE = log(logsInSeason$CPUE+1)
for(i in 1:length(yrs)){
cpuegrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR == yrs[i],c("LFA","GRID_NUM","CPUE")),FUN=median,lvls=cpueLevels)
# pdf(file.path(figdir,paste0("FishFootcpue", yrs[i],".pdf")))
saveRDS(cpuegrids,file=file.path(fd,paste('Figure5',yrs[i],'.rds')))
#
LobsterMap('27-33',poly.lst=cpuegrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=cpuegrids$lvls,Cont.data=cpuegrids,title="CPUE (kg/TH)",inset=0.02,cex=0.8,bg='white')
# dev.off()
}
## Fishery Footprint - Mean Pots Hauled
potLevels = c (0,1000,100000,200000,300000,400000,500000,600000)
yrs = 2011:2016
for(i in 1:length(yrs)){
potgrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR == yrs[i],c("LFA","GRID_NUM","NUM_OF_TRAPS")),FUN=sum,lvls=potLevels)
saveRDS(potgrids,file=file.path(fd,paste('Figure4',yrs[i],'.rds')))
#pdf(file.path(figdir,paste0("FishFootpot", yrs[i],".pdf")))
LobsterMap('27-33',poly.lst=potgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=potgrids$lvls/1000,Cont.data=potgrids,title="Pots Hauled (000s)",inset=0.02,cex=0.8,bg='white')
#dev.off()
}
## Fishery Footprint - Days Fished
daysLevels = c(0,500,1000,1500,2000,2500,3000)
daysFished<-aggregate(DATE_FISHED ~ SYEAR + LFA + GRID_NUM + LICENCE_ID, data=logsInSeason,FUN= function(x) length(unique(x)))
yrs = 2011:2016
for (i in 1: length(yrs)){
daysgrids = lobGridPlot(subset(daysFished, LFA%in%p$lfas&SYEAR == yrs[i],c("LFA", "GRID_NUM", "DATE_FISHED")),FUN=sum, lvls= daysLevels)
saveRDS(daysgrids,file=file.path(fd,paste('Figure6',yrs[i],'.rds')))
# pdf(file.path(figdir,paste0("FishFootDaysFished", yrs[i],".pdf")))
LobsterMap('27-33',poly.lst=daysgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=daysgrids$lvls,Cont.data=daysgrids,title="Total Days Fished",inset=0.02,cex=0.8,bg='white')
# dev.off()
}
## Fishery Footprint - Licences Fished
licenceLevels = c(0,15,30,45,60,75,90,105,120)
yrs=2011:2016
daysFished$LICENCE<-1
for(i in 1: length(yrs)){
licencegrids = lobGridPlot(subset(daysFished, LFA%in%p$lfas&SYEAR==yrs[i], c("LFA", "GRID_NUM", "LICENCE")), FUN=sum, lvls= licenceLevels)
saveRDS(licencegrids,file=file.path(fd,paste('Figure7',yrs[i],'.rds')))
#pdf(file.path(figdir,paste0("FishFootLicenceFished", yrs[i],".pdf")))
LobsterMap('27-33', poly.lst=licencegrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright', lvls=licencegrids$lvls, Cont.data=licencegrids, title= "Number of Licence Fished", inset =0.02,cex=0.8,bg='white')
dev.off()
}
###Models need to be fixed for following
## FSRS MOdels
FSRSvesday<-FSRSModelData()
FSRSModelResultsShort = list()
FSRSModelResultsLegal = list()
for(i in 1:length( p$subareas)){
mdata = subset(FSRSvesday,subarea==p$subareas[i])
FSRSModelResultsShort[[i]]=FSRSmodel(LFA27north, response="SHORTS")
FSRSModelResultsLegal[[i]]=FSRSmodel(LFA27north, response="LEGALS")
}
## Commercial CPUE MOdels
CPUE.data<-CPUEModelData()
CPUEModelResults = list()
for(i in 1:length( p$subareas)){
mdata = subset(CPUE.data,subarea==p$subareas[i])
CPUEModelResults[[i]]=CPUEmodel(LFA27north)
}
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