inst/Frameworks/LFA41Framework/FinalIndicators/20.pezzackIndicators.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
#Pezzack Indicators
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
require(bio.polygons)
la()
###DFO Summer RV
#MAP
LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
LFA41 = subset(LFA41,SID==1)
attr(LFA41,'projection') <- 'LL'
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
require(bio.polygons)
la()
pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('pezzacksummerstratamap.pdf',sep='.')))
LobsterMap(ylim=c(41.1,44.5), xlim=c(-68,-63.5) ,boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=F)
a = find.bio.gis('summer_strata_labels',return.one.match=F)
a = read.csv(a,header=T)
names(a)[4] <- 'label'
b = find.bio.gis('strat.gf',return.one.match=F)
b = read.table(b)
names(b) <- c('X','Y','PID')
b = b[which(b$PID %in% c(477,478,480:484)),]
b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
addPolys(b,lty=1,border='red',col=adjustcolor('yellow',alpha.f=1))
addPolys(LFA41,border='blue',lwd=2)
dev.off()
#ABUNDANCE
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('summer')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$strat = c(477,478,480:484)
p$years.to.estimate = c(1970:2016)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'pezzackRVDFObasenumbers.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim=c(0,30)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#identify productivity regime shifts
require(bcp)
b = bcp(aout$n.yst, w0 = 0.2, p0 = 0.05)
plot(b,xaxlab=aout$yr,xlab='Year')
#starting in 1994-1995
#DFO GEORGES
#MAP
LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
LFA41 = subset(LFA41,SID==1)
attr(LFA41,'projection') <- 'LL'
pdf(file=file.path(project.figuredirectory('bio.lobster'),'pezzackgeorgesmap41.pdf'))
LobsterMap(xlim=c(-70.5,-63.5),ylim=c(38.5,45),boundaries='LFAs',addGeorgesStrata=T,output='bio.lobster',fname='georgesmap41.pdf',save=F,labcex =0.8,labels=T)
addPolys(LFA41,border='blue',lwd=2)
b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
load(b)
addPolys(out,border='red')
addPolys(subset(out,PID %in% c(1,2,3,4)),lty=1,border='red',col='yellow')
addPolys(LFA41,border='blue',lwd=2)
dev.off()
#ABUNDANCE
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('georges')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$years.to.estimate = c(1987:2015)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = c('5Z1','5Z2','5Z3','5Z4')
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'pezzacklfa41georgesnumbers.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim=c(0,6)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,save=T)
###############################################
#Large Females
##############################################
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('summer')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$strat = c(480,481)
p$years.to.estimate = c(1999:2015)
p$length.based = T
p$by.sex = T
p$size.class = c(140,300)
p$sex = c(2,3)
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
p$reweight.strata =F
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
#Figure
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'pezzacklfa41largefemale.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim2 = c(0,500)
xx = aggregate(ObsLobs~yr,data=aout,FUN=sum)
names(xx) =c('x','y')
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p, x2 = xx, sampleSizes=T)
###map
LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
LFA41 = subset(LFA41,SID==1)
attr(LFA41,'projection') <- 'LL'
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
require(bio.polygons)
la()
pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('pezzack480481map.pdf',sep='.')))
LobsterMap(ylim=c(41.1,44.5), xlim=c(-68,-63.5) ,boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=F)
a = find.bio.gis('summer_strata_labels',return.one.match=F)
a = read.csv(a,header=T)
names(a)[4] <- 'label'
b = find.bio.gis('strat.gf',return.one.match=F)
b = read.table(b)
names(b) <- c('X','Y','PID')
b = b[which(b$PID %in% c(480:481)),]
b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
addPolys(b,lty=1,border='red',col=adjustcolor('yellow',alpha.f=1))
addPolys(LFA41,border='blue',lwd=2)
dev.off()
### Georges large females
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('georges')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$years.to.estimate = c(2007:2015)
p$length.based = T
p$by.sex = T
p$sex = c(2,3)
p$size.class = c(140,300)
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = c('5Z1','5Z2','5Z3','5Z4')
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'largefemalepezzackgeorges.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim=c(0,1.5)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,save=T)
###############################################
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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#Pezzack Indicators
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
require(bio.polygons)
la()
###DFO Summer RV
#MAP
LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
LFA41 = subset(LFA41,SID==1)
attr(LFA41,'projection') <- 'LL'
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
require(bio.polygons)
la()
pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('pezzacksummerstratamap.pdf',sep='.')))
LobsterMap(ylim=c(41.1,44.5), xlim=c(-68,-63.5) ,boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=F)
a = find.bio.gis('summer_strata_labels',return.one.match=F)
a = read.csv(a,header=T)
names(a)[4] <- 'label'
b = find.bio.gis('strat.gf',return.one.match=F)
b = read.table(b)
names(b) <- c('X','Y','PID')
b = b[which(b$PID %in% c(477,478,480:484)),]
b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
addPolys(b,lty=1,border='red',col=adjustcolor('yellow',alpha.f=1))
addPolys(LFA41,border='blue',lwd=2)
dev.off()
#ABUNDANCE
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('summer')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$strat = c(477,478,480:484)
p$years.to.estimate = c(1970:2016)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'pezzackRVDFObasenumbers.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim=c(0,30)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#identify productivity regime shifts
require(bcp)
b = bcp(aout$n.yst, w0 = 0.2, p0 = 0.05)
plot(b,xaxlab=aout$yr,xlab='Year')
#starting in 1994-1995
#DFO GEORGES
#MAP
LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
LFA41 = subset(LFA41,SID==1)
attr(LFA41,'projection') <- 'LL'
pdf(file=file.path(project.figuredirectory('bio.lobster'),'pezzackgeorgesmap41.pdf'))
LobsterMap(xlim=c(-70.5,-63.5),ylim=c(38.5,45),boundaries='LFAs',addGeorgesStrata=T,output='bio.lobster',fname='georgesmap41.pdf',save=F,labcex =0.8,labels=T)
addPolys(LFA41,border='blue',lwd=2)
b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
load(b)
addPolys(out,border='red')
addPolys(subset(out,PID %in% c(1,2,3,4)),lty=1,border='red',col='yellow')
addPolys(LFA41,border='blue',lwd=2)
dev.off()
#ABUNDANCE
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('georges')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$years.to.estimate = c(1987:2015)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = c('5Z1','5Z2','5Z3','5Z4')
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'pezzacklfa41georgesnumbers.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim=c(0,6)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,save=T)
###############################################
#Large Females
##############################################
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('summer')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$strat = c(480,481)
p$years.to.estimate = c(1999:2015)
p$length.based = T
p$by.sex = T
p$size.class = c(140,300)
p$sex = c(2,3)
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
p$reweight.strata =F
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
#Figure
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'pezzacklfa41largefemale.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim2 = c(0,500)
xx = aggregate(ObsLobs~yr,data=aout,FUN=sum)
names(xx) =c('x','y')
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p, x2 = xx, sampleSizes=T)
###map
LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
LFA41 = subset(LFA41,SID==1)
attr(LFA41,'projection') <- 'LL'
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
require(bio.polygons)
la()
pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('pezzack480481map.pdf',sep='.')))
LobsterMap(ylim=c(41.1,44.5), xlim=c(-68,-63.5) ,boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=F)
a = find.bio.gis('summer_strata_labels',return.one.match=F)
a = read.csv(a,header=T)
names(a)[4] <- 'label'
b = find.bio.gis('strat.gf',return.one.match=F)
b = read.table(b)
names(b) <- c('X','Y','PID')
b = b[which(b$PID %in% c(480:481)),]
b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
addPolys(b,lty=1,border='red',col=adjustcolor('yellow',alpha.f=1))
addPolys(LFA41,border='blue',lwd=2)
dev.off()
### Georges large females
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$series =c('georges')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$years.to.estimate = c(2007:2015)
p$length.based = T
p$by.sex = T
p$sex = c(2,3)
p$size.class = c(140,300)
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = c('5Z1','5Z2','5Z3','5Z4')
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'custom'
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$add.reference.lines = F
p$time.series.start.year = p$years.to.estimate[1]
p$time.series.end.year = p$years.to.estimate[length(p$years.to.estimate)]
p$metric = 'numbers' #weights
p$measure = 'stratified.mean' #'stratified.total'
p$figure.title = ""
p$reference.measure = 'median' # mean, geomean
p$file.name = 'largefemalepezzackgeorges.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$legend = FALSE
p$running.median = T
p$running.length = 3
p$running.mean = F #can only have rmedian or rmean
p$error.polygon=F
p$error.bars=T
p$ylim=c(0,1.5)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,save=T)
###############################################
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