inst/Updates/LFA41/2023/2.stratifiedAnalysis.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
require(bio.survey)
require(bio.lobster)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"assessments",'LFA41','2023')
#load_all('~/git/bio.survey/')
p$current.assessment.year = 2023
assessment.year = p$current.assessment.year ########### check the year ############### !!!!!!!!!!!
p$reweight.strata = F #this subsets
p$years.to.estimate = c(1969:assessment.year)
p$length.based = T
p$size.class= c(50,300)
p$by.sex = F
p$sex = c(1,2) # male female berried c(1,2,3)
p$bootstrapped.ci=T
p$strata.files.return=F
p$strata.efficiencies=F
p$clusters = c( rep( "localhost", 7) )
# Spring survey All stations including adjacent
p$season =c('spring')# p$series =c('spring');p$series =c('fall')
p$area = 'LFA41'
p$return.both = NULL
p = make.list(list(yrs=p$years.to.estimate),Y=p)
#Figure
p$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$reference.measure = 'median' # mean, geomean
#Spring restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figurea for Assessment Document
# p$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 = 'lfa41NEFSCSpringrestratifiednumbers.png'
#
# p$ylim=c(0,20)
# p$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$error.bars=T
#
#
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41NEFSCSpringrestratifiednumbersNOY.png'
# p$ylim=NULL
# p$box=T
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=c(0,50)
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCSpringrestratifiedweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=T
# p$ylim=NULL
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCSpringrestratifiedweightsNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=NULL
# p$file.name = 'lfa41NEFSCSpringrestratifiedDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$file.name = 'lfa41NEFSCSpringrestratifiedgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'NEFSC.Spring.Restratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.Restratified.All.csv'))
#Fall Survey All stations not pruned by polygon
p$season =c('fall')# p$series =c('spring');p$series =c('fall')
#Fall restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
p$years.to.estimate = c(1969:(assessment.year)) # -1 because update is in the Fall
p = make.list(list(yrs=p$years.to.estimate),Y=p)
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
# #Figures for assessments
# 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$file.name = 'lfa41NEFSCFallrestratifiednumbers.png'
#
# p$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(0,15)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$file.name = 'lfa41NEFSCFallrestratifiednumbersNOY.png'
# p$ylim=NULL
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$ylim=c(0,30)
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCFallrestratifiedweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=T
# p$ylim=NULL
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCFallrestratifiedweightsNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$file.name = 'lfa41NEFSCFallrestratifiedDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41NEFSCFallrestratifiedgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'NEFSC.Fall.Restratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.Restratified.All.csv'))
##############################################################
#DFO RV Setup
p$series =c('summer')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'LFA41'
p$years.to.estimate = c(1970:(assessment.year))
#p$years.to.estimate = c(assessment.year)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = NULL
p$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
#DFO restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #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$file.name = 'lfa41DFOrestratifiednumbers.png'
#
# p$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)
#
# p$ylim=NULL
# p$box=T
# p$file.name = 'lfa41DFOrestratifiednumbersNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=c(0,32)
# p$metric = 'weights'
# p$file.name = 'lfa41DFOrestratifiedweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=T
# p$ylim=NULL
# p$metric = 'weights'
# p$file.name = 'lfa41DFOrestratifiedweightsNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=NULL
# p$file.name = 'lfa41DFOrestratifiedDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41DFOrestratifiedgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'DFO.restratified.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.restratified.All.csv'))
#DFO Georges
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:assessment.year)
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 = NULL
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 = 'Georges.Canada'
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#
# #Figure for assessments
# p$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 = 'lfa41georgesnumbers.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
#
#
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$metric = 'weights'
# p$file.name = 'lfa41georgesweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$file.name = 'lfa41georgesDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41georgesgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'DFO.Georges.All.csv'
write.csv(aout,file=file.path(fp,'indicators','DFO.Georges.All.csv'))
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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require(bio.survey)
require(bio.lobster)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"assessments",'LFA41','2023')
#load_all('~/git/bio.survey/')
p$current.assessment.year = 2023
assessment.year = p$current.assessment.year ########### check the year ############### !!!!!!!!!!!
p$reweight.strata = F #this subsets
p$years.to.estimate = c(1969:assessment.year)
p$length.based = T
p$size.class= c(50,300)
p$by.sex = F
p$sex = c(1,2) # male female berried c(1,2,3)
p$bootstrapped.ci=T
p$strata.files.return=F
p$strata.efficiencies=F
p$clusters = c( rep( "localhost", 7) )
# Spring survey All stations including adjacent
p$season =c('spring')# p$series =c('spring');p$series =c('fall')
p$area = 'LFA41'
p$return.both = NULL
p = make.list(list(yrs=p$years.to.estimate),Y=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
#Spring restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figurea for Assessment Document
# 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$file.name = 'lfa41NEFSCSpringrestratifiednumbers.png'
#
# p$ylim=c(0,20)
# 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
#
#
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41NEFSCSpringrestratifiednumbersNOY.png'
# p$ylim=NULL
# p$box=T
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=c(0,50)
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCSpringrestratifiedweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=T
# p$ylim=NULL
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCSpringrestratifiedweightsNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=NULL
# p$file.name = 'lfa41NEFSCSpringrestratifiedDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$file.name = 'lfa41NEFSCSpringrestratifiedgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'NEFSC.Spring.Restratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.Restratified.All.csv'))
#Fall Survey All stations not pruned by polygon
p$season =c('fall')# p$series =c('spring');p$series =c('fall')
#Fall restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
p$years.to.estimate = c(1969:(assessment.year)) # -1 because update is in the Fall
p = make.list(list(yrs=p$years.to.estimate),Y=p)
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
# #Figures for assessments
# p$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 = 'lfa41NEFSCFallrestratifiednumbers.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$ylim=c(0,15)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$file.name = 'lfa41NEFSCFallrestratifiednumbersNOY.png'
# p$ylim=NULL
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$ylim=c(0,30)
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCFallrestratifiedweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=T
# p$ylim=NULL
# p$metric = 'weights'
# p$file.name = 'lfa41NEFSCFallrestratifiedweightsNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$file.name = 'lfa41NEFSCFallrestratifiedDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41NEFSCFallrestratifiedgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'NEFSC.Fall.Restratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.Restratified.All.csv'))
##############################################################
#DFO RV Setup
p$series =c('summer')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'LFA41'
p$years.to.estimate = c(1970:(assessment.year))
#p$years.to.estimate = c(assessment.year)
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 = NULL
p$clusters = c( rep( "localhost", 7) )
p$strata.efficiencies = F
p = make.list(list(yrs=p$years.to.estimate),Y=p)
# DFO survey All stations including adjacent
#DFO restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
# p$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 = 'lfa41DFOrestratifiednumbers.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$ylim=c(0,30)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$ylim=NULL
# p$box=T
# p$file.name = 'lfa41DFOrestratifiednumbersNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=c(0,32)
# p$metric = 'weights'
# p$file.name = 'lfa41DFOrestratifiedweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=T
# p$ylim=NULL
# p$metric = 'weights'
# p$file.name = 'lfa41DFOrestratifiedweightsNOY.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$box=NULL
# p$ylim=NULL
# p$file.name = 'lfa41DFOrestratifiedDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41DFOrestratifiedgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'DFO.restratified.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.restratified.All.csv'))
#DFO Georges
p$series =c('georges')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$years.to.estimate = c(1987:assessment.year)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = NULL
p$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$area = 'Georges.Canada'
p$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#
# #Figure for assessments
# 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$file.name = 'lfa41georgesnumbers.png'
#
# p$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$error.bars=T
#
#
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$metric = 'weights'
# p$file.name = 'lfa41georgesweights.png'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
#
# p$file.name = 'lfa41georgesDWAO.png'
# p$metric = 'dwao'
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$file.name = 'lfa41georgesgini.png'
# p$metric = 'gini'
# p$ylim =c(0,1)
# ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
# p$ylim = NULL
aout$subset = 'DFO.Georges.All.csv'
write.csv(aout,file=file.path(fp,'indicators','DFO.Georges.All.csv'))
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