inst/Frameworks/LFA41Framework/2.stratifiedAnalysis.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
#####need to rerun this full thing, to get the combined results and to get the gini and dwao running medians figured out for the dfo summer rv surey with missing years
####sept 23, 2016
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$reweight.strata = F #this subsets
p$years.to.estimate = c(1969:2015)
p$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$define.by.polygons = F
p$lobster.subunits=F
p$area = 'LFA41'
p$return.both = NULL
p = make.list(list(yrs=p$years.to.estimate),Y=p)
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = 'lfa41NEFSCSpringbasenumbers.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$file.name = 'lfa41NEFSCSpringbasenumbers.png'
p$ylim = c(0,20)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = c(0,50)
p$metric = 'weights'
p$file.name = 'lfa41NEFSCSpringbaseweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
p$file.name = 'lfa41NEFSCSpringbaseDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa41NEFSCSpringbasegini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'NEFSC.Spring.All'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.All.csv'))
#Spring restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = '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$subset = 'NEFSC.Spring.Restratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.Restratified.csv'))
#Spring restratified to adjacentlfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'adjacentLFA41'
p$reweight.strata = T #this subsets
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = 'adjacentlfa41NEFSCSpringrestratifiednumbers.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$error.bars=T
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=c(0,50)
p$metric = 'weights'
p$file.name = 'adjacentlfa41NEFSCSpringrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'adjacentlfa41NEFSCSpringrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'adjacentlfa41NEFSCSpringrestratifiedgini.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.adjRestratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.adjRestratified.csv'))
#Fall Survey All stations not pruned by polygon
p$season =c('fall')# p$series =c('spring');p$series =c('fall')
# Spring survey All stations including adjacent
p$season =c('fall')# p$series =c('fall');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'LFA41'
p = make.list(list(yrs=p$years.to.estimate),Y=p)
aout= nefsc.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$file.name = 'lfa41NEFSCFallbasenumbers.png'
p$y.maximum = NULL # NULL # if ymax is too high for one year
p$show.truncated.numbers = F #if using ymax and want to show the numbers that are cut off as values on figure
p$ylim=c(0,15)
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$metric = 'weights'
p$ylim=c(0,30)
p$file.name = 'lfa41NEFSCFallbaseweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'lfa41NEFSCFallbaseDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa41NEFSCFallbasegini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'NEFSC.Fall.All'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.All.csv'))
#Fall restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = '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.csv'))
#Fall restratified to adjacentlfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'adjacentLFA41'
p$reweight.strata = T #this subsets
aout= nefsc.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$file.name = 'adjacentlfa41NEFSCFallrestratifiednumbers.png'
p$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$ylim=c(0,30)
p$metric = 'weights'
p$file.name = 'adjacentlfa41NEFSCFallrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'adjacentlfa41NEFSCFallrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'adjacentlfa41NEFSCFallrestratifiedgini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'NEFSC.Fall.adjRestratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.adjRestratified.csv'))
##############################################################
#DFO RV Setup
p$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(1970:2016)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$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 = 'LFA41'
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 = 'lfa41DFObasenumbers.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=c(0,32)
p$metric = 'weights'
p$file.name = 'lfa41DFObaseweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'lfa41DFObaseDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa41DFObasegini.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.Base.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.Base.All.csv'))
#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)
#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$file.name = 'lfa41DFOrestratifiednumbers.png'
p$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 restratified to lfa40
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA40'
p$reweight.strata = T #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$file.name = 'lfa40DFOrestratifiednumbers.png'
p$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(0,70)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,save=T)
p$box=NULL
p$ylim=c(0,32)
p$metric = 'weights'
p$file.name = 'lfa40DFOrestratifiedweights.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 = 'lfa40DFOrestratifiedweightsNOY.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$box=NULL
p$ylim=NULL
p$file.name = 'lfa40DFOrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa40DFOrestratifiedgini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'DFO.restratified.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.restratified.All.csv'))
#DFO restratified to lfa41adjacent
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'adjacentLFA41'
p$reweight.strata = T #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = 'adjcentlfa41DFOrestratifiednumbers.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$ylim=c(0,30)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$metric = 'weights'
p$ylim=c(0,32)
p$file.name = 'adjacentlfa41DFOrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'adjacentlfa41DFOrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'adjacentlfa41DFOrestratifiedgini.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.adjrestratified.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.adjrestratified.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(1987:2015)
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 = 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$reweight.strata = F #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=T)
#Figure
p$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 = '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$subset = 'DFO.Georges.All.csv'
write.csv(aout,file=file.path(fp,'indicators','DFO.Georges.All.csv'))
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
R Package Documentation
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#####need to rerun this full thing, to get the combined results and to get the gini and dwao running medians figured out for the dfo summer rv surey with missing years
####sept 23, 2016
require(bio.survey)
require(bio.lobster)
require(bio.groundfish)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
load_all('~/git/bio.survey/')
p$reweight.strata = F #this subsets
p$years.to.estimate = c(1969:2015)
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$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'LFA41'
p$return.both = NULL
p = make.list(list(yrs=p$years.to.estimate),Y=p)
aout= nefsc.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$file.name = 'lfa41NEFSCSpringbasenumbers.png'
p$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$error.bars=T
p$file.name = 'lfa41NEFSCSpringbasenumbers.png'
p$ylim = c(0,20)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = c(0,50)
p$metric = 'weights'
p$file.name = 'lfa41NEFSCSpringbaseweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
p$file.name = 'lfa41NEFSCSpringbaseDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa41NEFSCSpringbasegini.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.All'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.All.csv'))
#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)
#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$file.name = 'lfa41NEFSCSpringrestratifiednumbers.png'
p$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.csv'))
#Spring restratified to adjacentlfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'adjacentLFA41'
p$reweight.strata = T #this subsets
aout= nefsc.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$file.name = 'adjacentlfa41NEFSCSpringrestratifiednumbers.png'
p$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$ylim=c(0,50)
p$metric = 'weights'
p$file.name = 'adjacentlfa41NEFSCSpringrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'adjacentlfa41NEFSCSpringrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'adjacentlfa41NEFSCSpringrestratifiedgini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'NEFSC.Spring.adjRestratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.adjRestratified.csv'))
#Fall Survey All stations not pruned by polygon
p$season =c('fall')# p$series =c('spring');p$series =c('fall')
# Spring survey All stations including adjacent
p$season =c('fall')# p$series =c('fall');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$area = 'LFA41'
p = make.list(list(yrs=p$years.to.estimate),Y=p)
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = 'lfa41NEFSCFallbasenumbers.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$ylim=c(0,15)
p$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$ylim=c(0,30)
p$file.name = 'lfa41NEFSCFallbaseweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'lfa41NEFSCFallbaseDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa41NEFSCFallbasegini.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.All'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.All.csv'))
#Fall 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)
#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$file.name = 'lfa41NEFSCFallrestratifiednumbers.png'
p$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$subset = 'NEFSC.Fall.Restratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.Restratified.csv'))
#Fall restratified to adjacentlfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'adjacentLFA41'
p$reweight.strata = T #this subsets
aout= nefsc.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = 'adjacentlfa41NEFSCFallrestratifiednumbers.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$ylim=c(0,15)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=c(0,30)
p$metric = 'weights'
p$file.name = 'adjacentlfa41NEFSCFallrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'adjacentlfa41NEFSCFallrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'adjacentlfa41NEFSCFallrestratifiedgini.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.adjRestratified'
write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.adjRestratified.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$years.to.estimate = c(1970:2016)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = NULL
p$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$area = 'LFA41'
p$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$file.name = 'lfa41DFObasenumbers.png'
p$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$ylim=c(0,32)
p$metric = 'weights'
p$file.name = 'lfa41DFObaseweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'lfa41DFObaseDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa41DFObasegini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'DFO.Base.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.Base.All.csv'))
#DFO restratified to lfa41
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA41'
p$reweight.strata = T #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = '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$subset = 'DFO.restratified.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.restratified.All.csv'))
######
#DFO restratified to lfa40
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'LFA40'
p$reweight.strata = T #this subsets
aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
#Figure
p$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 = 'lfa40DFOrestratifiednumbers.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$ylim=c(0,70)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,save=T)
p$box=NULL
p$ylim=c(0,32)
p$metric = 'weights'
p$file.name = 'lfa40DFOrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$box=T
p$ylim=NULL
p$metric = 'weights'
p$file.name = 'lfa40DFOrestratifiedweightsNOY.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$box=NULL
p$ylim=NULL
p$file.name = 'lfa40DFOrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'lfa40DFOrestratifiedgini.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 restratified to lfa41adjacent
p$define.by.polygons = T
p$lobster.subunits=F
p$area = 'adjacentLFA41'
p$reweight.strata = T #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$file.name = 'adjcentlfa41DFOrestratifiednumbers.png'
p$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$metric = 'weights'
p$ylim=c(0,32)
p$file.name = 'adjacentlfa41DFOrestratifiedweights.png'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim=NULL
p$file.name = 'adjacentlfa41DFOrestratifiedDWAO.png'
p$metric = 'dwao'
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$file.name = 'adjacentlfa41DFOrestratifiedgini.png'
p$metric = 'gini'
p$ylim =c(0,1)
ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
p$ylim = NULL
aout$subset = 'DFO.adjrestratified.All'
write.csv(aout,file=file.path(fp,'indicators','DFO.adjrestratified.All.csv'))
#DFO Georges
p$series =c('georges')# p$series =c('georges');p$series =c('fall')
p$define.by.polygons = F
p$lobster.subunits=F
p$years.to.estimate = c(1987:2015)
p$length.based = F
p$by.sex = F
p$bootstrapped.ci=T
p$strata.files.return=F
p$vessel.correction.fixed=1.2
p$strat = NULL
p$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,save=T)
#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$file.name = 'lfa41georgesnumbers.png'
p$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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