inst/Frameworks/LFA41Framework/2a.stratifiedAnalysisLargeFemales.r

In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes

require(bio.survey)
require(bio.lobster)
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
la()
load_all('~/git/bio.survey/')
#NEFSC Setup
#need to figureout DWAO boot strapping errors with the dfo survey....something not working
fpp = file.path(fp,'combinedResults')



      p$reweight.strata = F #this subsets 
      p$years.to.estimate = c(1969:2015)
      p$length.based = T
      p$size.class= c(140,300)
      p$by.sex = T
      p$sex = c(2,3) # 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 = 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 = 'lfa41NEFSCSpringbasenumberslargefemale.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)
     aout$subset = 'NEFSCSpringLargeFemale'
     write.csv(aout,file=file.path(fp,'indicators','NEFSC.Spring.LargeFemale.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 = 'lfa41NEFSCSpringrestratifiednumberslargefemale.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)
     
aout$subset = 'NEFSCSpringLargeFemale'
     
write.csv(aout,file=file.path(fp,'indicators','restratified.NEFSC.Spring.LargeFemale.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 = 'adjacentlfa41NEFSCSpringrestratifiednumberslargefemale.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)
     
      aout$subset = 'NEFSCSpringLargeFemale'
     write.csv(aout,file=file.path(fp,'indicators','adjrestratified.NEFSC.Spring.LargeFemale.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 = 'lfa41NEFSCFallbasenumberslargefemale.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)

      aout$subset = 'NEFSCFallLargeFemale'
     write.csv(aout,file=file.path(fp,'indicators','NEFSC.Fall.LargeFemale.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 = 'lfa41NEFSCFallrestratifiednumberslargefemale.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)
     
      aout$subset = 'NEFSCFallLargeFemale'
     write.csv(aout,file=file.path(fp,'indicators','restratified.NEFSC.Fall.LargeFemale.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 = 'adjacentlfa41NEFSCFallrestratifiednumberslargefemale.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)
     

      aout$subset = 'NEFSCFallLargeFemale'
     write.csv(aout,file=file.path(fp,'indicators','adjrestratified.NEFSC.Fall.LargeFemale.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$years.to.estimate = c(1970:2015)
      p$length.based = T
      p$by.sex = T
      p$size.class = c(140,300)
      p$sex = c(2,3)
      p$bootstrapped.ci=F
      p$strata.files.return=T
      p$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 = 'lfa41DFObasenumberslargefemale.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)
     

      aout$subset = 'DFOLargeFemale'
     write.csv(aout,file=file.path(fp,'indicators','DFO.Base.LargeFemale.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 = 'lfa41DFOrestratifiednumberslargefemale.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)
    
     aout$subset = 'DFOLargeFemale'
    write.csv(aout,file=file.path(fp,'indicators','DFO.restratified.LargeFemale.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 = 'adjcentlfa41DFOrestratifiednumberslargefemale.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)

      aout$subset = 'DFOLargeFemale'
write.csv(aout,file=file.path(fp,'indicators','DFO.adjrestratified.LargeFemale.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(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 = 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
                              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 = 'lfa41georgesnumberslargefemale.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)
    aout$subset = 'DFO.Georges.LargeFemale'  
write.csv(aout,file=file.path(fp,'indicators','DFO.Georges.LargeFemale.csv'))