inst/Frameworks/LFA3438Framework/LFA35-38Assessment/8.PredatorIndex.r

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

require(bio.survey)
require(bio.groundfish)
require(bio.lobster)
la()
ff = "LFA35-38Assessment"
fp1 = file.path(project.datadirectory('bio.lobster'),"analysis",ff)
fpf1 = file.path(project.figuredirectory('bio.lobster'),ff)

        p=list()
        p$strat=490:495
        p$series =c('summer')# p$series =c('4vswcod');p$series =c('georges')
        p$years.to.estimate = c(1970:2019)
        p$functional.groups = T
        yy = list()
        yy[['LobPred']] = c(10,11,12,13,40,50,200,201,203,204,300)
        p$species = 'LobPred'
        p$yy = yy
        p$vessel.correction = T
        p$vessel.correction.fixed = 1.2
        p$length.based = F
        p$by.sex = p$sex.based = F
        p$alpha = 0.05
        p$strata.efficiencies=F
        p$functional.groups = T
        p$bootstrapped.ci=T
        p$strata.files.return=F
        p$clusters = c( rep( "localhost", 7) )
        p = make.list(list(v=p$species, yrs=p$years.to.estimate),Y=p)
        p$runs = p$runs[order(p$runs$v),]

aout= groundfish.analysis(DS='stratified.estimates.redo',out.dir = 'bio.lobster',p=p)
write.csv(aout,file=file.path(fpf1,'LobPredators35-38.csv')
                        p$ylim = NULL
              				  p$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 =  file.path(ff,'LobPredatorsabundance35-38.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,wd=10,ht=8)
              


              				  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$metric = 'weights' #weights
                              p$measure = 'stratified.mean' #'stratified.total'
                              p$figure.title = ""
                              p$reference.measure = 'median' # mean, geomean
                              p$file.name =  file.path(ff,'LobPredatorsbiomass35-38.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=NULL

                       ref.out=   figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,wd=10,ht=8)