inst/Frameworks/LFA3438Framework/LFA35-38Assessment/3.stratifiedAnalysisCommercial.r

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

require(bio.survey)
require(bio.lobster)
require(bio.groundfish)

p = bio.lobster::load.environment()
p$libs = NULL
ff = "LFA35-38Assessment"
fp1 = file.path(project.datadirectory('bio.lobster'),"analysis",ff)
fpf1 = file.path(project.figuredirectory('bio.lobster'),ff)
dir.create(fpf1,showWarnings=F)
dir.create(fp1,showWarnings=F)
p1 = p
p1$yrs = 1970:2019

stratifiedAnalysesCommercial = function( p=p1, survey,lfa, fpf = fpf1, fp = fp1,f=ff,wd=10,ht=8){
    p$series =c('summer')# p$series =c('georges');p$series =c('fall')
    p$years.to.estimate = p$yrs
    p$length.based = T
    p$by.sex = T
    p$size.class = c(83,300)
    p$sex = c(1,2)
    p$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)
    p$define.by.polygons = T
    p$lobster.subunits=F
    p$area = lfa
    p$reweight.strata = T #this subsets 

    aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
    write.csv(aout,file=file.path(fpf, paste(lfa,'DFOCommB.csv')))

      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.total' #'stratified.total'
    p$figure.title = ""
    p$reference.measure = 'median' # mean, geomean
    p$file.name =  file.path(f,paste(lfa,'DFOrestratifiedtotalweightscommercial.png',sep=""))

    p$y.maximum = NULL # NULL # if ymax is too high for one year
    p$show.truncated.weights = F #if using ymax and want to show the weights 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
    require(bio.lobster)
     p$ylim2 = NULL
    xx = aggregate(ObsLobs~yr,data=aout,FUN=sum)
    names(xx) =c('x','y')
     p$ylim=NULL
     ref.out= figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p,wd=wd,ht=ht)
     return(aout)
  }



aout = stratifiedAnalysesCommercial(survey='DFO',lfa='LFA35-38')
write.csv(aout,file.path(fp1,'LFA3538CommercialB.csv'))