inst/Frameworks/LFA41Framework/2f.stratifiedAnalysisforCusum.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)
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis")
la()
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) )
      p$big.ci=T  
      

# Spring survey All stations including adjacent
                        p$season =c('spring')# p$series =c('spring');p$series =c('fall')
                        p$area = 'LFA41'
                      p = make.list(list(yrs=p$years.to.estimate),Y=p)
                    

#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)

save(aout,file=file.path(fp,'nefsc.spring.restratified.bigci.rdata'))

#Fall restratified to lfa41
      p$season='fall'
      p$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)
save(aout,file=file.path(fp,'nefsc.fall.restratified.bigci.rdata'))



##############################################################
#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 = 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)

      
      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)
      save(aout,file=file.path(fp,'dfo.summer.restratified.bigci.rdata'))


  #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(aout,file=file.path(fp,'dfo.georges.restratified.bigci.rdata'))