inst/Assessments/LFA41Assessment/2b.stratifiedSexRatios.r

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

# sex ratios surveys
require(bio.survey)
require(bio.groundfish)
require(bio.lobster)
la()
p = bio.lobster::load.environment()
p$libs = NULL
fp = file.path(project.datadirectory('bio.lobster'),"analysis",'lfa41Assessment')
la()
#load_all('~/git/bio.survey/')

assessment.year = p$current.assessment.year ########### check the year ############### !!!!!!!!!!!


#DFO RV Analysis

      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$reweight.strata = T
      p$years.to.estimate = c(1999:assessment.year)
      p$length.based = F
      p$by.sex = T
      p$bootstrapped.ci=F
      p$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)

      

#restratified

        a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
          }

        aa = do.call(rbind,out)
		aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'sexLFA41polygonSummerRV.rdata'))
    write.csv(aa,file=file.path(fp,'indicators','DFO.restratified.SexRatio.csv'))



#NEFSC spring
      p$years.to.estimate = c(1969:assessment.year)
      p$length.based = T
      p$size.class= c(50,300)
      p$by.sex = T
      p$sex = c(1,2) # male female berried c(1,2,3)
      p$bootstrapped.ci=F
      p$strata.files.return=F
      p$strata.efficiencies=F
      p$clusters = c( rep( "localhost", 7) )
  
         p = make.list(list(yrs=p$years.to.estimate),Y=p)

   

                 
# restratified
    p$season =c('spring')# p$series =c('spring');p$series =c('fall')
    p$define.by.polygons = T
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = T #this subsets 
      
   	    a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = nefsc.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'sexLFA41NEFSCspringrestratified.rdata'))
     write.csv(aa,file=file.path(fp,'indicators','NEFSC.spring.restratified.SexRatio.csv'))





# Fall restratified
    p$season =c('fall')# p$series =c('spring');p$series =c('fall')
    p$define.by.polygons = T
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = T #this subsets 
      p$years.to.estimate = c(1969:(assessment.year-1)) # -1 because update is in the Fall
      p = make.list(list(yrs=p$years.to.estimate),Y=p)
      
   	    a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = nefsc.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'sexLFA41NEFSCfallrestratified.rdata'))
        write.csv(aa,file=file.path(fp,'indicators','NEFSC.fall.restratified.SexRatio.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:assessment.year)
      p$length.based = F
      p$by.sex = T
      p$bootstrapped.ci=F
      p$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$define.by.polygons = F
      p$lobster.subunits=F
      p$area = 'Georges.Canada'
      p$reweight.strata = F #this subsets 
      

   	    a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'sexLFA41dfogeorges.rdata'))
        write.csv(aa,file=file.path(fp,'indicators','DFO.georges.SexRatio.csv'))

##################################### 
#####mature lobster sex ratios
# sex ratios surveys


#DFO RV Analysis
#restratified
        require(bio.lobster)
        p = bio.lobster::load.environment()
        p$libs = NULL

        la()
        #load_all('~/git/bio.survey/')

        p$series =c('summer')# p$series =c('georges');p$series =c('fall')
        p$define.by.polygons = T
        p$lobster.subunits=F
        p$area = 'LFA41'
        p$reweight.strata = T #this subsets 
        p$years.to.estimate = c(1999:assessment.year)
        p$length.based = T
        p$by.sex = T
        p$bootstrapped.ci=F
        p$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$years.to.estimate),Y=p)
        p$size.class = c(92,300)
        a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
          }

        aa = do.call(rbind,out)
		aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'maturesexLFA41polygonSummerRV.rdata'))
        load(file=file.path(fp,'maturesexLFA41polygonSummerRV.rdata'))
    write.csv(aa,file=file.path(fp,'indicators','DFO.restratified.Mature.SexRatio.csv'))


#NEFSC spring

      p$season  = 'spring'
      p$years.to.estimate = c(1969:assessment.year)
      p$length.based = T
      p$size.class= c(92,300)
      p$by.sex = T
      p$sex = c(1,2) # male female berried c(1,2,3)
      p$bootstrapped.ci=F
      p$strata.files.return=F
      p$strata.efficiencies=F
      p$clusters = c( rep( "localhost", 7) )
  
      p$define.by.polygons = T
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = T #this subsets 
    p = make.list(list(yrs=p$years.to.estimate),Y=p)
      
   	    a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = nefsc.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'maturesexLFA41NEFSCspringrestratified.rdata'))
  write.csv(aa,file=file.path(fp,'indicators','NEFSC.spring.restratified.Mature.SexRatio.csv'))

# Fall survey 
# restratified
    p$season =c('fall')# p$series =c('spring');p$series =c('fall')
    p$define.by.polygons = T
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = T #this subsets 
      p$years.to.estimate = c(1969:(assessment.year-1)) # -1 because update is in the Fall
      p = make.list(list(yrs=p$years.to.estimate),Y=p)
      
   	    a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = nefsc.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'maturesexLFA41NEFSCfallrestratified.rdata'))
  write.csv(aa,file=file.path(fp,'indicators','NEFSC.fall.restratified.Mature.SexRatio.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:assessment.year)
      p$length.based = T
      p$by.sex = T
      p$bootstrapped.ci=F
      p$strata.files.return=F
      p$vessel.correction.fixed=1.2
      p$strat = NULL
      p$clusters = c( rep( "localhost", 7) )
      p$strata.efficiencies = F
      p$size.class = c(92,300)
      p = make.list(list(yrs=p$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 
      

   	    a = list(1,c(2,3))
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'maturesexLFA41dfogeorges.rdata'))
write.csv(aa,file=file.path(fp,'indicators','DFO.Georges.Mature.SexRatio.csv'))
    


#####immature lobster sex ratios
# sex ratios surveys
        require(bio.lobster)
        p = bio.lobster::load.environment()
        p$libs = NULL

        p$series =c('summer')# p$series =c('georges');p$series =c('fall')
        p$define.by.polygons = T
        p$lobster.subunits=F
        p$area = 'LFA41'
        p$reweight.strata = T #this subsets 
        p$years.to.estimate = c(1999:assessment.year)
        p$length.based = T
        p$by.sex = T
        p$bootstrapped.ci=F
        p$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$years.to.estimate),Y=p)
        p$size.class = c(0,91)
        a = list(1,2)
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
          }

        aa = do.call(rbind,out)
    aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'immaturesexLFA41polygonSummerRV.rdata'))
     write.csv(aa,file=file.path(fp,'indicators','DFO.restratified.immature.SexRatio.csv'))

#NEFSC spring


      p$reweight.strata = F #this subsets 
      p$years.to.estimate = c(1969:assessment.year)
      p$length.based = T
      p$size.class= c(50,91)
      p$by.sex = T
      p$sex = c(1,2) # male female berried c(1,2,3)
      p$bootstrapped.ci=F
      p$strata.files.return=F
      p$strata.efficiencies=F
      p$clusters = c( rep( "localhost", 7) )
       p = make.list(list(yrs=p$years.to.estimate),Y=p)
      

# restratified
    p$season =c('spring')# p$series =c('spring');p$series =c('fall')
    p$define.by.polygons = T
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = T #this subsets 
      
        a = list(1,2)
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = nefsc.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'immaturesexLFA41NEFSCspringrestratified.rdata'))
     write.csv(aa,file=file.path(fp,'indicators','NEFSC.spring.restratified.immature.SexRatio.csv'))



# restratified
      p$season =c('fall')# p$series =c('spring');p$series =c('fall')
      p$define.by.polygons = T
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = T #this subsets 
      p$years.to.estimate = c(1969:(assessment.year-1)) # -1 because update is in the Fall
      p = make.list(list(yrs=p$years.to.estimate),Y=p)
      
        a = list(1,2)
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = nefsc.analysis(DS='stratified.estimates.redo',p=p)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'immaturesexLFA41NEFSCfallrestratified.rdata'))
write.csv(aa,file=file.path(fp,'indicators','NEFSC.fall.restratified.immature.SexRatio.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:assessment.year)
      p$length.based = T
      p$by.sex = T
      p$bootstrapped.ci=F
      p$strata.files.return=F
      p$vessel.correction.fixed=1.2
      p$strat = NULL
      p$clusters = c( rep( "localhost", 7) )
      p$strata.efficiencies = F
      p$size.class = c(0,91)
      p = make.list(list(yrs=p$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 
      

        a = list(1,2)
        out = list()
        for(i in 1:length(a)) {
          p$sex=a[[i]]
          out[[i]] = dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
          }

        aa = do.call(rbind,out)
        aa$sex = rep(c('male','femberr'),each=length(p$years.to.estimate))
        save(aa,file=file.path(fp,'immaturesexLFA41dfogeorgeshi.rdata'))
      write.csv(aa,file=file.path(fp,'indicators','DFO.Georges.base.immature.SexRatio.csv'))




#adding sex ratios combined data frames

fp = file.path(fp,"indicators")
h = dir(fp)

hi = h[grep('SexRatio',h)]
hi = hi[grep('restratified',hi)]
hi = hi[grep('adj',hi,invert=T)]
hi = c(hi,"DFO.Georges.Mature.SexRatio.csv  ")

for(i in hi) {
    j = read.csv(file.path(fp,i))
    g = aggregate(cbind(n.yst,ObsLobs)~yr,data=j,FUN=sum)
    k = subset(j,sex=='femberr',select=c('yr','n.yst'))
  
    l = merge(g,k,by='yr')

    l$sexratio = l$n.yst.y / l$n.yst.x
    l = l[,c('yr','sexratio','ObsLobs')]
    write.csv(l,file=file.path(fp,i))

}