inst/Assessments/LFA41Assessment/11.environmentalConditions.r

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

#environmental conditions

#AMO capture from web
options(stringsAsFactors=F)

url <- "http://www.esrl.noaa.gov/psd/data/correlation//amon.us.long.data"
a = readLines(url,skip=1)
k = length(a)
a = a[-c(1,(k-4):k)]
g = length(a)

a = matrix(scan(url,skip=1,nlines=g),nrow=g,ncol=13,byrow=T)
p = rowMeans(a[,2:13])
fn = file.path(project.figuredirectory('bio.lobster'))
png(file=file.path(fn,'AMO.png'),units='in',width=15,height=12,pointsize=18, res=300,type='cairo')
plot(1856:(1856+length(p)-1),p,type='h',ylab='AMO anomaly',xlab='Year')
dev.off()
aa = data.frame(yr=1856:(1856+length(p)-1),amo=p)
write.csv(aa,file=file.path(project.datadirectory('bio.lobster'),'analysis','lfa41Assessment','indicators','amo.csv'))



#temperature trends from the surveys
require(bio.survey)

require(bio.lobster)
p = bio.lobster::load.environment()
assessment.year = p$current.assessment.year ########### check the year ############### !!!!!!!!!!!
p$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:assessment.year)
      p$length.based = F
      p$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) )
  
      

# 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$temperature=T
                      p = make.list(list(yrs=p$years.to.estimate),Y=p)
                    
                        aout= nefsc.analysis(DS='stratified.estimates.redo',p=p,save=F)
write.csv(aout,file=file.path(project.datadirectory('bio.lobster'),'analysis','lfa41Assessment','indicators','lfa41NEFSCSpringTemps.csv'))
              #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$metric = 'temperature' #weights
                              p$measure = 'stratified.mean' #'stratified.total'
                              p$figure.title = ""
                              p$reference.measure = 'median' # mean, geomean
                              p$file.name = 'lfa41NEFSCSpringTemps.png'
                              p$ylim = c(5,12)
                          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)
 #### fall
         p$season =c('fall')# p$series =c('spring');p$series =c('fall')
      p$years.to.estimate = c(1969:(assessment.year-1))
       p = make.list(list(yrs=p$years.to.estimate),Y=p)
                        
	                        aout= nefsc.analysis(DS='stratified.estimates.redo',p=p,save=F)
                          write.csv(aout,file=file.path(project.datadirectory('bio.lobster'),'analysis','lfa41Assessment','indicators','lfa41NEFSCFallTemps.csv'))

                            p$file.name = 'lfa41NEFSCFallTemps.png'
                            ref.out=   figure.stratified.analysis(x=aout,out.dir = 'bio.lobster', p=p)
 

 ###dfo
    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$years.to.estimate = c(1970:assessment.year)
      p$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$temperature=T
      

# DFO survey All stations including adjacent
      p$define.by.polygons = F
      p$lobster.subunits=F
      p$area = 'LFA41'
      p$reweight.strata = F #this subsets 
      require(bio.groundfish)
      la()
      aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p,save=F)
write.csv(aout,file=file.path(project.datadirectory('bio.lobster'),'analysis','lfa41Assessment','indicators','lfa41DFOSummerTemps.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$metric = 'temperature' #weights
                              p$measure = 'stratified.mean' #'stratified.total'
                              p$figure.title = ""
                              p$reference.measure = 'median' # mean, geomean
                              p$file.name = 'lfa41DFOTemp.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)
       

       #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:assessment.year)
      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 
      p$temperature=T
      aout= dfo.rv.analysis(DS='stratified.estimates.redo',p=p)
write.csv(aout,file=file.path(project.datadirectory('bio.lobster'),'analysis','lfa41Assessment','indicators','lfa41DFOGeorgesTemps.csv'))
      

         #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$metric = 'temperature' #weights
                              p$measure = 'stratified.mean' #'stratified.total'
                              p$figure.title = ""
                              p$reference.measure = 'median' # mean, geomean
                              p$file.name = 'lfa41georgestemperature.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,save=T)