inst/Frameworks/LFA41Framework/maps.r

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

#maps

#Fishing Area
		logs41   = lobster.db('logs41')
		logs41$YEAR = year(logs41$FV_FISHED_DATETIME)
  		logs41 = makePBS(logs41,polygon=F)
        logs41 = logs41[-which(is.na(logs41[,c('X','Y','EID')])),]
		yr = unique(logs41$YEAR)

		#prune to polygons
				LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
				LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
				LFA41 = subset(LFA41,SID==1)
				attr(LFA41,'projection') <- 'LL'

				l = findPolys(logs41,LFA41)$EID
			logs41 = subset(logs41,EID %in% l)

			LFA41<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
				y = c(2002,2007,2013)
			for(i in y) {
					pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('lfa41Logs',i,i+5,'.pdf',sep='.')))
					LobsterMap('41')
					addPoints(subset(logs41,YEAR %in% c(i:(i+5))),pch='.',col='green')
					addPolys(LFA41,border='red')		
					dev.off()
				}


#Survey Maps
		LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
				LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
				LFA41 = subset(LFA41,SID==1)
				attr(LFA41,'projection') <- 'LL'


LobsterMap(xlim=c(-69,-56.8),ylim=c(41.2,47.5),boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=T,labcex =0.8,labels=F)


pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('summerstratamap41.pdf',sep='.')))
		LobsterMap('41',boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname='summerstratamap41.pdf',save=F,labcex =0.8,labels=F,subsetSummerStrata=c(472,473,477,478,481,482,483,484,485))
		addPolys(LFA41,border='blue',lwd=2)
	 dev.off()

pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('georgesmap41.pdf',sep='.')))
LobsterMap(xlim=c(-70.5,-63.5),ylim=c(38.5,45),boundaries='LFAs',addGeorgesStrata=T,output='bio.lobster',fname='georgesmap41.pdf',save=F,labcex =0.8,labels=T)
	addPolys(LFA41,border='blue',lwd=2)
	b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
	 load(b)
	 addPolys(subset(out,PID %in% c(1,2)),lty=1,border='green')
	dev.off()


pdf(file=file.path(project.figuredirectory('bio.lobster'),paste('americanmap41.pdf',sep='.')))
LobsterMap(xlim=c(-71,-63.5),ylim=c(38,45),boundaries='LFAs',addAmericanStrata=F,output='bio.lobster',fname='americanmapfull41.pdf',save=F,labcex =0.8,labels=T)
a = importShapefile(find.bio.gis('BTS_Strata'),readDBF=T) 
                          l = attributes(a)$PolyData[,c('PID','STRATA')]
                          a = merge(a,l,by='PID',all.x=T)
   # addPolys(a,border='red')                      
    addPolys(subset(a,STRATA %in% c(1160, 1170, 1180, 1190, 1200, 1210, 1220, 1290, 1300, 1340, 1360,1330,1360,1351,1352,3920,3900)),lty=1,border='red',col=adjustcolor('white',alpha.f=1))
			
         
	addPolys(LFA41,border='blue',lwd=2)

	

	dev.off()



#areas within each polygon

#LFA41 total
		LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
		LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
		
		addPolys(subset(a,STRATA %in% c(1160, 1170, 1180, 1190, 1200, 1210, 1220, 1290, 1300, 1340, 1360,1330,1360,1351,1352,3920,3900)),lty=1,border='red',col=adjustcolor('white',alpha.f=1))
		
		
				LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
				LFA41 = subset(LFA41,SID==1)
				attr(LFA41,'projection') <- 'LL'

a41 = calcArea(LFA41)$area
#32686

#Summer strata
			  a = find.bio.gis('summer_strata_labels',return.one.match=F)
			  a = read.csv(a,header=T)
			  names(a)[4] <- 'label'
			  b = find.bio.gis('strat.gf',return.one.match=F)
			  b = read.table(b)
			  names(b) <- c('X','Y','PID')
			  b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
			  d = joinPolys(LFA41,b,'INT')
			  attr(d,'projection') <- "LL"
			  d = joinPolys(d,operation='UNION')
			  d = calcArea(d)
			  RVa = sum(d$area)
# 14597 / 32686 = 0.446
 

			  b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
			  load(b)
			  d = joinPolys(LFA41,out,'INT')
			  attr(d,'projection') <- "LL"
			  d = joinPolys(d,operation='UNION')
			  d = calcArea(d)
			  GBa = sum(d$area)
# 7274 / 32686 = 0.222

     		   b = importShapefile(find.bio.gis('bts',return.one.match=F))
     		   addPolys(subset(a,STRATA %in% c(1160, 1170, 1180, 1190, 1200, 1210, 1220, 1290, 1300, 1340, 1360,1330,1360,1351,1352,3920,3900)),lty=1,border='red',col=adjustcolor('white',alpha.f=1))
     		   
     		   
			  d = joinPolys(LFA41,b,'INT')
			  attr(d,'projection') <- "LL"
			  d = joinPolys(d,operation='UNION')
			  d = calcArea(d)
			USa = sum(d$area)
#194119 / 32686 = 0.594 

  # 

  ###Overlap map
require(PBSmapping)
require(bio.utilities)
require(bio.lobster)
require(bio.polygons)

LobsterMap(xlim=c(-69.5,-63.5),ylim=c(40.5,45),boundaries='LFAs',addGeorgesStrata=F,output='bio.lobster',fname='georgesmap41.pdf',save=F,labcex =0.8,labels=T)

  		LFA41 = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
				LFA41 = joinPolys(as.PolySet(LFA41),operation='UNION')
				LFA41 = subset(LFA41,SID==1)
				attr(LFA41,'projection') <- 'LL'

#NEFSC
a = importShapefile(find.bio.gis('BTS_Strata'),readDBF=T) 
                          l = attributes(a)$PolyData[,c('PID','STRATA')]
                          a = merge(a,l,by='PID',all.x=T)
   # addPolys(a,border='red')                      
   	Ne = subset(a,STRATA %in% c(1160, 1170, 1180, 1190, 1200, 1210, 1220, 1290, 1300, 1340, 1360))
   	Ne = joinPolys(Ne,operation='UNION')
   	Ne = joinPolys(Ne,LFA41,operation='INT')
    addPolys(Ne,col= rgb(1,0,0,.15))


##DFO Summer
  			  a = find.bio.gis('summer_strata_labels',return.one.match=F)
			  a = read.csv(a,header=T)
			  names(a)[4] <- 'label'
			  b = find.bio.gis('strat.gf',return.one.match=F)
			  b = read.table(b)
			  names(b) <- c('X','Y','PID')
			  b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
			  d = joinPolys(LFA41,b,'INT')
			  d = joinPolys(d,operation='UNION')
			
			  d = subset(d,SID %in% c(1,4))
  			  d = d[c(-251,-252),]
			  d = within(d,{POS <- ave(SID,list(SID),FUN=seq_along)})
			  attr(d,'projection') <- "LL"
			addPolys(d,col= rgb(1,0,0,.15))			  
		#Georges
		  b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
			  load(b)
			  d = joinPolys(LFA41,out,'INT')
			  attr(d,'projection') <- "LL"
			  dd = joinPolys(d,operation='UNION')
		addPolys(dd,col= rgb(1,0,0,.15))

		addPolys(LFA41,border='blue')

		savePlot(file=file.path(project.figuredirectory('bio.lobster'),'AllSurveyCoverage.png'))



		#LFA40

				LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
				a = subset(LFAs,PID==40)