inst/Frameworks/LFA3438Framework/LFA34-38Framework/maps.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
#maps
require(bio.lobster)
require(bio.utilities)
require(bio.polygons)
la()
#Survey Maps
fp = file.path(project.datadirectory('bio.lobster'),"analysis","LFA34-38")
fpf = file.path(project.figuredirectory('bio.lobster'),'LFA3438Framework2019')
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA34 = subset(LFAs,PID %in% c(34,35,36,38))
attr(LFA34,'projection') <- 'LL'
LobsterMap('34-38',boundaries='LFAs',addSummerStrata=F,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=T)
savePlot(file.path(fpf,'LFAMap34-38.png'),)
LobsterMap('34-38',boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=T,addGrids=F)
savePlot(file.path(fpf,'LFAMap34-38DFOSummerSurvey.png'),)
LobsterMap('34-38',boundaries='LFAs',addSummerStrata=F,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=T,addAmericanStrata=T,addGrids=F)
savePlot(file.path(fpf,'LFAMap34-38AmericanSurvey.png'),)
##
##Areas by maps
a = importShapefile(find.bio.gis('BTS_Strata'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','STRATA')]
a = merge(a,l,by='PID',all.x=T)
# addPolys(a,border='red')
addPolys(subset(a,STRATA %in% c(3900,3920,1352,1351,1360,1330,1340,1310)),lty=1,border='green',col=adjustcolor('white',alpha.f=1))
#3900 and 3920 are in LFA 38
#areas within each LFA
#LFA34 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA34 = subset(LFAs,PID %in% c(34))
LFA34 = joinPolys(LFA34,operation='UNION')
LFA34 = subset(LFA34,SID==1)
attr(LFA34,'projection') <- 'LL'
a34 = calcArea(LFA34)$area
#20364 km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 13316 / 20364 = 0.655
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA35 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA35 = subset(LFAs,PID %in% c(35))
LFA35 = joinPolys(LFA35,operation='UNION')
LFA35 = subset(LFA35,SID==1)
attr(LFA35,'projection') <- 'LL'
a35 = sum(calcArea(LFA35)$area)
#5396 km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA35,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 2304.03 / 5396 = 0.427
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA35,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA36 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA36 = subset(LFAs,PID %in% c(36))
LFA36 = subset(LFA36,SID==1)
attr(LFA36,'projection') <- 'LL'
a36 = sum(calcArea(LFA36)$area)
#4408/ km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA36,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 3081.5 / 4408 = 0.699
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA36,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA38 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA38 = subset(LFAs,PID %in% c(38))
LFA38 = subset(LFA38,SID==1)
attr(LFA38,'projection') <- 'LL'
a38 = sum(calcArea(LFA38)$area)
#4277/ km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 2962.77 / 4277 = 0.693
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA36-38 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA38 = subset(LFAs,PID %in% c(35,36,38))
LFA38 = subset(LFA38,SID==1)
LFA38 = joinPolys(LFA38,operation = "UNION")
attr(LFA38,'projection') <- 'LL'
a38 = sum(calcArea(LFA38)$area)
#14089/ km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 8350.751 / 4277 = 0.693
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#######################################################################################
#American surveys
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA34 = subset(LFAs,PID %in% c(34))
LFA34 = joinPolys(LFA34,operation='UNION')
LFA34 = subset(LFA34,SID==1)
attr(LFA34,'projection') <- 'LL'
a34 = calcArea(LFA34)$area
#LFA34 total
#20364 km2
a = importShapefile(find.bio.gis('BTS_Strata'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','STRATA')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
USa = sum(d$area)
# 13273 / 20364 = 0.652
##strata by strata areas
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA35 total -- no overlap
#LFA36 total - 56km2 of overlap, not worth including
#LFA38 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA38 = subset(LFAs,PID %in% c(38))
LFA38 = subset(LFA38,SID==1)
attr(LFA38,'projection') <- 'LL'
a38 = sum(calcArea(LFA38)$area)
#4277/ km2
#Summer strata
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 4070 / 4277 = 0.9517
##strata by strata areas
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA36-38 total
#194119 / 32686 = 0.651
#since 2009
#
#######################################################################################
lobster.db( DS="fsrs", p=p) # FSRS recruitment traps
LobsterMap('34-38')
fsrs$EID = 1:nrow(fsrs)
fsrs$X = fsrs$LONG_DD
fsrs$Y = fsrs$LAT_DD
fsrs = subset(fsrs,HAUL_YEAR>2014 & LFA >33)
addPoints(fsrs,pch=16,col='red',cex=0.5)
savePlot(file.path(fpf,'LFAMap34-38FSRSgr2014.png'),)
##ff mapos
require(bio.lobster)
require(bio.utilities)
require(PBSmapping)
p = bio.lobster::load.environment()
p$syr = 2005
p$yrs = p$syr:2018
figdir = fpf
p$lfas = c("34", "35", "36", "38") # specify lfas for data summary
logsInSeason<-lobster.db('process.logs')
catchLevels = c(0,100000,200000,300000,400000,500000,600000,700000,800000)
yrs = c(2003:2018)
outs = list()
for(i in 1:length(yrs)){
catchgrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR==yrs[i],c("LFA","GRID_NUM","TOTAL_WEIGHT_KG")),FUN=sum,lvls=catchLevels)
a = catchgrids$grid
b = catchgrids$pdata
a = calcCentroid(a)
d = merge(a,b)
outs[[i]] = with(subset(d,PID==34),{
Xc = sum(X*Z)/sum(Z)
Yc = sum(Y*Z)/sum(Z)
return(c(Xc,Yc))
})
# saveRDS(catchgrids,file=file.path(fd,paste('Figure3',yrs[i],'.rds')))
pdf(file.path(figdir,paste0("FisheryFootprintLandings",yrs[i],".pdf")))
LobsterMap('34-38',poly.lst=catchgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=catchgrids$lvls/1000,Cont.data=catchgrids,title="Catch (tons)",inset=0.02,cex=0.8,bg='white')
dev.off()
}
##fishery moving ? weighted centroids of landings
xx = as.data.frame(do.call(rbind,outs))
names(xx) = c('X','Y')
xx$POS=1:nrow(xx)
xx$PID = 1
LobsterMap('34')
addLines(xx,col='red')
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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#maps
require(bio.lobster)
require(bio.utilities)
require(bio.polygons)
la()
#Survey Maps
fp = file.path(project.datadirectory('bio.lobster'),"analysis","LFA34-38")
fpf = file.path(project.figuredirectory('bio.lobster'),'LFA3438Framework2019')
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA34 = subset(LFAs,PID %in% c(34,35,36,38))
attr(LFA34,'projection') <- 'LL'
LobsterMap('34-38',boundaries='LFAs',addSummerStrata=F,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=T)
savePlot(file.path(fpf,'LFAMap34-38.png'),)
LobsterMap('34-38',boundaries='LFAs',addSummerStrata=T,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=T,addGrids=F)
savePlot(file.path(fpf,'LFAMap34-38DFOSummerSurvey.png'),)
LobsterMap('34-38',boundaries='LFAs',addSummerStrata=F,output='bio.lobster',fname = 'summerstratamap.pdf',save=F,labcex =0.8,labels=T,addAmericanStrata=T,addGrids=F)
savePlot(file.path(fpf,'LFAMap34-38AmericanSurvey.png'),)
##
##Areas by maps
a = importShapefile(find.bio.gis('BTS_Strata'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','STRATA')]
a = merge(a,l,by='PID',all.x=T)
# addPolys(a,border='red')
addPolys(subset(a,STRATA %in% c(3900,3920,1352,1351,1360,1330,1340,1310)),lty=1,border='green',col=adjustcolor('white',alpha.f=1))
#3900 and 3920 are in LFA 38
#areas within each LFA
#LFA34 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA34 = subset(LFAs,PID %in% c(34))
LFA34 = joinPolys(LFA34,operation='UNION')
LFA34 = subset(LFA34,SID==1)
attr(LFA34,'projection') <- 'LL'
a34 = calcArea(LFA34)$area
#20364 km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 13316 / 20364 = 0.655
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA35 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA35 = subset(LFAs,PID %in% c(35))
LFA35 = joinPolys(LFA35,operation='UNION')
LFA35 = subset(LFA35,SID==1)
attr(LFA35,'projection') <- 'LL'
a35 = sum(calcArea(LFA35)$area)
#5396 km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA35,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 2304.03 / 5396 = 0.427
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA35,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA36 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA36 = subset(LFAs,PID %in% c(36))
LFA36 = subset(LFA36,SID==1)
attr(LFA36,'projection') <- 'LL'
a36 = sum(calcArea(LFA36)$area)
#4408/ km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA36,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 3081.5 / 4408 = 0.699
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA36,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA38 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA38 = subset(LFAs,PID %in% c(38))
LFA38 = subset(LFA38,SID==1)
attr(LFA38,'projection') <- 'LL'
a38 = sum(calcArea(LFA38)$area)
#4277/ km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 2962.77 / 4277 = 0.693
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA36-38 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA38 = subset(LFAs,PID %in% c(35,36,38))
LFA38 = subset(LFA38,SID==1)
LFA38 = joinPolys(LFA38,operation = "UNION")
attr(LFA38,'projection') <- 'LL'
a38 = sum(calcArea(LFA38)$area)
#14089/ km2
#Summer strata
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 8350.751 / 4277 = 0.693
##strata by strata areas
a = importShapefile(find.bio.gis('MaritimesRegionEcosystem'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','StrataID')]
a = merge(a,l,by='PID',all.x=T)
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#######################################################################################
#American surveys
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA34 = subset(LFAs,PID %in% c(34))
LFA34 = joinPolys(LFA34,operation='UNION')
LFA34 = subset(LFA34,SID==1)
attr(LFA34,'projection') <- 'LL'
a34 = calcArea(LFA34)$area
#LFA34 total
#20364 km2
a = importShapefile(find.bio.gis('BTS_Strata'),readDBF=T)
l = attributes(a)$PolyData[,c('PID','STRATA')]
a = merge(a,l,by='PID',all.x=T)
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
USa = sum(d$area)
# 13273 / 20364 = 0.652
##strata by strata areas
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA34,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA35 total -- no overlap
#LFA36 total - 56km2 of overlap, not worth including
#LFA38 total
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
LFA38 = subset(LFAs,PID %in% c(38))
LFA38 = subset(LFA38,SID==1)
attr(LFA38,'projection') <- 'LL'
a38 = sum(calcArea(LFA38)$area)
#4277/ km2
#Summer strata
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
d = joinPolys(d,operation='UNION')
d = calcArea(d)
RVa = sum(d$area)
# 4070 / 4277 = 0.9517
##strata by strata areas
attr(a,'projection') <- "LL"
bb = calcArea(a)
bb = aggregate(area~PID,data=bb,FUN=sum)
bb = rename.df(bb,'area','totalarea')
d = joinPolys(LFA38,a,'INT')
attr(d,'projection') <- "LL"
dd = calcArea(d)
dd = aggregate(area~PID,data=dd, FUN=sum)
dd = merge(dd,bb,all.x=T)
dd = merge(dd,l,by='PID',all.x=T)
dd$prop = dd$area / dd$totalarea
#LFA36-38 total
#194119 / 32686 = 0.651
#since 2009
#
#######################################################################################
lobster.db( DS="fsrs", p=p) # FSRS recruitment traps
LobsterMap('34-38')
fsrs$EID = 1:nrow(fsrs)
fsrs$X = fsrs$LONG_DD
fsrs$Y = fsrs$LAT_DD
fsrs = subset(fsrs,HAUL_YEAR>2014 & LFA >33)
addPoints(fsrs,pch=16,col='red',cex=0.5)
savePlot(file.path(fpf,'LFAMap34-38FSRSgr2014.png'),)
##ff mapos
require(bio.lobster)
require(bio.utilities)
require(PBSmapping)
p = bio.lobster::load.environment()
p$syr = 2005
p$yrs = p$syr:2018
figdir = fpf
p$lfas = c("34", "35", "36", "38") # specify lfas for data summary
logsInSeason<-lobster.db('process.logs')
catchLevels = c(0,100000,200000,300000,400000,500000,600000,700000,800000)
yrs = c(2003:2018)
outs = list()
for(i in 1:length(yrs)){
catchgrids = lobGridPlot(subset(logsInSeason,LFA%in%p$lfas&SYEAR==yrs[i],c("LFA","GRID_NUM","TOTAL_WEIGHT_KG")),FUN=sum,lvls=catchLevels)
a = catchgrids$grid
b = catchgrids$pdata
a = calcCentroid(a)
d = merge(a,b)
outs[[i]] = with(subset(d,PID==34),{
Xc = sum(X*Z)/sum(Z)
Yc = sum(Y*Z)/sum(Z)
return(c(Xc,Yc))
})
# saveRDS(catchgrids,file=file.path(fd,paste('Figure3',yrs[i],'.rds')))
pdf(file.path(figdir,paste0("FisheryFootprintLandings",yrs[i],".pdf")))
LobsterMap('34-38',poly.lst=catchgrids)
title(yrs[i],line=-3,cex.main=2,adj=0.3)
SpatialHub::contLegend('bottomright',lvls=catchgrids$lvls/1000,Cont.data=catchgrids,title="Catch (tons)",inset=0.02,cex=0.8,bg='white')
dev.off()
}
##fishery moving ? weighted centroids of landings
xx = as.data.frame(do.call(rbind,outs))
names(xx) = c('X','Y')
xx$POS=1:nrow(xx)
xx$PID = 1
LobsterMap('34')
addLines(xx,col='red')
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