inst/Projects/Vic Map and Figs/FootPrintsDepthPruned_vh.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
require(devtools)
require(bio.lobster)
require(bio.utilities)
require(sf)
la()
wd = ('E:/Nova Scotia/Lobster Job/Stock Assessment/LFA 41/LFA 41 Evaluation')
setwd(wd)
layerDir=file.path(project.datadirectory("bio.lobster"), "data","maps")
##from inst/IP/FootprintMapping/1.EstimatingTrapHaulsFromSlipsandSplit2Grids.r
Tot = readRDS('DiscretizedData/PrivacyScreened_TrapHauls_Landings_Trips_Gridand.rds')
Tot$LFA = ifelse(Tot$LFA=='31B',312,Tot$LFA)
Tot$LFA = ifelse(Tot$LFA=='31A',311,Tot$LFA)
#making plots of Tot
GrMap = readRDS(file.path(project.datadirectory('bio.lobster'),'data','maps','LFA27-38GridsPrunedtoDepth-sf.rds'))
coa = st_as_sf(readRDS(file.path( project.datadirectory("bio.lobster"), "data","maps","CoastlineSF_NY_NL.rds")))
GrMap1 = GrMap
GrMap1$area = st_area(GrMap1)/1000000
GrMap1$V2 = paste(GrMap1$LFA, GrMap1$GRID_NO,sep="-")
st_geometry(GrMap1)<- NULL
gg = aggregate(area~LFA+GRID_NO,data=GrMap1,FUN=function(x) abs(sum(x)))
GrMap2 =merge(GrMap,gg)
gTot = merge(GrMap2,Tot,by.x=c('LFA','GRID_NO'),by.y=c('LFA','Grid'),all.x=T)
###################################################################################################################
makeNewFootPrints <- function(x,data,grmap=GrMap){
LFA1=x
gTot=data
gTot$LandingsT = gTot$Landings/1000
g27 = subset(gTot,LFA==LFA1 & FishingYear>2018 )
g27p = subset(gTot,LFA==LFA1 & FishingYear>2018 &PrivacyScreen==1)
g27n = subset(gTot,LFA==LFA1 & FishingYear>2018 &PrivacyScreen==0)
ok1 = ggplot(g27p,aes(fill=TrapHauls))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
width_inch <- 8.5 * 0.7 # 80% of the paper width
height_inch <- 11 * 0.7 # 80% of the paper height
# Save the plot with the specified dimensions
nm = paste('LFA', LFA1,'- Logbook reported number of trap hauls by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$TrapHaulspkm2 = as.numeric(g27p$TrapHauls/g27p$area)
ok1 = ggplot(g27p,aes(fill=TrapHaulspkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA', LFA1,'- Logbook reported number of trap hauls (TH) by grid corrected by the area of the grid (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
ok1 = ggplot(g27p,aes(fill=LandingsT))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported Landings (t) by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$Landingspkm2 = as.numeric(g27p$LandingsT/g27p$area)
ok1 = ggplot(g27p,aes(fill=Landingspkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported Landings (t) by grid adjusted by area (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
ok1 = ggplot(g27p,aes(fill=Trips))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported number of trips by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$Tripspkm2 = as.numeric(g27p$Trips/g27p$area)
ok1 = ggplot(g27p,aes(fill=Tripspkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported number of trips by grid adjusted by area (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
ok1 = ggplot(g27p,aes(fill=NLics))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA', LFA1,'- Logbook reported number of licences fishing by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$Licencespkm2 = as.numeric(g27p$NLics/g27p$area)
ok1 = ggplot(g27p,aes(fill=Licencespkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported number of licences fishing by grid corrected by area (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$CPUE = g27p$Landings/g27p$TrapHauls
ok1 = ggplot(g27p,aes(fill=CPUE))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
nm = paste('LFA',LFA1,'- Logbook reported catch (kg) per unit effort (trap haul) by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
#Trends
g27 = subset(gTot,LFA==LFA1 & FishingYear>2005 )
g27p = subset(gTot,LFA==LFA1 & FishingYear>2005 &PrivacyScreen==1)
g27n = subset(gTot,LFA==LFA1 & FishingYear>2005 &PrivacyScreen==0)
g27$CPUE = g27$Landings/g27$TrapHauls
ui = unique(g27$GRID_NO)
out = list()
j=0
for(i in 1:length(ui)){
b=subset(g27,GRID_NO==ui[i])
b1 = subset(g27,GRID_NO==ui[i]& FishingYear==max(b$FishingYear))
bp=aggregate(CPUE~FishingYear,data=b,FUN=mean)
base = mean(bp$CPUE[which(bp$FishingYear %in% 2006:2010)])
p4b = p3b = p2b = p1b = b1
p1b$PercentDiff = percentDifference(c(mean(bp$CPUE[6:8]),base))
p2b$PercentDiff = percentDifference(c(mean(bp$CPUE[9:11]),base))
p3b$PercentDiff = percentDifference(c(mean(bp$CPUE[12:14]),base))
p4b$PercentDiff = percentDifference(c(mean(bp$CPUE[15:17]),base))
p1b$label = '2011-2013'
p2b$label = '2014-2016'
p3b$label = '2017-2019'
p4b$label = '2020-2022'
if(nrow(bp)<14){
p1b$PercentDiff =p2b$PercentDiff = p3b$PercentDiff = p4b$PercentDiff = NA
}
bp = do.call(rbind,list(p1b,p2b,p3b,p4b))
out[[i]] = bp
}
o = do.call(rbind,out)
ok1 = ggplot(o,aes(fill=PercentDiff))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~label)+
#geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(o)$xmin,st_bbox(o)$xmax),
ylim = c(st_bbox(o)$ymin,st_bbox(o)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
nm = paste('LFA',LFA1,'- Logbook reported grid estimates of percent difference in catch per unit effort (CPUE) relative to mean CPUE between 2006 and 2010.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
}
wd = ('E:/Nova Scotia/Lobster Job/Stock Assessment/LFA 41/LFA 41 Evaluation/Figures')
setwd(wd)
makeNewFootPrints(x='27',data=gTot)
makeNewFootPrints(x='29',data=gTot)
makeNewFootPrints(x='30',data=gTot)
makeNewFootPrints(x='32',data=gTot)
makeNewFootPrints(x='33',data=gTot)
makeNewFootPrints(x='34',data=gTot)
makeNewFootPrints(x='35',data=gTot)
makeNewFootPrints(x='36',data=gTot)
makeNewFootPrints(x='38',data=gTot)
makeNewFootPrints(x='311',data=gTot)
makeNewFootPrints(x='312',data=gTot)
r<-readRDS(file.path( layerDir,"GridPolysSF.rds"))
b=subset(r,LFA %in% c(27,28,29,30,311,312,32))
o=subset(GrMap,LFA %in% c(27,28,29,30,311,312,32))
ggplot(b)+
geom_sf()+
geom_sf(data=coa,fill='grey')+
geom_sf(data=o,fill='red')+
coord_sf(xlim = c(st_bbox(b)$xmin,st_bbox(b)$xmax),
ylim = c(st_bbox(b)$ymin,st_bbox(b)$ymax),
expand = FALSE)
###
gTot$CPUE = gTot$Landings/gTot$TrapHauls
g27p = subset(gTot, FishingYear%in%2022:2023)
ok1 = ggplot(g27p,aes(fill=CPUE))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
# geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=GrMap,fill=NA)+
coord_sf(xlim = c(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax),
ylim = c(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax,length.out=2),2)))
gp = subset(g27p,FishingYear==2022)
gl = subset(g27p,FishingYear==2023)
gl$geometry<- NULL
gg = merge(gp,gl[,c('LFA','GRID_NO','CPUE')],by=c('LFA','GRID_NO'))
percent_diff <- function(row) {
row$geometry<- NULL
abs_diff <- (as.numeric(row[1]) - as.numeric(row[2]))
mean_val <- mean(as.numeric(row))
percent_diff <- (abs_diff / mean_val) * 100
return(percent_diff)
}
gg$percentChange = apply(gg[,c('CPUE.y','CPUE.x')],1,percent_diff)
require(colorspace)
ggplot(subset(gg,PrivacyScreen==1),aes(fill=percentChange))+
geom_sf() +
scale_fill_continuous_diverging(palette='Purple-Green') +
#facet_wrap(~FishingYear)+
# geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=GrMap,fill=NA)+
coord_sf(xlim = c(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax),
ylim = c(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax,length.out=2),2)))
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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require(devtools)
require(bio.lobster)
require(bio.utilities)
require(sf)
la()
wd = ('E:/Nova Scotia/Lobster Job/Stock Assessment/LFA 41/LFA 41 Evaluation')
setwd(wd)
layerDir=file.path(project.datadirectory("bio.lobster"), "data","maps")
##from inst/IP/FootprintMapping/1.EstimatingTrapHaulsFromSlipsandSplit2Grids.r
Tot = readRDS('DiscretizedData/PrivacyScreened_TrapHauls_Landings_Trips_Gridand.rds')
Tot$LFA = ifelse(Tot$LFA=='31B',312,Tot$LFA)
Tot$LFA = ifelse(Tot$LFA=='31A',311,Tot$LFA)
#making plots of Tot
GrMap = readRDS(file.path(project.datadirectory('bio.lobster'),'data','maps','LFA27-38GridsPrunedtoDepth-sf.rds'))
coa = st_as_sf(readRDS(file.path( project.datadirectory("bio.lobster"), "data","maps","CoastlineSF_NY_NL.rds")))
GrMap1 = GrMap
GrMap1$area = st_area(GrMap1)/1000000
GrMap1$V2 = paste(GrMap1$LFA, GrMap1$GRID_NO,sep="-")
st_geometry(GrMap1)<- NULL
gg = aggregate(area~LFA+GRID_NO,data=GrMap1,FUN=function(x) abs(sum(x)))
GrMap2 =merge(GrMap,gg)
gTot = merge(GrMap2,Tot,by.x=c('LFA','GRID_NO'),by.y=c('LFA','Grid'),all.x=T)
###################################################################################################################
makeNewFootPrints <- function(x,data,grmap=GrMap){
LFA1=x
gTot=data
gTot$LandingsT = gTot$Landings/1000
g27 = subset(gTot,LFA==LFA1 & FishingYear>2018 )
g27p = subset(gTot,LFA==LFA1 & FishingYear>2018 &PrivacyScreen==1)
g27n = subset(gTot,LFA==LFA1 & FishingYear>2018 &PrivacyScreen==0)
ok1 = ggplot(g27p,aes(fill=TrapHauls))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
width_inch <- 8.5 * 0.7 # 80% of the paper width
height_inch <- 11 * 0.7 # 80% of the paper height
# Save the plot with the specified dimensions
nm = paste('LFA', LFA1,'- Logbook reported number of trap hauls by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$TrapHaulspkm2 = as.numeric(g27p$TrapHauls/g27p$area)
ok1 = ggplot(g27p,aes(fill=TrapHaulspkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA', LFA1,'- Logbook reported number of trap hauls (TH) by grid corrected by the area of the grid (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
ok1 = ggplot(g27p,aes(fill=LandingsT))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported Landings (t) by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$Landingspkm2 = as.numeric(g27p$LandingsT/g27p$area)
ok1 = ggplot(g27p,aes(fill=Landingspkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported Landings (t) by grid adjusted by area (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
ok1 = ggplot(g27p,aes(fill=Trips))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported number of trips by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$Tripspkm2 = as.numeric(g27p$Trips/g27p$area)
ok1 = ggplot(g27p,aes(fill=Tripspkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported number of trips by grid adjusted by area (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
ok1 = ggplot(g27p,aes(fill=NLics))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA', LFA1,'- Logbook reported number of licences fishing by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$Licencespkm2 = as.numeric(g27p$NLics/g27p$area)
ok1 = ggplot(g27p,aes(fill=Licencespkm2))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
# Save the plot with the specified dimensions
nm = paste('LFA',LFA1,'- Logbook reported number of licences fishing by grid corrected by area (km2).png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
g27p$CPUE = g27p$Landings/g27p$TrapHauls
ok1 = ggplot(g27p,aes(fill=CPUE))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(g27)$xmin,st_bbox(g27)$xmax),
ylim = c(st_bbox(g27)$ymin,st_bbox(g27)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
nm = paste('LFA',LFA1,'- Logbook reported catch (kg) per unit effort (trap haul) by grid.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
#Trends
g27 = subset(gTot,LFA==LFA1 & FishingYear>2005 )
g27p = subset(gTot,LFA==LFA1 & FishingYear>2005 &PrivacyScreen==1)
g27n = subset(gTot,LFA==LFA1 & FishingYear>2005 &PrivacyScreen==0)
g27$CPUE = g27$Landings/g27$TrapHauls
ui = unique(g27$GRID_NO)
out = list()
j=0
for(i in 1:length(ui)){
b=subset(g27,GRID_NO==ui[i])
b1 = subset(g27,GRID_NO==ui[i]& FishingYear==max(b$FishingYear))
bp=aggregate(CPUE~FishingYear,data=b,FUN=mean)
base = mean(bp$CPUE[which(bp$FishingYear %in% 2006:2010)])
p4b = p3b = p2b = p1b = b1
p1b$PercentDiff = percentDifference(c(mean(bp$CPUE[6:8]),base))
p2b$PercentDiff = percentDifference(c(mean(bp$CPUE[9:11]),base))
p3b$PercentDiff = percentDifference(c(mean(bp$CPUE[12:14]),base))
p4b$PercentDiff = percentDifference(c(mean(bp$CPUE[15:17]),base))
p1b$label = '2011-2013'
p2b$label = '2014-2016'
p3b$label = '2017-2019'
p4b$label = '2020-2022'
if(nrow(bp)<14){
p1b$PercentDiff =p2b$PercentDiff = p3b$PercentDiff = p4b$PercentDiff = NA
}
bp = do.call(rbind,list(p1b,p2b,p3b,p4b))
out[[i]] = bp
}
o = do.call(rbind,out)
ok1 = ggplot(o,aes(fill=PercentDiff))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~label)+
#geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=subset(grmap,LFA==LFA1),fill=NA)+
coord_sf(xlim = c(st_bbox(o)$xmin,st_bbox(o)$xmax),
ylim = c(st_bbox(o)$ymin,st_bbox(o)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27)$xmin,st_bbox(g27)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27)$ymin,st_bbox(g27)$ymax,length.out=2),2)))
nm = paste('LFA',LFA1,'- Logbook reported grid estimates of percent difference in catch per unit effort (CPUE) relative to mean CPUE between 2006 and 2010.png',sep="")
ggsave(nm, plot = ok1, width = width_inch, height = height_inch, units = "in")
}
wd = ('E:/Nova Scotia/Lobster Job/Stock Assessment/LFA 41/LFA 41 Evaluation/Figures')
setwd(wd)
makeNewFootPrints(x='27',data=gTot)
makeNewFootPrints(x='29',data=gTot)
makeNewFootPrints(x='30',data=gTot)
makeNewFootPrints(x='32',data=gTot)
makeNewFootPrints(x='33',data=gTot)
makeNewFootPrints(x='34',data=gTot)
makeNewFootPrints(x='35',data=gTot)
makeNewFootPrints(x='36',data=gTot)
makeNewFootPrints(x='38',data=gTot)
makeNewFootPrints(x='311',data=gTot)
makeNewFootPrints(x='312',data=gTot)
r<-readRDS(file.path( layerDir,"GridPolysSF.rds"))
b=subset(r,LFA %in% c(27,28,29,30,311,312,32))
o=subset(GrMap,LFA %in% c(27,28,29,30,311,312,32))
ggplot(b)+
geom_sf()+
geom_sf(data=coa,fill='grey')+
geom_sf(data=o,fill='red')+
coord_sf(xlim = c(st_bbox(b)$xmin,st_bbox(b)$xmax),
ylim = c(st_bbox(b)$ymin,st_bbox(b)$ymax),
expand = FALSE)
###
gTot$CPUE = gTot$Landings/gTot$TrapHauls
g27p = subset(gTot, FishingYear%in%2022:2023)
ok1 = ggplot(g27p,aes(fill=CPUE))+
geom_sf() +
scale_fill_distiller(trans='identity',palette='Spectral') +
facet_wrap(~FishingYear)+
# geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=GrMap,fill=NA)+
coord_sf(xlim = c(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax),
ylim = c(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax,length.out=2),2)))
gp = subset(g27p,FishingYear==2022)
gl = subset(g27p,FishingYear==2023)
gl$geometry<- NULL
gg = merge(gp,gl[,c('LFA','GRID_NO','CPUE')],by=c('LFA','GRID_NO'))
percent_diff <- function(row) {
row$geometry<- NULL
abs_diff <- (as.numeric(row[1]) - as.numeric(row[2]))
mean_val <- mean(as.numeric(row))
percent_diff <- (abs_diff / mean_val) * 100
return(percent_diff)
}
gg$percentChange = apply(gg[,c('CPUE.y','CPUE.x')],1,percent_diff)
require(colorspace)
ggplot(subset(gg,PrivacyScreen==1),aes(fill=percentChange))+
geom_sf() +
scale_fill_continuous_diverging(palette='Purple-Green') +
#facet_wrap(~FishingYear)+
# geom_sf(data=g27n,fill='white')+
geom_sf(data=coa,fill='grey')+
geom_sf(data=GrMap,fill=NA)+
coord_sf(xlim = c(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax),
ylim = c(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax),
expand = FALSE)+
scale_x_continuous(breaks = c(round(seq(st_bbox(g27p)$xmin,st_bbox(g27p)$xmax,length.out=2),2)))+
scale_y_continuous(breaks = c(round(seq(st_bbox(g27p)$ymin,st_bbox(g27p)$ymax,length.out=2),2)))
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