inst/Projects/Vic Map and Figs/LFA33-38FootPrints_VH.r

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

#combined footprints 33-38 & 41
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)


r<-readRDS(file.path( layerDir,"GridPolysSF.rds"))
b=subset(r,LFA %in% c(33:38))

o=subset(GrMap,LFA %in% c(33:38))

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, LFA%in% 33:38 & 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)))