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report4_SAG.r
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library(icesTAF)
library(icesFO)
library(sf)
library(ggplot2)
library(dplyr)
## Run utilies
source("boot/utilities.r")
# set values for automatic naming of files:
cap_year <- 2024
cap_month <- "November"
ecoreg_code <- "BtS"
##########
#Load data
##########
trends <- read.taf("model/sag_trends.csv")
catch_current <- read.taf("model/sag_catch_current.csv")
catch_trends <- read.taf("model/sag_catch_trends.csv")
#error with number of columns, to check
clean_status <- read.taf("data/clean_status.csv")
###########
## 3: SAG #
###########
#~~~~~~~~~~~~~~~#
# A. Trends by guild
#~~~~~~~~~~~~~~~#
unique(sag_trends$FisheriesGuild)
# 1. Demersal
#~~~~~~~~~~~
plot_stock_trends(sag_trends, guild="demersal", cap_year , cap_month , return_data = FALSE)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Trends_demersal", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_stock_trends(sag_trends, guild="demersal", cap_year , cap_month , return_data = TRUE)
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Trends_demersal", ext = "csv", dir = "report"))
# 2. Pelagic
#~~~~~~~~~~~
plot_stock_trends(sag_trends, guild="pelagic", cap_year, cap_month , return_data = FALSE)
#remove her.27.1-24a514a in NrS
sag_trends_bis <- sag_trends %>% filter(StockKeyLabel != "her.27.1-24a514a")
plot_stock_trends(sag_trends_bis, guild="pelagic", cap_year, cap_month , return_data = FALSE)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Trends_pelagic", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_stock_trends(sag_trends_bis, guild="pelagic", cap_year, cap_month , return_data = TRUE)
write.taf(dat,file =file_name(cap_year,ecoreg_code,"SAG_Trends_pelagic", ext = "csv", dir = "report"))
unique(sag_trends$FisheriesGuild)
# 3. Crustacean
#~~~~~~~~~~~
plot_stock_trends(sag_trends, guild="crustacean", cap_year , cap_month ,return_data = FALSE )
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Trends_crustacean", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_stock_trends(sag_trends, guild="crustacean", cap_year , cap_month , return_data = TRUE)
write.taf(dat,file =file_name(cap_year,ecoreg_code,"SAG_Trends_crustacean", ext = "csv", dir = "report"))
# 4. Benthic
#~~~~~~~~~~~
plot_stock_trends(sag_trends, guild="benthic", cap_year, cap_month , return_data = FALSE)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Trends_benthic", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_stock_trends(sag_trends, guild="benthic", cap_year, cap_month , return_data = TRUE)
write.taf(dat,file =file_name(cap_year,ecoreg_code,"SAG_Trends_benthic", ext = "csv", dir = "report"))
# 5. Elasmobranch
#~~~~~~~~~~~
plot_stock_trends(sag_trends, guild="elasmobranch", cap_year, cap_month , return_data = FALSE)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Trends_elasmobranch", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_stock_trends(sag_trends, guild="elasmobranch", cap_year, cap_month , return_data = TRUE)
write.taf(dat,file =file_name(cap_year,ecoreg_code,"SAG_Trends_elasmobranch", ext = "csv", dir = "report"))
unique(sag_trends$FisheriesGuild)
#~~~~~~~~~~~~~~~~~~~~~~~~~#
# Ecosystem Overviews plot
#~~~~~~~~~~~~~~~~~~~~~~~~~#
guild <- read.taf("model/guild.csv")
# trends2 <- trends%>% filter (StockKeyLabel %in% c("cod.2127.1f14",
# "ghl.27.561214",
# "mac.27.nea",
# "her.27.1-24a514a",
# "reg.27.561214"))
# trends2 <- trends2 [,-1]
# colnames(trends2) <- c("FisheriesGuild", "Year", "Metric", "Value")
# trends3 <- trends2%>% filter(Metric == "F_FMSY")
# # guild2 <- guild %>% filter(Metric == "F_FMSY")
# plot_guild_trends(trends3, cap_year, cap_month,return_data = FALSE )
# # guild2 <- guild2 %>% filter(FisheriesGuild != "MEAN")
# # plot_guild_trends(guild2, cap_year , cap_month,return_data = FALSE )
# ggplot2::ggsave(paste0(cap_year, "_", ecoreg_code, "_EO_SAG_GuildTrends_F.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
# # ggplot2::ggsave("2019_BtS_EO_GuildTrends_noMEAN_F.png", path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
trends2 <- sag_trends%>% filter(Metric == "F_FMSY")
plot_guild_trends(trends2, cap_year, cap_month,return_data = FALSE )
trends2 <- trends2 %>% filter(StockKeyLabel == "MEAN")
# trends2 <- trends2 %>% filter(Year > 1960)
plot_guild_trends(trends2, cap_year, cap_month,return_data = FALSE )
# guild2 <- guild2 %>% filter(FisheriesGuild != "MEAN")
# plot_guild_trends(guild2, cap_year , cap_month,return_data = FALSE )
ggplot2::ggsave(paste0(cap_year, "_", ecoreg_code, "_EO_SAG_GuildTrends_F.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
trends2 <- sag_trends%>% filter(Metric == "SSB_MSYBtrigger")
trends2 <- trends2 %>% filter(StockKeyLabel == "MEAN")
trends2 <- trends2 %>% filter(Year > 1960)
plot_guild_trends(trends2, cap_year, cap_month,return_data = FALSE )
# guild2 <- guild2 %>% filter(FisheriesGuild != "MEAN")
# plot_guild_trends(guild2, cap_year , cap_month,return_data = FALSE )
ggplot2::ggsave(paste0(cap_year, "_", ecoreg_code, "_EO_SAG_GuildTrends_SSB.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
# trends3 <- trends2%>% filter(Metric == "SSB_MSYBtrigger")
# guild2 <- guild %>% filter(Metric == "SSB_MSYBtrigger")
# guild3 <- guild2 %>% dplyr::filter(FisheriesGuild != "MEAN")
trends3 <- trends3 %>% filter(Year > 1960)
plot_guild_trends(trends3, cap_year, cap_month,return_data = FALSE )
ggplot2::ggsave(paste0(cap_year, "_", ecoreg_code, "_EO_SAG_GuildTrends_SSB_1960.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
# ggplot2::ggsave(paste0(year_cap, "_", ecoreg, "_EO_SAG_GuildTrends_SSB_1900.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_guild_trends(sag_trends, cap_year, cap_month ,return_data = TRUE)
write.taf(dat, file =paste0(cap_year, "_", ecoreg_code, "_EO_SAG_GuildTrends.csv"), dir = "report" )
dat <- sag_trends[,1:2]
dat <- unique(dat)
dat <- dat %>% filter(StockKeyLabel != "MEAN")
colnames(dat) <- c("StockKeyLabel", "Year")
dat2 <- sid %>% select(c(StockKeyLabel, StockKeyDescription))
dat <- left_join(dat,dat2)
write.taf(dat, file =paste0(year_cap, "_", ecoreg_code, "_EO_SAG_SpeciesGuildList.csv"), dir = "report", quote = TRUE )
#~~~~~~~~~~~~~~~#
# B.Current catches
#~~~~~~~~~~~~~~~#
## Bar plots are not in order, check!!
# 1. Demersal
#~~~~~~~~~~~
bar <- plot_CLD_bar(sag_catch_current, guild = "demersal", caption = T, cap_year , cap_month , return_data = FALSE)
# bar <- plot_CLD_bar(catch_current, guild = "demersal", caption = T, cap_year = 2019, cap_month = "September", return_data = FALSE)
bar_dat <- plot_CLD_bar(sag_catch_current, guild = "demersal", caption = T, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_demersal", ext = "csv", dir = "report"))
sag_catch_current <- unique(sag_catch_current)
kobe <- plot_kobe(sag_catch_current, guild = "demersal", caption = T, cap_year , cap_month , return_data = FALSE)
#kobe_dat is just like bar_dat with one less variable
#kobe_dat <- plot_kobe(catch_current, guild = "Demersal", caption = T, cap_year = 2019, cap_month = "September", return_data = TRUE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_demersal", ext = "png", dir = "report"),
width = 131.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "demersal")
dev.off()
#for top 20 demersal (NrS and CS)
top_20 <- bar_dat %>% top_n(20, total)
bar <- plot_CLD_bar(top_20, guild = "demersal", caption = TRUE, cap_year = 2024, cap_month = "October", return_data = FALSE)
bar_dat <- plot_CLD_bar(top_20, guild = "demersal", caption = T, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_demersal_top20", ext = "csv", dir = "report"))
kobe <- plot_kobe(top_20, guild = "demersal", caption = T, cap_year, cap_month , return_data = FALSE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_demersal_top20", ext = "png", dir = "report"),
width = 131.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "Top 20 demersal")
dev.off()
# 2. Pelagic
#~~~~~~~~~~~
#Only for Baltic
sag_catch_current <- sag_catch_current %>% filter(StockKeyLabel != "sal.27.32")
sag_catch_current$Status[which(sag_catch_current$StockKeyLabel == "her.27.28")] <- "GREEN"
#only for North Sea
sag_catch_current <- sag_catch_current %>% filter(StockKeyLabel != "her.27.1-24a514a")
bar <- plot_CLD_bar(sag_catch_current, guild = "pelagic", caption = T, cap_year, cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(sag_catch_current, guild = "pelagic", caption = T, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_pelagic", ext = "csv", dir = "report"))
kobe <- plot_kobe(sag_catch_current, guild = "pelagic", caption = T, cap_year , cap_month, return_data = FALSE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_pelagic", ext = "png", dir = "report"),
width = 131.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "pelagic")
dev.off()
# 3. Crustacean
#~~~~~~~~~~~
bar <- plot_CLD_bar(sag_catch_current, guild = "crustacean", caption = T, cap_year, cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(sag_catch_current, guild = "crustacean", caption = T, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_crustacean", ext = "csv", dir = "report"))
#not work
#write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_crustacean", ext = "csv"), dir = "report")
kobe <- plot_kobe(sag_catch_current, guild = "crustacean", caption = T, cap_year , cap_month , return_data = FALSE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_crustacean", ext = "png", dir = "report"),
width = 131.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "crustacean")
dev.off()
# 2. Benthic
#~~~~~~~~~~~
bar <- plot_CLD_bar(sag_catch_current, guild = "benthic", caption = T, cap_year, cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(sag_catch_current, guild = "benthic", caption = T, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_benthic", ext = "csv", dir = "report"))
kobe <- plot_kobe(sag_catch_current, guild = "benthic", caption = T, cap_year , cap_month, return_data = FALSE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_benthic", ext = "png", dir = "report"),
width = 300.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "benthic")
dev.off()
# 6. All
#~~~~~~~~~~~
bar <- plot_CLD_bar(sag_catch_current, guild = "All", caption = T, cap_year , cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(sag_catch_current, guild = "All", caption = T, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_all", ext = "csv", dir = "report" ))
kobe <- plot_kobe(sag_catch_current, guild = "All", caption = T, cap_year, cap_month , return_data = FALSE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_All", ext = "png", dir = "report"),
width = 131.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "All")
dev.off()
#Only top 10
top_10 <- bar_dat %>% top_n(10, total)
bar <- plot_CLD_bar_top(top_10, guild = "All", caption = TRUE, cap_year = 2024, cap_month = "October", return_data = FALSE)
# top_10 <- unique(top_10)
kobe <- plot_kobe(top_10, guild = "All", caption = T, cap_year, cap_month , return_data = FALSE)
png(file_name(cap_year,ecoreg_code,"SAG_Current_top10", ext = "png", dir = "report"),
width = 131.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(kobe,
bar, ncol = 2,
respect = TRUE, top = "All Top 10")
dev.off()
#~~~~~~~~~~~~~~~#
# C. Discards
#~~~~~~~~~~~~~~~#
# No discards at all
discardsA <- plot_discard_trends(sag_catch_trends, 2024, cap_year , cap_month )
#for North sea and CS
sag_catch_trends <- sag_catch_trends %>% filter(FisheriesGuild != "elasmobranch")
discardsA <- plot_discard_trends(sag_catch_trends, 2024, cap_year , cap_month )
dat <- plot_discard_trends(sag_catch_trends, 2024, cap_year , cap_month , return_data = TRUE)
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_trends_noelasmo", ext = "csv", dir = "report" ))
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_trends", ext = "csv", dir = "report" ))
discardsC <- plot_discard_current(sag_catch_trends, 2024,position_letter = "b)", cap_year, cap_month )
dat <- plot_discard_current(sag_catch_trends, 2024, cap_year, cap_month , return_data = TRUE)
#this does not work
#write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_current_all", ext = "csv"), dir = "report" )
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_current_all_noelasmo", ext = "csv", dir = "report" ))
catch_trends2 <- sag_catch_trends %>% filter(Discards > 0)
discardsB <- plot_discard_current_order(catch_trends2, 2024,dat,position_letter = "c)", cap_year , cap_month , caption = TRUE)
dat <- plot_discard_current(catch_trends2, 2024, cap_year, cap_month , return_data = TRUE)
#this does not work
# write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_", ext = "csv"), dir = "report" )
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_current_onlydiscardsexist", ext = "csv", dir = "report" ))
#this does not work
# cowplot::plot_grid(discardsA, discardsB,discardsC, align = "h", nrow = 1, rel_widths = 1, rel_heights = 1)
# ggplot2::ggsave(file_name(cap_year,ecoreg_code,"_FO_SAG_Discards", ext = "png"), path = "report/", width = 220.32, height = 88.9, units = "mm", dpi = 300)
png(file_name(cap_year,ecoreg_code,"SAG_Discards_noelasmo", ext = "png", dir = "report"),
width = 220.32,
height = 88.9,
units = "mm",
res = 300)
p1_plot<-gridExtra::grid.arrange(discardsA,
discardsC,
discardsB, ncol = 3,
respect = TRUE)
dev.off()
# png("report/2019_BI_FO_Figure7.png",
# width = 137.32,
# height = 88.9,
# units = "mm",
# res = 300)
# p1_plot<-gridExtra::grid.arrange(discardsA,
# discardsB, ncol = 2,
# respect = TRUE)
# dev.off()
#~~~~~~~~~~~~~~~#
#D. ICES pies
#~~~~~~~~~~~~~~~#
plot_status_prop_pies(clean_status, cap_month,cap_year)
# will make qual_green just green
unique(clean_status$StockSize)
clean_status$StockSize <- gsub("qual_GREEN", "GREEN", clean_status$StockSize)
clean_status$StockSize <- gsub("qual_RED", "RED", clean_status$StockSize)
clean_status$StockSize <- gsub("UNDEFINED", "GREY", clean_status$StockSize)
unique(clean_status$FishingPressure)
clean_status$FishingPressure <- gsub("qual_RED", "RED", clean_status$FishingPressure)
clean_status$FishingPressure <- gsub("qual_GREEN", "GREEN", clean_status$FishingPressure)
clean_status$FishingPressure <- gsub("UNDEFINED", "GREY", clean_status$FishingPressure)
plot_status_prop_pies(clean_status, cap_month,cap_year)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_ICESpies", ext = "png", dir = "report"), width = 178, height = 178, units = "mm", dpi = 300)
dat <- plot_status_prop_pies(clean_status, cap_month,cap_year, return_data = TRUE)
write.taf(dat, file= file_name(cap_year,ecoreg_code,"SAG_ICESpies", ext = "csv", dir = "report"))
#~~~~~~~~~~~~~~~#
#E. GES pies
#~~~~~~~~~~~~~~~#
#Need to change order and fix numbers
plot_GES_pies(clean_status, sag_catch_current, cap_month,cap_year)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_GESpies", ext = "png", dir = "report"), width = 178, height = 178, units = "mm", dpi = 300)
dat <- plot_GES_pies(clean_status, sag_catch_current, cap_month,cap_year, return_data = TRUE)
write.taf(dat, file= file_name(cap_year,ecoreg_code,"SAG_GESpies", ext = "csv", dir = "report"))
#~~~~~~~~~~~~~~~#
#F. ANNEX TABLE
#~~~~~~~~~~~~~~~#
# write.csv(clean_status, file= file_name(cap_year,ecoreg_code,"SAG_StockStatus", ext = "csv", dir = "report"))
dat <- format_annex_table(clean_status, 2024)
# format_annex_table_html(dat,ecoreg_code,cap_year)
write.taf(dat, file = file_name(cap_year,ecoreg_code,"annex_table", ext = "csv", dir = "report"), quote=TRUE)
# This annex table has to be edited by hand,
# For SBL and GES only one values is reported,
# the one in PA for SBL and the one in MSY for GES