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report4_SAG.R
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library(icesTAF)
library(icesFO)
library(sf)
library(ggplot2)
library(dplyr)
## Run utilies
source("bootstrap/utilities.r")
# set values for automatic naming of files:
cap_year <- 2022
cap_month <- "October"
ecoreg_code <- "ONA"
ecoreg <- "ONA"
##########
#Load data
##########
trends <- read.taf("model/trends.csv")
catch_current <- read.taf("model/catch_current.csv")
catch_trends <- read.taf("model/catch_trends.csv")
clean_status <- read.taf("data/clean_status.csv")
# set year for plot calculations
year = 2022
###########
## 3: SAG #
###########
#~~~~~~~~~~~~~~~#
# A. Trends by guild
#~~~~~~~~~~~~~~~#
unique(trends$FisheriesGuild)
# 1. Demersal
#~~~~~~~~~~~
plot_stock_trends(trends, guild="demersal", cap_year, cap_month , return_data = FALSE)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Trends_demersal", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_stock_trends(trends, guild="demersal", cap_year , cap_month, return_data = TRUE)
write.taf(dat, file = file_name(cap_year,ecoreg_code,"SAG_Trends_demersal", ext = "csv", dir = "report"))
# 2. Pelagic
#~~~~~~~~~~~
trends2 <- trends %>% filter(StockKeyLabel != "bsf.27.nea")
trends2 <- trends2 %>% filter(StockKeyLabel != "her.27.6aS7bc")
##### eliminate year 2022 for F and 2023 for SSB for whb.27.1-91214
trends2 <- trends2[!(trends2$StockKeyLabel == "whb.27.1-91214" & trends2$Metric == "F_FMEAN" & trends2$Year == 2022) &
!(trends2$StockKeyLabel == "whb.27.1-91214" & trends2$Metric == "F_FMSY" & trends2$Year == 2022) &
!(trends2$StockKeyLabel == "MEAN" & trends2$Metric == "F_FMSY" & trends2$Year == 2022) &
!(trends2$StockKeyLabel == "whb.27.1-91214" & trends2$Metric == "SSB_MSYBtrigger" & trends2$Year == 2023) &
!(trends2$StockKeyLabel == "MEAN" & trends2$Metric == "SSB_MSYBtrigger" & trends2$Year == 2023),]
plot_stock_trends(trends2, 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(trends, 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"))
# 3. Benthic
#~~~~~~~~~~~
trends2 <- trends %>% filter(StockKeyLabel != "anf.27.3a46")
plot_stock_trends(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(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"))
# 4. Elasmobranch
#~~~~~~~~~~~
plot_stock_trends(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(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"))
# 5. Crustacean
#~~~~~~~~~~~
# plot_stock_trends(trends, guild="crustacean", cap_year, cap_month ,return_data = FALSE )
# ggplot2::ggsave(paste0(year_cap, "_", ecoreg, "_FO_SAG_Trends_crustacean.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
#
# dat <- plot_stock_trends(trends, guild="crustacean", cap_year , cap_month , return_data = TRUE)
# write.taf(dat, file =paste0(year_cap, "_", ecoreg, "_FO_SAG_Trends_crustacean.csv"), dir = "report" )
#
#~~~~~~~~~~~~~~~~~~~~~~~~~#
# Ecosystem Overviews plot
#~~~~~~~~~~~~~~~~~~~~~~~~~#
guild <- read.taf("model/guild.csv")
trends <- read.taf("model/trends.csv")
# For this EO, they need separate plots with all info
guild2 <- guild %>% filter(Metric == "F_FMSY")
plot_guild_trends(guild, 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(file_name(cap_year,ecoreg_code,"EO_SAG_GuildTrends_F", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
# ggplot2::ggsave(paste0(year_cap, "_", ecoreg, "_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)
guild2 <- guild %>% filter(Metric == "SSB_MSYBtrigger")
guild3 <- guild2 %>% dplyr::filter(FisheriesGuild != "MEAN")
guild3 <- guild3 %>% filter(Year > 1980)
plot_guild_trends(guild3, cap_year, cap_month,return_data = FALSE )
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"EO_SAG_GuildTrends_SSB", ext = "png", dir = "report"), width = 178, height = 130, units = "mm", dpi = 300)
# ggplot2::ggsave(paste0(year_cap, "_", ecoreg, "_EO_SAG_GuildTrends_SSB.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
dat <- plot_guild_trends(guild, cap_year, cap_month ,return_data = TRUE)
write.taf(dat, file = file_name(cap_year,ecoreg_code,"EO_SAG_GuildTrends", ext = "csv", dir = "report"))
# write.taf(dat, file =paste0(year_cap, "_", ecoreg, "_EO_SAG_GuildTrends.csv"), dir = "report" )
dat <- trends[,1:2]
dat <- unique(dat)
dat <- dat %>% filter(StockKeyLabel != "MEAN")
dat2 <- sid %>% select(c(StockKeyLabel, StockKeyDescription))
dat <- left_join(dat,dat2)
write.taf(dat, file = file_name(cap_year,ecoreg_code,"EO_SAG_SpeciesGuildList", ext = "csv", dir = "report"), quote = TRUE)
# write.taf(dat, file =paste0(year_cap, "_", ecoreg, "_EO_SAG_SpeciesGuildList.csv"), dir = "report", quote = TRUE )
#~~~~~~~~~~~~~~~#
# B.Current catches
#~~~~~~~~~~~~~~~#
# 1. Demersal
#~~~~~~~~~~~
bar <- plot_CLD_bar(catch_current, guild = "demersal", caption = TRUE, cap_year, cap_month, return_data = FALSE)
catch_current <- catch_current %>% filter(StockKeyLabel != "ele.2737.nea")
bar <- plot_CLD_bar(catch_current, guild = "demersal", caption = TRUE, cap_year, cap_month, return_data = FALSE)
bar_dat <- plot_CLD_bar(catch_current, guild = "demersal", caption = TRUE, 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"))
# write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_demersal", ext = "csv"), dir = "report" )
kobe <- plot_kobe(catch_current, guild = "demersal", caption = TRUE, 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 , cap_month , return_data = TRUE)
#Check this file name
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()
# 2. Pelagic
#~~~~~~~~~~~
bar <- plot_CLD_bar(catch_current, guild = "pelagic", caption = TRUE, cap_year, cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(catch_current, guild = "pelagic", caption = TRUE, 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"))
# write.taf(bar_dat, file = file_name(cap_year,ecoreg_code,"SAG_Current_pelagic", ext = "csv"), dir = "report")
catch_current <- unique(catch_current)
kobe <- plot_kobe(catch_current, guild = "pelagic", caption = TRUE, cap_year , cap_month , return_data = FALSE)
#check this file name
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. Benthic
#~~~~~~~~~~~
# catch_current$Status[which(catch_current$StockKeyLabel == "sol.27.20-24")] <- "GREEN"
bar <- plot_CLD_bar(catch_current, guild = "benthic", caption = TRUE, cap_year , cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(catch_current, guild = "benthic", caption = TRUE, 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"))
# write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_benthic", ext = "csv"), dir = "report" )
kobe <- plot_kobe(catch_current, guild = "benthic", caption = TRUE, cap_year , cap_month , return_data = FALSE)
#check this file name
png(file_name(cap_year,ecoreg_code,"SAG_Current_benthic", 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 = "benthic")
dev.off()
# 4. Elasmobranch
#~~~~~~~~~~~
# catch_current$Status[which(catch_current$StockKeyLabel == "sol.27.20-24")] <- "GREEN"
bar <- plot_CLD_bar(catch_current, guild = "elasmobranch", caption = TRUE, cap_year , cap_month , return_data = FALSE)
catch_current <- catch_current %>% filter(StockKeyLabel != "syt.27.67")
bar <- plot_CLD_bar(catch_current, guild = "elasmobranch", caption = TRUE, cap_year , cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(catch_current, guild = "elasmobranch", caption = TRUE, cap_year , cap_month , return_data = TRUE)
write.taf(bar_dat, file = file_name(cap_year,ecoreg_code,"SAG_Current_elasmobranch", ext = "csv", dir = "report"))
# write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_elasmobranch", ext = "csv"), dir = "report" )
kobe <- plot_kobe(catch_current, guild = "elasmobranch", caption = TRUE, cap_year , cap_month , return_data = FALSE)
#check this file name
png(file_name(cap_year,ecoreg_code,"SAG_Current_elasmobranch", 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 = "elasmobranch")
dev.off()
# 5. Crustacean
#~~~~~~~~~~~
# catch_current$Status[which(catch_current$StockKeyLabel == "sol.27.20-24")] <- "GREEN"
#
# bar <- plot_CLD_bar(catch_current, guild = "crustacean", caption = TRUE, cap_year , cap_month , return_data = FALSE)
#
# bar_dat <- plot_CLD_bar(catch_current, guild = "crustacean", caption = TRUE, cap_year , cap_month , return_data = TRUE)
# write.taf(bar_dat, file =paste0(year_cap, "_", ecoreg, "_FO_SAG_Current_crustacean.csv"), dir = "report" )
#
# kobe <- plot_kobe(catch_current, guild = "crustacean", caption = TRUE, cap_year , cap_month , return_data = FALSE)
# #check this file name
# png("report/2020_ONA_FO_SAG_Current_crustacean.png",
# width = 131.32,
# 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(catch_current, guild = "All", caption = TRUE, cap_year , cap_month , return_data = FALSE)
bar_dat <- plot_CLD_bar(catch_current, guild = "All", caption = TRUE, 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"))
# write.taf(bar_dat, file =file_name(cap_year,ecoreg_code,"SAG_Current_All", ext = "csv"), dir = "report" )
top_10 <- bar_dat %>% top_n(10, total)
bar <- plot_CLD_bar(top_10, guild = "All", caption = TRUE, cap_year , cap_month , return_data = FALSE)
kobe <- plot_kobe(top_10, guild = "All", caption = TRUE, cap_year, cap_month , return_data = FALSE)
# kobe <- plot_kobe(catch_current, guild = "All", caption = TRUE, cap_year, cap_month , return_data = FALSE)
#check this file name
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 stocks top 10")
dev.off()
#~~~~~~~~~~~~~~~#
# C. Discards
#~~~~~~~~~~~~~~~#
discardsA <- plot_discard_trends(catch_trends, year, cap_year, cap_month )
catch_trends <- unique(catch_trends)
catch_trends$ID <- paste0(catch_trends$Year,catch_trends$StockKeyLabel,catch_trends$FisheriesGuild)
catch_trends <- catch_trends %>% arrange(rowSums(is.na(.))) %>% distinct(ID, .keep_all = TRUE)
catch_trends2 <- catch_trends %>% filter(FisheriesGuild != "elasmobranch")
discardsA <- plot_discard_trends(catch_trends2, year, cap_year, cap_month )
dat <- plot_discard_trends(catch_trends2, year, cap_year , cap_month , return_data = TRUE)
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_trends", ext = "csv", dir = "report" ))
catch_trends3 <- catch_trends2 %>% filter(Discards > 0)
df5 <- catch_trends3
discardsB <- plot
# discardsB <- plot_discard_current(catch_trends3, year,position_letter = "b)", cap_year , cap_month , caption = FALSE)
df5 <- catch_trends2
discardsC <- plot
# discardsC <- plot_discard_current(catch_trends2, year,position_letter = "c)", cap_year , cap_month , caption = TRUE)
#Need to change order?
dat <- plot_discard_current(catch_trends, year, cap_year, cap_month , return_data = TRUE)
write.taf(dat, file =file_name(cap_year,ecoreg_code,"SAG_Discards_current", ext = "csv", dir = "report" ))
cowplot::plot_grid(discardsA, discardsB, discardsC, align = "h",nrow = 1, rel_widths = 1, rel_heights = 1)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Discards", ext = "png", dir = "report"), width = 220.32, height = 88.9, units = "mm", dpi = 300)
# ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_Discards", ext = "png"),path = "report/", width = 220.32, height = 88.9, units = "mm", dpi = 300)
#~~~~~~~~~~~~~~~#
#D. ICES pies
#~~~~~~~~~~~~~~~#
plot_status_prop_pies(clean_status, cap_month, cap_year)
unique(clean_status$StockSize)
clean_status$StockSize <- gsub("qual_RED", "RED", clean_status$StockSize)
clean_status_updated$StockSize <- gsub("qual_RED", "RED", clean_status_updated$StockSize)
plot_status_prop_pies(clean_status, cap_month, cap_year)
plot_status_prop_pies(clean_status_updated, cap_month, cap_year)
ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_ICESpies", ext = "png", dir = "report"), width = 178, height = 178, units = "mm", dpi = 300)
# ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_ICESpies", ext = "png"), path= "report/", width = 178, height = 178, units = "mm", dpi = 300)
dat <- plot_status_prop_pies(clean_status, cap_month, cap_year, return_data = TRUE)
write.taf(dat, file= file_name(cap_year,ecoreg_code,"SAG_ICESpies", ext = "csv",dir ="report"))
#~~~~~~~~~~~~~~~#
#E. GES pies
#~~~~~~~~~~~~~~~#
# need to check what is that weird zero!!
#Need to change order and fix numbers
plot_GES_pies(clean_status, catch_current, cap_month, cap_year)
plot_GES_pies(clean_status_updated, catch_current, cap_month, cap_year)
unique(clean_status$FishingPressure)
unique(clean_status$StockSize)
# clean_status2 <- clean_status
# clean_status2$StockSize <- gsub("qual_RED", "RED", clean_status2$StockSize)
# plot_GES_pies(clean_status2, 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)
# ggplot2::ggsave(file_name(cap_year,ecoreg_code,"SAG_GESpies", ext = "png"),path = "report", width = 178, height = 178, units = "mm",dpi = 300)
dat <- plot_GES_pies(clean_status, 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
#~~~~~~~~~~~~~~~#
################################################# NOT WORKING unless I copy and run the devel
#### version of format_annex_table
dat <- format_annex_table(clean_status_updated, year)
write.taf(dat, file = file_name(cap_year,ecoreg_code,"SAG_annex_table", ext = "csv", dir = "report"), quote = TRUE)
format_annex_table_html(dat, cap_year, ecoreg_code)
# 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