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report2_Catches.R
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library(icesTAF)
taf.library(icesFO)
library(sf)
library(ggplot2)
library(dplyr)
# set values for automatic naming of files:
year_cap = "2022"
ecoreg = "NwS"
cap_year <- 2022
##########
#Load data
##########
catch_dat <- read.taf("data/catch_dat.csv")
#################################################
##1: ICES nominal catches and historical catches#
#################################################
#~~~~~~~~~~~~~~~#
# By common name
#~~~~~~~~~~~~~~~#
#Plot
plot_catch_trends(catch_dat, type = "COMMON_NAME", line_count = 7, plot_type = "line")
ggplot2::ggsave(paste0(year_cap, "_", ecoreg,"_FO_Catches_species.png"), path = "report/", width = 170, height = 100.5, units = "mm", dpi = 300)
#data
dat <- plot_catch_trends(catch_dat, type = "COMMON_NAME", line_count = 7, plot_type = "line", return_data = TRUE)
write.taf(dat, paste0(year_cap, "_", ecoreg,"_FO_Catches_species.csv"), dir = "report")
#~~~~~~~~~~~~~~~#
# By country
#~~~~~~~~~~~~~~~#
#Plot
catch_dat$COUNTRY[which(catch_dat$COUNTRY == "Russian Federation")] <- "Russia"
plot_catch_trends(catch_dat, type = "COUNTRY", line_count = 5, plot_type = "area")
ggplot2::ggsave(paste0(year_cap, "_", ecoreg,"_FO_Catches_country.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
#data
dat <- plot_catch_trends(catch_dat, type = "COUNTRY", line_count = 9, plot_type = "area", return_data = TRUE)
write.taf(dat, file= paste0(year_cap, "_", ecoreg,"_FO_Catches_country.csv"), dir = "report")
#~~~~~~~~~~~~~~~#
# By guild
#~~~~~~~~~~~~~~~#
#Plot
plot_catch_trends(catch_dat, type = "GUILD", line_count = 6, plot_type = "line")
# Undefined is too big, will try to assign guild to the biggest ones
check <- catch_dat %>% filter (GUILD == "undefined")
unique(check$COMMON_NAME)
catch_dat$GUILD[which(catch_dat$COMMON_NAME == "Polar cod")] <- "Demersal"
# Redfishes of Sebastes spp attributed to pelagic
catch_dat$GUILD[which(catch_dat$COMMON_NAME == "Atlantic redfishes nei")] <- "Pelagic"
plot_catch_trends(catch_dat, type = "GUILD", line_count = 6, plot_type = "line")
ggplot2::ggsave(paste0(year_cap, "_", ecoreg,"_FO_Catches_guild.png"), path = "report/", width = 178, height = 130, units = "mm", dpi = 300)
#data
dat <- plot_catch_trends(catch_dat, type = "GUILD", line_count = 6, plot_type = "line", return_data = TRUE)
write.taf(dat, file= paste0(year_cap, "_", ecoreg,"_FO_Catches_guild.csv"), dir = "report")