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data.R
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# Initial formatting of the data
library(icesTAF)
library(icesFO)
library(icesFO)
library(dplyr)
mkdir("data")
# load species list
species_list <- read.taf("bootstrap/initial/data/FAO_ASFIS_species/species_list.csv")
sid <- read.taf("bootstrap/initial/data/ICES_StockInformation/sid.csv")
# 1: ICES official cath statistics
hist <- read.taf("bootstrap/initial/data/ICES_nominal_catches/ICES_historical_catches.csv")
official <- read.taf("bootstrap/initial/data/ICES_nominal_catches/ICES_2006_2019_catches.csv")
prelim <- read.taf("bootstrap/initial/data/ICES_nominal_catches/ICES_preliminary_catches.csv")
catch_dat <-
format_catches(2022, "Greenland Sea",
hist, official, NULL, species_list, sid)
write.taf(catch_dat, dir = "data", quote = TRUE)
# 2: STECF effort and landings
effort <- read.taf("bootstrap/data/STECF_effort_data.csv", check.names = TRUE)
landings <- read.taf("bootstrap/initial/data/STECF_landings_data.csv", check.names = TRUE)
frmt_effort <- format_stecf_effort(effort)
effort <- effort %>% rename('regulated.area' = 'regulated area')
effort <- effort %>% rename('regulated.gear' = 'regulated gear')
frmt_effort <- format_stecf_effort(effort)
frmt_landings <- format_stecf_landings(landings)
landings <- landings %>% rename('regulated.area' = 'regulated area')
landings <- landings %>% rename('regulated.gear' = 'regulated gear')
frmt_landings <- format_stecf_landings(landings)
write.taf(frmt_effort, dir = "data", quote = TRUE)
write.taf(frmt_landings, dir = "data", quote = TRUE)
# 3: SAG
sag_sum <- read.taf("bootstrap/initial/data/SAG_data/SAG_summary.csv")
sag_refpts <- read.taf("bootstrap/initial/data/SAG_data/SAG_refpts.csv")
sag_status <- read.taf("bootstrap/initial/data/SAG_data/SAG_status.csv")
# clean_sag <- format_sag(summary, refpts, 2021, "Greenland")
clean_sag <- format_sag(sag_complete, sid)
clean_status <- format_sag_status(status, 2022, "Greenland Sea")
# list of stocks
GS_stocks <- c("aru.27.5a14",
"usk.27.5a14",
"her.27.1-24a514a",
"rng.27.1245a8914ab",
"cod.2127.1f14",
"rhg.27.nea",
# "cap.27.2a514",
# "whb.27.1-91214",
"bli.27.5a14",
# "pra.27.1-2",
"ghl.27.561214",
"mac.27.nea",
"reb.2127.dp",
"reb.2127.sp",
"reb.27.14b",
"reg.27.561214"
)
clean_sag <- dplyr::filter(clean_sag, StockKeyLabel %in% GS_stocks)
clean_status <- dplyr::filter(clean_status, StockKeyLabel %in% GS_stocks)
write.taf(clean_sag, dir = "data", quote = TRUE)
write.taf(clean_status, dir = "data", quote = TRUE)