load_raw_data <- function(raw_data = c("all",
"stock_list_raw",
"sag_summary_raw", "sag_refpts_raw", "sag_keys_raw", "sag_stock_status_raw",
"ices_catch_official_raw", "ices_catch_historical_raw",
"species_list_raw",
"stecf_effort_raw", "stecf_landings_raw",
"europe_shape", "ices_shape", "eco_shape")) {
raw_names <- c("stock_list_raw",
"sag_summary_raw", "sag_refpts_raw", "sag_keys_raw", "sag_stock_status_raw",
"ices_catch_official_raw", "ices_catch_historical_raw",
"species_list_raw",
"stecf_effort_raw", "stecf_landings_raw",
"europe_shape", "ices_shape", "eco_shape")
raw_data <- match.arg(tolower(raw_data), c("all", raw_names),
several.ok = TRUE)
if(any(raw_data %in% "all")) {
raw_data <- raw_names
}
data("date_data", package = "fisheryO")
# date_data$data_file <- as.character(date_data$data_file)
# date_data$date <- as.Date(as.character(date_data$date))
date_data_names <- raw_data[!raw_data %in% grep("stecf", raw_data, value = TRUE)]
date_data$date[date_data$data_file %in% date_data_names] <- as.Date(as.character(Sys.Date()))
devtools::use_data(date_data, overwrite = TRUE)
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: ICES Stock Database ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("stock_list_raw" %in% raw_data) {
stock_list_raw <- jsonlite::fromJSON("http://sd.ices.dk/services/odata3/StockListDWs3",
simplifyDataFrame = TRUE)$value
devtools::use_data(stock_list_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: ICES Stock Assessment Graphs Database ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("sag_summary_raw" %in% raw_data){
sag_summary_raw <- icesSAG::getSAG(stock = NULL,
year = 2014:2017,
data = "summary",
combine = TRUE)
devtools::use_data(sag_summary_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: ICES Stock Assessment Graphs Database ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("sag_refpts_raw" %in% raw_data) {
sag_refpts_raw <- icesSAG::getSAG(stock = NULL,
year = 2014:2017,
data = "refpts",
combine = TRUE)
devtools::use_data(sag_refpts_raw, overwrite = TRUE)
}
if("sag_keys_raw" %in% raw_data) {
sag_keys_raw <- do.call("rbind", lapply(2014:2017,
function(x) icesSAG::findAssessmentKey(stock = NULL,
year = x,
full = TRUE)[, c("AssessmentYear",
"AssessmentKey",
"StockKeyLabel")]))
devtools::use_data(sag_keys_raw, overwrite = TRUE)
}
if("sag_stock_status_raw" %in% raw_data){
get_stock_status <- function(assessmentKey) {
dat <- icesSAG::getStockStatusValues(assessmentKey)[[1]]
if(is.null(dat)) stop(paste0("NULL value returned for assessmentKey = ", assessmentKey))
dat
}
sag_stock_status_raw <- sag_keys_raw %>%
mutate(stock_status = purrr::map(.x = AssessmentKey, purrr::possibly(get_stock_status, otherwise = NA_real_))) %>%
filter(!is.na(stock_status)) %>%
tidyr::unnest(stock_status)
devtools::use_data(sag_stock_status_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: ICES official catch statistics (1950-2010) ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("ices_catch_historical_raw" %in% raw_data){
historicURL <- "http://ices.dk/marine-data/Documents/CatchStats/HistoricalLandings1950-2010.zip"
tmpFileHistoric <- tempfile(fileext = ".zip")
download.file(historicURL, destfile = tmpFileHistoric, mode = "wb", quiet = TRUE)
ices_catch_historical_raw <- read.csv(unz(tmpFileHistoric, "ICES_1950-2010.csv"),
stringsAsFactors = FALSE,
header = TRUE,
fill = TRUE,
na.strings = c("...", "-", "ns", "."))
devtools::use_data(ices_catch_historical_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: ICES official catch statistics (2006-2015) ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("ices_catch_official_raw" %in% raw_data) {
catchURL <- "http://ices.dk/marine-data/Documents/CatchStats/OfficialNominalCatches.zip"
tmpFileCatch <- tempfile(fileext = ".zip")
download.file(catchURL, destfile = tmpFileCatch, mode = "wb", quiet = TRUE)
ices_catch_official_raw <- read.csv(unz(tmpFileCatch,
grep("ICESCatchDataset.*.csv", unzip(tmpFileCatch,
list = TRUE)$Name,
value = TRUE)),
stringsAsFactors = FALSE,
header = TRUE,
fill = TRUE)
# remove columns with all NA
ices_catch_official_raw <- Filter(function(x)!all(is.na(x)), ices_catch_official_raw)
devtools::use_data(ices_catch_official_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: FAO species names and labels ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("species_list_raw" %in% raw_data){
spURL <- "http://www.fao.org/fishery/static/ASFIS/ASFIS_sp.zip"
tmpFileSp <- tempfile(fileext = ".zip")
download.file(spURL, destfile = tmpFileSp, mode = "wb", quiet = TRUE)
FAO_file <- grep(".*txt", unzip(tmpFileSp,list = TRUE)$Name, value = TRUE)
species_list_raw <- read.delim(unz(tmpFileSp, FAO_file),
fill = TRUE,
stringsAsFactors = FALSE,
header = TRUE,
na.strings = "")
devtools::use_data(species_list_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: STECF Effort and Catch tables ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("stecf_effort_raw" %in% raw_data) {
stecf_effort_raw <- readRDS("data-raw/STECF_effort_data.rds")
devtools::use_data(stecf_effort_raw, overwrite = TRUE)
}
if("stecf_landings_raw" %in% raw_data) {
stecf_landings_raw <- readRDS("data-raw/STECF_landings_data.rds")
devtools::use_data(stecf_landings_raw, overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: ICES Area and ecoregion shapefiles ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
get_map <- function(URL) {
tmp_file <- tempfile(fileext = ".zip")
download.file(url = URL,
destfile = tmp_file,
mode = "wb", quiet = TRUE)
unzip(tmp_file, exdir = tmp_path)
}
if("ices_shape" %in% raw_data) {
tmp_path <- tempdir()
get_map("http://gis.ices.dk/shapefiles/ICES_areas.zip")
layer_name <- grep("ICES_Areas", gsub("\\..*", "", list.files(tmp_path)), value = TRUE)[1]
ices_shape <- sf::st_read(dsn = tmp_path, layer = layer_name, quiet = FALSE)
devtools::use_data(ices_shape, compress='xz', overwrite = TRUE)
}
if("ices_eco" %in% raw_data) {
tmp_path <- tempdir()
get_map("http://gis.ices.dk/shapefiles/ICES_ecoregions.zip")
layer_name <- grep("ICES_ecoregions", gsub("\\..*", "", list.files(tmp_path)), value = TRUE)[1]
eco_shape <- sf::st_read(dsn = tmp_path, layer = layer_name, quiet = FALSE)
devtools::use_data(eco_shape, compress='xz', overwrite = TRUE)
}
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
#### DATA SOURCE: rnaturalearth 10 ####
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if("europe_shape" %in% raw_data) {
europe_shape <- rnaturalearth::ne_countries(scale = 10,
type = "countries",
continent = "europe",
returnclass = "sf")[, c("iso_a3", "iso_n3", "admin", "geometry")]
devtools::use_data(europe_shape, compress='xz', overwrite = TRUE)
}
}
load_raw_data(raw_data = c("stock_list_raw",
"sag_summary_raw", "sag_refpts_raw", "sag_keys_raw", "sag_stock_status_raw",
"ices_catch_official_raw", "ices_catch_historical_raw",
"species_list_raw"))
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