# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# DATA SOURCE: ICES Stock Database #
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
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 #
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
#
# 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 #
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
sag_refpts_raw <- icesSAG::getSAG(stock = NULL,
year = 2014:2017,
data = "refpts",
combine = TRUE)
devtools::use_data(sag_refpts_raw, overwrite = TRUE)
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)
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) %>%
select(-AssessmentKey1)
devtools::use_data(sag_stock_status_raw, overwrite = TRUE)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# DATA SOURCE: FAO species names and labels #
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
spURL <- "http://www.fao.org/fishery/static/ASFIS/ASFIS_sp.zip"
tmpFileSp <- tempfile(fileext = ".zip")
download.file(spURL, destfile = tmpFileSp, mode = "wb", quiet = TRUE)
species_list_raw <- read.delim(unzip(tmpFileSp, "ASFIS_sp_Feb_2017.txt"),
fill = TRUE,
stringsAsFactors = FALSE,
header = TRUE,
na.strings = "")
devtools::use_data(species_list_raw, overwrite = TRUE)
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