R/species_codes.R

In rfisheries: 'Programmatic Interface to the 'openfisheries.org' API'

#' Download species data including three-letter ASFIS species code.
#'
#' Returns a data frame with scientific_name, taxocode, a3_code, isscaap, and English name. The a3_code is required by \code{\link{landings}} to return species specific landing data.
#'
#' @param foptions additional optional parameters
#' @export
#' @importFrom httr GET content stop_for_status
#' @importFrom data.table rbindlist
#' @export
#' @return data.frame
#' @examples \dontrun{
#' of_species_list <- of_species_codes()
#'}
of_species_codes <- function(foptions = list()) {
    url <- "http://openfisheries.org/api/landings/species.json"
    species <- GET(url, foptions)
    stop_for_status(species)
    species_data <- content(species)
    species_data <- lapply(species_data, spfillnull)
    species_data_frame <- data.frame(rbindlist(species_data), stringsAsFactors = FALSE)
    species_data_frame
} 

# Internal function used inside species_code2
#' @noRd
spfillnull <- function(x) {
  x[["isscaap"]] <- ifelse(is.null(x[["isscaap"]]), NA, x[["isscaap"]])
 as.list(x, stringsAsFactors = FALSE)
}

#' species_codes
#'
#' Function now replaced by \code{of_species_code}
#' @rdname species_codes-deprecated
#' @export
species_codes <- function()
{
  .Deprecated(new="of_species_codes", package="rfisheries", msg="This function is deprecated, and will be removed in a future version. See ?of_species_codes")
}