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#' Taxonomy of GIFT
#'
#' Retrieves the taxonomy of GIFT.
#'
#' @template GIFT_version_api
#'
#' @return A data frame with 6 columns.
#'
#' @details Here is what each column refers to:
#'
#' \emph{taxon_ID} - the identification number of each taxonomic entry.\cr
#' \emph{taxon_name} - names describing taxa.\cr
#' \emph{taxon_name} - author name for a given taxon.\cr
#' \emph{taxon_lvl} - splits every taxon in genus, family, order or
#' superior orders. Taxonomy is a linear sequence of left and right borders
#' for each taxon. This is nested, for example left and right borders of a
#' genus would fall between the left and right borders of the corresponding
#' family. \cr
#' \emph{lft} - left border of one taxon in the taxonomic sequence.\cr
#' \emph{rgt} - right border of one taxon in the taxonomic sequence.\cr
#'
#' @references
#' Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
#' access the Global Inventory of Floras and Traits. Methods in Ecology
#' and Evolution, 14, 2738-2748.
#' https://doi.org/10.1111/2041-210X.14213
#'
#' Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
#' Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
#' https://doi.org/10.1111/jbi.13623
#'
#' @seealso [GIFT::GIFT_checklists()]
#'
#' @examples
#' \donttest{
#' ex <- GIFT_taxonomy()
#' }
#'
#' @importFrom jsonlite read_json
#' @importFrom dplyr mutate_at
#'
#' @export
GIFT_taxonomy <- function(
GIFT_version = "latest",
api = "https://gift.uni-goettingen.de/api/extended/"){
api_check <- check_api(api)
if(is.null(api_check)){
return(NULL)
} else{
GIFT_version <- check_gift_version_simple(GIFT_version)
taxonomy <- read_json(paste0(
api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
".php?query=taxonomy"), simplifyVector = TRUE)
# Convert columns as numeric
taxonomy <- dplyr::mutate_at(taxonomy, c("taxon_ID", "lft", "rgt"),
as.numeric)
return(taxonomy)
}
}
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