R/GIFT_references.R

In GIFT: Access to the Global Inventory of Floras and Traits (GIFT)

#' Metadata for references available in GIFT
#'
#' Retrieve the metadata of every reference accessible in GIFT.
#'
#' @template GIFT_version_api
#' 
#' @return
#' A data frame with 14 columns.
#'
#' @details Here is what each column refers to:
#' 
#' \emph{ref_ID} - Identification number of the reference\cr
#' \emph{ref_long} - Full reference for the reference\cr
#' \emph{geo_entity_ref} - Name of the location\cr
#' \emph{type} - What type the source is\cr
#' \emph{subset} - What information regarding the status of species is
#'  available\cr
#' \emph{taxon_ID} - Identification number of the group of taxa available\cr
#' \emph{taxon_name} - Name of the group of taxa available\cr
#' \emph{checklist} - Is the source a checklist\cr
#' \emph{native_indicated} - Whether native status of species is available in
#'  the source\cr
#' \emph{natural_indicated} - Whether naturalized status of species is
#' available in the source\cr
#' \emph{end_ref} - Whether endemism information is available in the source\cr
#' \emph{traits} - Whether trait information is available in the source\cr
#' \emph{restricted} - Whether the access to this reference is restricted\cr
#' \emph{proc_date} - When the source was processed
#'
#' @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_references()
#' }
#' 
#' @importFrom jsonlite read_json
#' @importFrom dplyr mutate_at
#' 
#' @export

GIFT_references <- function(
    api = "https://gift.uni-goettingen.de/api/extended/",
    GIFT_version = "latest"){
  api_check <- check_api(api)
  if(is.null(api_check)){
    return(NULL)
  } else{
    GIFT_version <- check_gift_version(GIFT_version)
    
    tmp <- jsonlite::read_json(paste0(
      api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
      ".php?query=references"), simplifyVector = TRUE)
    
    tmp <- dplyr::mutate_at(
      tmp, c("ref_ID","taxon_ID","checklist","native_indicated",
             "natural_indicated","end_ref","traits"), as.numeric)
    
    if("restricted" %in% names(tmp)){
      tmp$restricted <- as.numeric(tmp$restricted)
    }
    
    return(tmp)
  }
}