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#' Spatial overlap between GIFT polygons and external polygons
#'
#' Calculate the spatial overlap between GIFT polygons and shapefiles coming
#' from other resources
#'
#' @param resource A character string indicating from which resource the
#' spatial overlap is calculated. Available options are `glonaf` and `gmba`.
#' glonaf stands for Global Naturalized Alien Flora and gmba for Global
#' Mountain Biodiversity Assessment.
#'
#' @template GIFT_version_api
#'
#' @return A data frame with the spatial overlap.
#'
#' @details The columns of the data.frame are the following:
#'
#' \emph{entity_ID} - Identification number of the GIFT polygon\cr
#' \emph{glonaf_ID} (or \emph{gmba_ID}) - Identification number of the polygon
#' from the other resource\cr
#' \emph{overlap12} - Spatial overlap in percentage between GIFT polygon and
#' the external polygon\cr
#' \emph{overlap21} - The other way around
#'
#' @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_lists()]
#'
#' @examples
#' \donttest{
#' glonaf <- GIFT_overlap(resource = "glonaf")
#' gmba <- GIFT_overlap(resource = "gmba")
#' }
#'
#' @importFrom jsonlite read_json
#' @importFrom dplyr select mutate_all
#'
#' @export
GIFT_overlap <- function(
resource = "glonaf", GIFT_version = "latest",
api = "https://gift.uni-goettingen.de/api/extended/"){
# 1. Controls ----
api_check <- check_api(api)
if(is.null(api_check)){
return(NULL)
} else{
if(length(resource) != 1 || !is.character(resource) ||
!(resource %in% c("glonaf", "gmba", "gaptani", "wdpa"))){
stop("resource must be a character string indicating from which external
resource you want to calculate the spatial overlap. Available options
are 'glonaf', 'gmba' or 'wdpa'.")
}
GIFT_version <- check_gift_version(GIFT_version)
ID <- NULL
# 2. Query ----
tmp <- jsonlite::read_json(paste0(
api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
".php?query=overlap_misc&layer=", resource), simplifyVector = TRUE)
tmp <- dplyr::select(tmp, -ID)
tmp <- dplyr::mutate_all(tmp, as.numeric)
return(tmp)
}
}
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