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#' Species richness per geographic region and taxonomic group in GIFT
#'
#' Retrieve species richness of all species, native species, naturalized
#' species and endemic species per taxonomic group and geographic region
#' combination.
#'
#' @param taxon_name Taxonomic group to retrieve species richness for.
#'
#' @template GIFT_version_api
#'
#' @return A data frame with species richness values for different floristic
#' subsets per geographic region in GIFT.
#'
#' @details The output has 5 columns:
#'
#' \emph{entity_ID} - Identification number of the geographic region\cr
#' \emph{total} - total species richness\cr
#' \emph{native} - number of native species\cr
#' \emph{naturalized} - number of naturalized species\cr
#' \emph{endemic_min} - number of endemic species
#'
#' The number of endemic species is a conservative count not counting
#' occurrences of species which go back to infraspecific taxa.
#'
#' @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_traits_meta()]
#'
#' @examples
#' \donttest{
#' ex <- GIFT_richness(taxon_name = "Angiospermae")
#' }
#'
#' @importFrom jsonlite read_json
#' @importFrom dplyr mutate_at
#'
#' @export
GIFT_richness <- function(taxon_name = "Embryophyta", 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(taxon_name) != 1 || is.na(taxon_name) ||
!is.character(taxon_name)){
stop(
"'taxon_name' is incorrect. It must be a character string among one of
the taxonomic groups available in GIFT. To check them all, run
'GIFT_taxonomy()'.")
}
GIFT_version <- check_gift_version_simple(GIFT_version)
# 2. Query ----
# Taxonomy query
taxonomy <- jsonlite::read_json(
paste0(api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
".php?query=taxonomy"), simplifyVector = TRUE)
# Define tax_group
tax_group <- taxonomy[which(taxonomy$taxon_name == taxon_name), "taxon_ID"]
# Query
tmp <- jsonlite::read_json(paste0(
api, "index", ifelse(GIFT_version == "beta", "", GIFT_version),
".php?query=species_num&taxonid=", tax_group), simplifyVector = TRUE)
tmp <- dplyr::mutate_at(tmp, c("entity_ID", "total", "native",
"naturalized", "endemic_min"), as.numeric)
return(tmp)
}
}
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