GIFT checklists

Raw checklists, to combine with other functions.

Usage

GIFT_checklists_raw(
  ref_ID = NULL,
  list_ID = NULL,
  namesmatched = FALSE,
  taxon_name = "Tracheophyta",
  floristic_group = "all",
  list_set = NULL,
  taxonomy = NULL,
  GIFT_version = "latest",
  api = "https://gift.uni-goettingen.de/api/extended/"
)

Arguments

ref_ID: A vector defining the IDs of the references to retrieve. NULL by default.
list_ID: A vector defining the IDs of the lists to retrieve. NULL by default. These lists are retrieved in addition to the lists contained in the references in ref_ID.
namesmatched: Logical. FALSE by default, set to TRUE if you want the original species name as they came in the references as well as details on the taxonomic harmonization.
taxon_name: Character string corresponding to the taxonomic group of interest.
floristic_group: Character string among these options: all, native, naturalized, endemic_list, endemic_ref.
list_set: NULL by default. If not, it has to be the list table (see GIFT_lists()). Used internally in GIFT_checklists() to avoid downloading the table of lists many times.
taxonomy: NULL by default. If not, it has to be the taxonomy table (see GIFT_taxonomy()). Used internally in GIFT_checklists() to avoid downloading the taxonomy table many times.#'
GIFT_version: character string defining the version of the GIFT database to use. The function retrieves by default the latest stable version. If set to beta, the most up-to-date version which is still subject to changes and edits is used.
api: character string defining from which API the data will be retrieved.

Value

A data frame with 15 or 29 columns (depending on namesmatched). This data frame contains the species checklist for a given reference/list.

Details

Here is what each column refers to:

ref_ID - Identification number of each reference
list_ID - Identification number of each list
orig_ID - Identification number of each species name, unchanged from the sources
name_ID - Identification number of each reference
genus - Genus of each species
species_epithet - Epithet of each species
subtaxon - If needed, subtaxon of the species
author - Name of the author who described the species
matched - Whether a match was found when using a taxonomic backbone
epithetscore - Matching score for the epithet
overallscore - Matching score for the overall species name
resolved - Whether the species name was resolved
service - Service used for the taxonomic harmonization
work_ID - Identification number of each species name, after taxonomic harmonization
genus_ID - Identification number of each genus, after taxonomic harmonization
species - Species name, after taxonomic harmonization
questionable - Whether the species occurrence is questionable
native - Whether the species is native
quest_native - Whether the native information is questionable
naturalized - Whether the species is naturalized
endemic_ref - Whether the species is endemic within the reference
quest_end_ref - Whether the endemic_ref information is questionable
endemic_list- Whether the species is endemic within the list
quest_end_list - Whether the endemic_list information is questionable
cons_status - Conservation status of the species

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

Examples