GIFT_checklists_raw {GIFT}

GIFT checklists

Description

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.

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

Value

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

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

See Also

GIFT_checklists()

Examples

ex <- GIFT_checklists_raw(list_ID = c(1,5))