GIFT_checklists_conditional {GIFT}

GIFT checklists meta data

Description

Retrieve meta data of GIFT checklists for regions that are covered by checklists jointly fulfilling specific criteria.

Usage

GIFT_checklists_conditional(
  taxon_name = "Tracheophyta",
  floristic_scope = c("all", "native", "native and naturalized",
    "native and historically introduced", "endangered", "endemic", "naturalized",
    "other subset")[1:4],
  ref_excluded = NULL,
  type_ref = c("Account", "Catalogue", "Checklist", "Flora", "Herbarium collection",
    "Key", "Red list", "Report", "Species Database", "Survey"),
  entity_class = c("Island", "Island/Mainland", "Mainland", "Island Group",
    "Island Part"),
  native_indicated = FALSE,
  natural_indicated = FALSE,
  end_ref = FALSE,
  end_list = FALSE,
  suit_geo = FALSE,
  complete_taxon = TRUE,
  GIFT_version = "latest",
  api = "https://gift.uni-goettingen.de/api/extended/",
  list_set = NULL,
  taxonomy = NULL
)

Arguments

taxon_name

Character string corresponding to the taxonomic group of interest.

floristic_scope

A vector listing floristic scopes of the references to be considered. Options are: all, native, ⁠native and naturalized⁠, ⁠native and historically introduced⁠, endangered, endemic, naturalized, ⁠other subset⁠.

ref_excluded

A vector listing potential ref_IDs that shall be ignored when assembling the set of regions and checklists fulfilling the given criteria. Checklists from these references will not be returned. NULL by default.

type_ref

Character, options are Account, Catalogue, Checklist, Flora, ⁠Herbarium collection⁠, Key, ⁠Red list⁠, Report, ⁠Species Database⁠, Survey.

entity_class

Character, options are Island, Island/Mainland, Mainland, ⁠Island Group⁠, ⁠Island Part⁠.

native_indicated

Logical, whether only lists where native status is available should be retrieved.

natural_indicated

Logical, whether only lists where natural status is available should be retrieved.

end_ref

Logical, whether only lists where endemism at the reference level is available should be retrieved.

end_list

Logical, whether only lists where endemism at the list level is available should be retrieved.

suit_geo

logical indicating whether only regions classified as suit_geo should be considered (see details).

complete_taxon

Logical, default TRUE.

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.

list_set

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

default NULL. If not, it has to be the taxonomy table (see GIFT_taxonomy()).

Details

Here is what each column refers to:

ref_ID - Identification number of each reference.
type - What type the source is.
subset - What information regarding the status of species is available.
native_indicated - Whether native status of species is available in the source.
natural_indicated - Whether naturalized status of species is available in the source.
end_ref - Whether endemism information is available in the source.
restricted - Whether the access to this reference is restricted.
taxon_ID - Identification number of species.
list_ID - Identification number of each list.
end_list - Whether endemism information is available in the list.
entity_ID - Identification number of the polygon of the list.
geo_entity - Name of the location.
suit_geo - Is the polygon suitable.
entity_class - Type of polygon.
entity_type - Name of the location.
taxon_name - Name of the group of taxa available.

Value

A data frame with 16 columns.

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_raw()

Examples

ex <- GIFT_checklists_conditional(taxon_name = "Embryophyta", 
floristic_scope = c("all", "native", "native and naturalized",
"native and historically introduced", "endangered",
"endemic", "naturalized", "other subset")[7],
type_ref = c("Account", "Catalogue", "Checklist","Flora",
"Herbarium collection", "Key", "Red list", "Report", "Species Database",
 "Survey"),
 entity_class = c("Island", "Island/Mainland", "Mainland", "Island Group",
 "Island Part"),
 native_indicated = FALSE, natural_indicated = FALSE, end_ref = FALSE,
 end_list = FALSE, suit_geo = TRUE, complete_taxon = TRUE,
 list_set = NULL, taxonomy = NULL)