GIFT_checklists {GIFT}

GIFT checklists

Description

Retrieve GIFT checklists that fulfill specific criteria.

Usage

GIFT_checklists(
  taxon_name = "Tracheophyta",
  complete_taxon = TRUE,
  floristic_group = c("all", "native", "endemic", "naturalized")[2],
  complete_floristic = TRUE,
  geo_type = c("All", "Mainland", "Island")[1],
  ref_excluded = NULL,
  suit_geo = FALSE,
  shp = NULL,
  coordinates = NULL,
  overlap = "centroid_inside",
  remove_overlap = FALSE,
  area_threshold_island = 0,
  area_threshold_mainland = 100,
  overlap_threshold = 0.1,
  by_ref_ID = FALSE,
  taxonomic_group = TRUE,
  namesmatched = FALSE,
  list_set_only = FALSE,
  GIFT_version = "latest",
  api = "https://gift.uni-goettingen.de/api/extended/"
)

Arguments

taxon_name

Character string corresponding to the taxonomic group of interest.

complete_taxon

logical stating you want to retrieve checklists that only contain the exhaustive list of the taxon_name argument or as well incomplete lists.

floristic_group

Character among the following options: all, native, endemic, naturalized.

complete_floristic

logical stating you want to retrieve checklists that only contain the exhaustive list of the floristic_group argument or as well incomplete lists.

geo_type

Character string, either Mainland, Island or All. Island gets you to Island, Island Group & Island Part. Mainland gets you to Mainland & Island/Mainland. All gets you all types.

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.

suit_geo

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

shp

Shapefile provided by the user.

coordinates

Custom set of coordinates. The format is a two columns, the first one being longitudes and the second being latitudes. If 4 coordinates are given, the function assumes that these are the four corners of a bounding box.

overlap

A character string defining the criteria to use in order to retrieve checklists. Available options are centroid_inside, extent_intersect, shape_intersect and shape_inside. For example, extent_intersect means that every polygon from GIFT for which the extent intersects the provided shape/coordinates will be retrieved.

remove_overlap

a logical stating whether you want to retrieve checklists that overlap or not.

area_threshold_island

A number stating from which surface the smallest overlapping polygon is kept. By default set to 0 square kilometer (meaning that by default the smallest islands will be conserved).

area_threshold_mainland

When two polygons overlap, the smallest or the biggest one can be kept. When the surface of the smallest polygon exceeds this number, the smallest polygon is kept. Otherwise, we keep the bigger one. Set by default 100 square-kilometers.

overlap_threshold

A number ranging from 0 to 1, indicating at what percentage of overlap, partially overlapping polygons should be kept.

by_ref_ID

logical indicating whether the removal of overlapping regions shall be applied by ref_ID only. Note that regions overlapping with other regions from the same resource will be removed even if there are other references available for those regions.

taxonomic_group

logical. When set to TRUE, two additional columns (family and tax_group) are available in the checklists.

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.

list_set_only

logical stating whether you only want the metadata or if you also want to retrieve the species lists.

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 the detail of each data.frame and their columns:

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.

For the second data frame with the species, each column refers to:

ref_ID - Identification number of each reference.
list_ID - Identification number of each list
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.
family - Family of the species.
tax_group - Taxonomic group of the species.

While the arguments taxon_name in combination with complete_taxon = TRUE and floristic_group in combination with complete_floristic = TRUE make sure to only get back checklists for regions for which GIFT has lists aiming at covering both the entire taxonomic group and floristic subset (for example native vascular plants), it does not mean that the checklists are complete (include all species). We therefore flagged regions in GIFT for which the combination of all checklists is obviously incomplete as suit_geo = 0. This has however only been done only for native angiosperms and the assessment has been subjective. Set suit_geo = TRUE if you only want to consider regions classified as suit_geo.

Value

List with two data frames: the checklist with species and the list of ID.

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

data("western_mediterranean")
ex <- GIFT_checklists(shp = western_mediterranean,
overlap = "centroid_inside", taxon_name = "Angiospermae",
list_set_only = TRUE) # set to FALSE to get species composition