Taxonomic and trait coverage per geographic region and taxonomic group in GIFT

Retrieve taxonomic or trait coverage (for a given trait) of all species, native species, naturalized species and endemic species per taxonomic group and geographic region combination. This function works with taxonomic groups above the genus level.

Usage

GIFT_coverage(
  what = "taxonomic_coverage",
  taxon_name = "Embryophyta",
  trait_ID = "1.1.1",
  GIFT_version = "latest",
  api = "https://gift.uni-goettingen.de/api/extended/"
)

Arguments

what: character indicating whether taxonomic_coverage or trait_coverage shall be retrieved.
taxon_name: Name of the taxonomic group you want to retrieve coverage for. See GIFT_taxonomy() for options. The function accepts family names and higher taxonomic groups.
trait_ID: Identification number of the trait you want to retrieve coverage for. See GIFT_traits_meta() for details.
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 either taxonomic or trait coverage per GIFT polygon.

Details

The output has 9 columns:

entity_ID - Identification number of GIFT polygons
total - taxonomic or trait coverage for all species
total_rst - taxonomic or coverage for all species considering restricted resources
native - taxonomic or trait coverage for native species
native_rst - taxonomic or trait coverage for native species considering restricted resources
naturalized - taxonomic or trait coverage for naturalized species
naturalized_rst - taxonomic or trait coverage for naturalized species considering restricted resources
endemic_min - taxonomic or trait coverage for endemic species
endemic_min_rst - taxonomic or trait coverage for endemic species considering restricted resources

In the case of taxonomic coverage, a '1' means that species composition data is available for the given combination of taxonomic group and geographic region while 'NA' means that no data is available. This can differ depending on whether restricted data in GIFT is considered or not (columns with or without _rst at the end).

In the case of trait coverage, the proportion of species of a given taxonomic group with information on the defined trait is reported per geographic region.

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

# \donttest{
ex <- GIFT_coverage(what = "taxonomic_coverage", taxon_name = "Angiospermae")
#> You are asking for the latest stable version of GIFT which is 3.2.
ex2 <- GIFT_coverage(what = "trait_coverage", taxon_name = "Angiospermae",
trait_ID = "1.2.1")
#> You are asking for the latest stable version of GIFT which is 3.2.
# }