GIFT_species_distribution {GIFT}

GIFT species distribution

Description

Retrieve the distribution of one species from GIFT checklists.

Usage

GIFT_species_distribution(
  genus = "Fagus",
  epithet = "sylvatica",
  namesmatched = FALSE,
  remove_overlap = FALSE,
  area_th_island = 0,
  area_th_mainland = 100,
  overlap_th = 0.1,
  by_ref_ID = FALSE,
  aggregation = FALSE,
  GIFT_version = "latest",
  api = "https://gift.uni-goettingen.de/api/extended/"
)

Arguments

genus

Character string corresponding to the genus of the species of interest.

epithet

Character string corresponding to the epithet of the species of interest.

namesmatched

Logical FALSE by default, set to TRUE if you want to look for the species not only in the standardized species names but also in the original species names as they came in the original resources.

remove_overlap

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

area_th_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_th_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_th

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.

aggregation

A logical stating whether you want to aggregate in a simpler way the floristic status of species per entity_ID. For example, two lists associated to the same entity_ID could describe a species both as native and non-native. In that case, the aggregation would consider the species to be native. Reverse for naturalized and alien.

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 the reference
list_ID - Identification number of the list
entity_ID - Identification number of the polygon
name_ID - Identification number of the genus before taxonomic harmonization
cf_genus - Whether the genus name is uncertain
cf_species - Whether the species' epithet is uncertain
aff_species - Species' epithet uncertain
questionable - Whether the species name is questionable
native - Is the species native
quest_native - Is the native status questionable
naturalized - Is the species naturalized
endemic_ref - Is the species endemic at the reference level
quest_end_ref - Is the endemic_ref status questionable
endemic_list - Is the species endemic at the list level
quest_end_list - Is the endemic_list status questionable
genus - Genus name before taxonomic harmonization
species_epithet - Epithet before taxonomic harmonization
subtaxon - Subtaxon name before taxonomic harmonization
author - Author who described the species before taxonomic harmonization
matched - Is the species name matched in the taxonomic backbone
epithetscore - Matching score for the epithet
overallscore - Overall matching score for the species
resolved - Is the species name resolved in the taxonomic backbone
synonym -Is the species a synonym in the taxonomic backbone
matched_subtaxon -Is the sub-species name matched in the taxonomic backbone
accepted - Is the species name accepted in the taxonomic backbone
service - Service use for the taxonomic harmonization
work_ID -Identification number of the species after taxonomic harmonization
taxon_ID -Identification number of the taxonomic group
work_genus - Identification number of the genus after taxonomic harmonization
work_species_epithet - Identification number of the species epithet after taxonomic harmonization
work_species - Species name (after taxonomic harmonization)
work_author - Author who described the species (after taxonomic harmonization)

Value

A data frame with 33 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_species_lookup()

Examples

ex <- GIFT_species_distribution()