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Raw trait values

Source: R/GIFT_traits_raw.R
GIFT_traits_raw.Rd

Retrieve non-aggregated trait values at the level of the bibliographic references and un-standardized species names in GIFT.

Usage

GIFT_traits_raw(
  trait_IDs = "",
  derived = TRUE,
  bias_ref = TRUE,
  bias_deriv = TRUE,
  api = "https://gift.uni-goettingen.de/api/extended/",
  GIFT_version = "latest"
)

Arguments

trait_IDs

a character string indicating which traits you want to retrieve. Traits must belong to the available list of traits. See GIFT_traits_meta().

derived

include logically derived traits.

bias_ref

When FALSE, exclude entries that are only based on a resource that potentially introduces a bias (e.g. a resource only including trees).

bias_deriv

When FALSE, exclude entries that are only based on a derivation that potentially introduces a bias (e.g. all phanerophytes being woody but some life forms being ambiguous).

api

character string defining from which API the data will be retrieved.

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.

Value

A data.frame with 28 columns.

Details

Here is the detail of each column:

trait_derived_ID - Identification number of the trait record in the database
ref_ID - Identification number of the reference
orig_ID - Identification number of the species, as it came in the source
trait_ID - Identification number of the trait
trait_value - Value of the trait (coded as character, even for continuous trait)
derived - Is the trait value derived from another information (e.g. phanerophytes are woody)
bias_deriv - Is the derivation potentially introducing a bias
bias_ref - Is the resource potentially introducing a bias
name_ID - Identification number of the species before being resolved
cf_genus - Whether the genus name is uncertain
genus - Genus of the species
cf_species - Whether the species' epithet is uncertain
aff_species - Species' epithet uncertain
species_epithet - Epithet of the species
subtaxon - Sub-taxon name
author - Author who described the species
matched - Was the species name matched in the taxonomic backbone
epithetscore - Matching score for the epithet
overallscore - Overall matching score
resolved - Was the species name resolved in the taxonomic backbone
service - Taxonomic backbone used for taxonomic harmonization
work_ID - Identification number of the taxonomically harmonized species
genus_ID - Identification number of the taxonomically harmonized genus
work_genus - Genus name (after taxonomic harmonization)
work_species - Species name (after taxonomic harmonization)
work_author - Name of the author who described the species
geo_entity _ref - Name of the region of the reference
ref_long - Full reference to cite

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_traits_meta() and GIFT_traits()

Examples

# \donttest{
succulence <- GIFT_traits_raw(trait_IDs = c("4.10.1"))
#> ================================================================================
# }