Queries in the API"
In GIFT: Access to the Global Inventory of Floras and Traits (GIFT)

knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE,
                      fig.width = 8, fig.height = 8)
# Packages --------------------------------------------------------------------
suppressPackageStartupMessages({
  suppressWarnings({
    library("GIFT")
    library("knitr")
    library("kableExtra")
  })
})

options(tinytex.verbose = TRUE)

knitr::include_graphics("../man/figures/biodiv_gottingen_logo.png")
knitr::include_graphics("../man/figures/GIFT.png")

This vignette shows how to work with the API, how it relates to the GIFT R package, and how the R functions in the package are interdependent.

API

The API endpoint is https://gift.uni-goettingen.de/api/extended/index.php. We then have several queries, listed in the table below, that allow retrieving distinct tables. The name in the Query column of the table below has to be used as the query argument. As an example, here is the query that leads to the environmental raster metadata table:
https://gift.uni-goettingen.de/api/extended/index.php?query=env_raster

Note that the endpoint changes depending on the version of GIFT you are querying. For example, with the same table as above, we can retrieve the table as it was in GIFT version 2.0:
https://gift.uni-goettingen.de/api/extended/index2.0.php?query=env_raster

While this API does not require authentication, there is a password-protected API leading to some restricted content in the different tables. Restricted content can be,for example, some checklists that need the approval of their provider before being used. This API can be communicated upon request.

Here is the list of the 24 available queries, their arguments and the GIFT R functions in which they are called. There is no rate-limitation for any of these queries except for species and phylogeny, which retrieves the data in chunks.

# GIFT_traits_raw => reference_traits traits_raw
# GIFT_traits_meta => traits_meta
# GIFT_traits => traits
# GIFT_taxonomy => taxonomy
# GIFT_taxgroup => taxonomy
# GIFT_species_lookup => names_matched names_matched_unique
# GIFT_species_distribution => species_distr overlap
# GIFT_species => species
# GIFT_richness => taxonomy, traits_cov, species_num
# GIFT_regions => regions
# GIFT_references => references
# GIFT_overlap => overlap_misc
# GIFT_no_overlap => overlap
# GIFT_lists => lists
# GIFT_env_meta_raster => env_raster, references_citavi
# GIFT_env_meta_misc => env_misc, references_citavi
# GIFT_env => geoentities_env_misc, geoentities_env_raster
# GIFT_checklists_raw => taxonomy, checklists
# GIFT_checklists_conditional => lists, taxonomy
# GIFT_checklists => lists, taxonomy, overlap
# GIFT_phylogeny => phylogeny

query_table <-
  data.frame(
    Query = c("checklists", "env_misc", "env_raster", "geoentities_env_misc",
              "geoentities_env_raster", "lists", "names_matched",
              "names_matched_unique", "overlap", "overlap_misc", "phylogeny",
              "references_citavi", "references", "reference_traits", "regions",
              "species", "species_distr", "species_num", "taxonomy", "traits",
              "traits_cov", "traits_meta", "traits_raw", "versions"),
    Arguments = c("listid (integer)\n, taxonid, namesmatched, filter", "", "",
                  "envvar",
                  "layername, sumstat", "", "genus, epithet", "genus, epithet",
                  "taxon, startat",
                  "layer", "taxon, startat, limit", "", "", "", "",
                  "startat, limit", "nameid",
                  "taxonid",
                  "", "traitid, biasref, biasderiv, startat, limit",
                  "traitid, taxonid", "", "traitid, deriv, biasderiv, refid",
                  ""
    ),
    R_function = c(
      "GIFT_checklists_raw()",  "GIFT_env_meta_misc()",
      "GIFT_env_meta_raster()", "GIFT_env()", "GIFT_env()",
      "GIFT_lists(), GIFT_checklists_conditional(), GIFT_checklists()",
      "GIFT_species_lookup()", "GIFT_species_lookup()",
      "GIFT_species_distribution(), GIFT_no_overlap(), GIFT_checklists()",
      "GIFT_overlap()",
      "GIFT_phylogeny()",
      "GIFT_env_meta_raster(), GIFT_env_meta_misc()",
      "GIFT_references()", "GIFT_traits_raw()", "GIFT_regions()",
      "GIFT_species()", "GIFT_species_distribution()", "GIFT_richness()",
      "GIFT_taxonomy(), GIFT_taxgroup(), GIFT_richness(),
      GIFT_checklists_raw(), GIFT_checklists(), GIFT_checklists_conditional()",
      "GIFT_traits()", "GIFT_richness()", "GIFT_traits_meta()",
      "GIFT_traits_raw()", "All GIFT functions"
    )
  )

kable(query_table, "html") %>%
  kable_styling(full_width = FALSE)

Some more details:

# Query for trait and chunks
# Default value for end is 10000
# https://gift.uni-goettingen.de/api/extended/index.php?query=traits&
# traitid=1.1.1&biasref=1&biasderiv=1&startat=100000&limit=10

# To retrieve the geojson
paste0("https://gift.uni-goettingen.de/geojson/geojson_smaller", 
       ifelse(GIFT_version == "beta", "", GIFT_version), "/",
       entity_ID[i], ".geojson")

Dependency graph of R functions

Arrows in the figure below connect interdependent functions, i.e. functions that call other functions. Function names are colored according to the larger category to which they belong.

knitr::include_graphics("../man/figures/GIFT_network_functions.png")

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, 00, 1–11. https://doi.org/10.1111/2041-210X.14213.

Weigelt, P., König, C. & Kreft, H. (2020) GIFT – A Global Inventory of Floras and Traits for macroecology and biogeography. Journal of Biogeography, https://doi.org/10.1111/jbi.13623.