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Download a list of species recorded inside a spatial polygon from GBIF.

Source: R/request_gbif_specieslist.R
request_gbif_specieslist.Rd

Download a list of species recorded inside a spatial polygon from GBIF, with support for optional higher-taxon filtering.

Usage

request_gbif_specieslist(
  spatial_polygon,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  family = NULL,
  genus = NULL,
  species = NULL,
  tolerance = 0.01,
  gbif_user = NULL,
  gbif_pwd = NULL,
  gbif_email = NULL,
  verbose = TRUE
)

Arguments

spatial_polygon

an object of class SpatVector representing the area of interest.

kingdom, phylum, class, order, family, genus, species

(character) optional taxonomic filters. Default is NULL.

tolerance

(numeric) tolerance in degrees for geometry simplification. Default is 0.01.

gbif_user

(character) user name within GBIF's website. Default is NULL, meaning it will try to obtain this information from the R enviroment. (check set_gbif_credentials()) for more details.

gbif_pwd

(character) user password within GBIF's website. Default is NULL, meaning it will try to obtain this information from the R enviroment.

gbif_email

(character) user email within GBIF's website. Default is NULL, meaning it will try to obtain this information from the R enviroment.

verbose

(logical) if TRUE, prints messages about the progress. Default is FALSE.

Value

A download request key returned by the GBIF API, which can be used to monitor or retrieve the download of the species list.

Details

This function converts the input SpatVector polygon into Well-Known Text (WKT) format and submits an asynchronous query using GBIF's SPECIES_LIST download format.

You can use the object returned by this function to check the download request progress with rgbif::occ_download_wait()

Note

This function requires an active internet connection and valid GBIF credentials. Set them in advance using set_gbif_credentials().

Examples

if (FALSE) { # \dontrun{
# Set your GBIF credentials (required before running this function)
# set_gbif_credentials(gbif_username = "your_username",
#                       gbif_email = "your_email@example.com",
#                       gbif_password = "your_password")

# Create a sample polygon
coords <- matrix(c(-48, -16, -47, -16, -47, -15, -48, -15, -48, -16),
                 ncol = 2, byrow = TRUE)
poly <- vect(coords, type = "polygons", crs = "EPSG:4326")

# Submit a request to download list of Malvaceae species in the area
gbif_requested_sl <- request_gbif_specieslist(spatial_polygon = poly,
                                            family = "Malvaceae")
# Monitor download progress
rgbif::occ_download_wait(gbif_requested_sl)

# Import completed species list
sl <- import_gbif(gbif_requested_sl, select_columns = FALSE)
} # }