Access 'gbif' recordings and metadata

query_gbif searches for metadata from gbif.

Usage

query_gbif(
  species = getOption("species"),
  format = c("sound", "image", "video", "interactive resource"),
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  verbose = getOption("verbose", TRUE),
  dataset = NULL,
  all_data = getOption("all_data", FALSE),
  raw_data = getOption("raw_data", FALSE)
)

Arguments

species: Character string with the scientific name of a species in the format: "Genus epithet". Required. Can be set globally for the current R session via the "term" option (e.g. options(term = "Hypsiboas rufitelus")).
format: Character vector with the media format to query for. Options are 'sound', 'image', 'video' and 'interactive resource'. Required.
cores: Numeric vector of length 1. Controls whether parallel computing is applied by specifying the number of cores to be used. Default is 1 (i.e. no parallel computing). Can be set globally for the current R session via the "mc.cores" option (e.g. options(mc.cores = 2)). Note that some repositories might not support parallel queries from the same IP address as it might be identified as denial-of-service cyberattack.
pb: Logical argument to control if progress bar is shown. Default is TRUE. Can be set globally for the current R session via the "pb" option ( options(pb = TRUE)).
verbose: Logical argument that determines if text is shown in console. Default is TRUE. Can be set globally for the current R session via the "verbose" option ( options(verbose = TRUE)).
dataset: see https://www.gbif.org/dataset/search?q=.
all_data: Logical argument that determines if all data available from database is shown in the results of search. Default is FALSE. Can be set globally for the current R session via the "all_data" option ( options(all_data = TRUE)).
raw_data: Logical argument that determines if the raw data from the API is returned (e.g. without any manipulation). Default is FALSE. Can be set globally for the current R session via the "raw_data" option ( options(raw_data = TRUE)). If TRUE all_data is set to TRUE internally. Useful for developers, or if users suspect that some data is mishandled during processing (i.e. date information is lost). Note that the metadata obtained when raw_data = TRUE is not standardized, so most suwo functions for downstream steps will not work on them.

Value

The function returns a data frame with the metadata of the media files matching the search criteria. If all_data = TRUE, all metadata fields (columns) are returned. If raw_data = TRUE, the raw data as obtained from the repository is returned (without any formatting).

Details

This function queries for species observation info in the open-access online repository gbif. GBIF (the Global Biodiversity Information Facility) is an international network and data infrastructure funded by the world's governments and aimed at providing open access to data about all types of life on Earth. Note that some of the records returned by this function could be duplicates of records returned by other suwo functions (e.g., query_inaturalist).

References

GBIF.org (2024), GBIF Home Page. Available from: https://www.gbif.org [13 January 2020].

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

Examples

if (FALSE) { # \dontrun{
# search sound files
View(df1)
} # }