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Access 'gbif' media file metadata

Source: R/query_gbif.R
query_gbif.Rd

query_gbif searches for metadata from gbif.

Usage

query_gbif(
  species = getOption("species"),
  format = getOption("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'. Can be set globally for the current R session via the "format" option (e.g. options(format = "sound")). 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

The name of a specific dataset in which to focus the query (by default it searchs across all available datasets). Users can check available dataset names by downloading this csv file https://api.gbif.org/v1/dataset/search/export?format=CSV&. See https://www.gbif.org/dataset/search?q= for more details.

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 repository 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/

See also

query_inaturalist

Author

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

Examples

# search dink frog sound files