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Access 'WikiAves' media file metadata

Source: R/query_wikiaves.R
query_wikiaves.Rd

query_wikiaves searches for metadata from WikiAves.

Usage

query_wikiaves(
  species = getOption("species"),
  format = getOption("format", c("sound", "image")),
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  verbose = getOption("verbose", TRUE),
  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' or 'image'. 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)).

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 avian digital media in the open-access online repository WikiAves and returns its metadata. WikiAves is a Brazilian online platform and citizen science project that serves as the largest community for birdwatchers in Brazil. It functions as a collaborative, interactive encyclopedia of Brazilian birds, where users contribute georeferenced photographs and sound recordings, which are then used to build a vast database for research and conservation.

References

Schubert, Stephanie Caroline, Lilian Tonelli Manica, and André De Camargo Guaraldo. 2019. Revealing the potential of a huge citizen-science platform to study bird migration. Emu-Austral Ornithology 119.4: 364-373.

Author

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

Examples

# search
p_nattereri <- query_wikiaves(species = "Phaethornis nattereri",
    format = "image")