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Access 'iNaturalist' media file metadata

Source: R/query_inaturalist.R
query_inaturalist.Rd

query_inaturalist searches for metadata from iNaturalist.

Usage

query_inaturalist(
  species = getOption("species"),
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  verbose = getOption("verbose", TRUE),
  format = getOption("format", c("sound", "image")),
  identified = FALSE,
  verifiable = FALSE,
  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")).

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)).

format

Character vector with the media format to query for. Currently 'image' and 'sound' are available. Can be set globally for the current R session via the "format" option (e.g. options(format = "sound")). Required.

identified

Logical argument to define if search results are categorized as identified by inaturalist.

verifiable

Logical argument to define if search results are categorized as verifiable by inaturalist.

all_data

Logical argument that determines if all data available from database is shown in the results of search. Default is 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 iNaturalist. iNaturalist is a free, crowdsourced online platform for nature enthusiasts to document and identify plants, animals, fungi, and other organisms in the wild. Note that Inaturalist observations do not include a 'country' field.

References

iNaturalist. Available from https://www.inaturalist.org. Accessed [date]

Author

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

Examples

# search Bleeding Tooth mushroom images