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Access 'observation' recordings and metadata

Source: R/query_observation.R
query_observation.Rd

query_observation searches for metadata from observation.

Usage

query_observation(
  species = getOption("species"),
  format = c("sound", "image"),
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  verbose = getOption("verbose", TRUE),
  token = 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. Currently 'image' and 'sound' are available.

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)).

token

Character refering to the token assigned by Observation.org as authorization for searches. Required.

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 observation. It can return media metadata.

References

Observation.org, Observation International and local partners. Available at https://observation.org. Retrieved June 30, 2022

Author

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

Examples

if (FALSE) { # \dontrun{
# search without downloading
View(df1)
} # }