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Transform ETN data to Darwin Core

Source: R/write_dwc.R
write_dwc.Rd

Transforms and downloads data from a European Tracking Network animal project to Darwin Core. The resulting CSV file(s) can be uploaded to an IPT for publication to OBIS and/or GBIF. A meta.xml or eml.xml file are not created.

Usage

write_dwc(
  connection = con,
  animal_project_code,
  directory = ".",
  rights_holder = NULL,
  license = "CC-BY"
)

Arguments

connection

Connection to the ETN database.

animal_project_code

Animal project code.

directory

Path to local directory to write file(s) to. If NULL, then a list of data frames is returned instead, which can be useful for extending/adapting the Darwin Core mapping before writing with readr::write_csv().

rights_holder

Acronym of the organization owning or managing the rights over the data.

license

Identifier of the license under which the data will be published.

Value

CSV file(s) written to disk or list of data frames when directory = NULL.

Transformation details

Data are transformed into an Occurrence core. This follows recommendations discussed and created by Peter Desmet, Jonas Mortelmans, Jonathan Pye, John Wieczorek and others. See the SQL file(s) used by this function for details.

Key features of the Darwin Core transformation:

  • Deployments (animal+tag associations) are parent events, with capture, surgery, release, recapture (human observations) and acoustic detections (machine observations) as child events. No information about the parent event is provided other than its ID, meaning that data can be expressed in an Occurrence Core with one row per observation and parentEventID shared by all occurrences in a deployment.

  • The release event often contains metadata about the animal (sex, lifestage, comments) and deployment as a whole.

  • Acoustic detections are downsampled to the first detection per hour, to reduce the size of high-frequency data. Duplicate detections (same animal, tag and timestamp) are excluded. It is possible for a deployment to contain no detections, e.g. if the tag malfunctioned right after deployment.