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Transform a GeoLocator Data Package to Darwin Core

Source: R/gldp_to_dwc.R
gldp_to_dwc.Rd

Transforms a GeoLocator Data Package to a Darwin Core Archive. The resulting CSV files can be uploaded to an IPT for publication to GBIF. A meta.xml file is included as well. See gldp_to_eml() to create an eml.xml file.

Usage

gldp_to_dwc(package, directory, path_type = "most_likely")

Arguments

package

A GeoLocator Data Package object.

directory

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

path_type

The type of path to use for the occurrence data. One of "most_likely", "mean_simulation", "median_simulation", or "geopressureviz". For simulation types, the mean or median position (lat/lon) is calculated for each tag_id-stap_id combination across all simulated paths. Defaults to "most_likely". See paths for more details.

Value

occurrence.csv file written to disk. Invisibly, an occurrence data frame.

Transformation details

Data are transformed into an Occurrence core. This transformation combines data from three resources:

  • tags: metadata about the device and deployment

  • staps: stationary periods with temporal information

  • paths: spatial positions estimated for each stationary period

The following terms are set from the package metadata:

  • datasetName: Title as provided in package$title.

  • datasetID: Identifier as provided in package$id.

  • rightsHolder: Rights holder as provided in package$contributors (contributor with "rightsHolder" role). If no rightsHolder role is found, this field will be NA.

  • license: License name as provided in package$licenses.

Key features of the Darwin Core transformation:

  • Stationary periods (staps) are treated as events, with each position as an occurrence representing the bird's location during that period.

  • Each occurrence represents one stationary period from the path data, filtered by path_type.

  • The eventDate is expressed as an ISO 8601 interval (start/end) representing the duration of the stationary period.

  • basisOfRecord is set to "MachineObservation" as data are derived from automated geolocator sensors.

  • samplingProtocol is set to "geolocator".

  • geodeticDatum is "EPSG:4326" (WGS84).

  • scientificName is taken from tags$scientific_name.

  • organismID is set to ring_number to track individual birds across multiple observations and deployments.

  • occurrenceID is a unique identifier combining tag_id and stap_id.

  • individualCount is set to 1.

  • occurrenceStatus is set to "present".

  • sex and lifeStage are included if available in the tags resource.

  • coordinateUncertaintyInMeters is calculated for simulation path types ("mean_simulation" or "median_simulation") as the 95th percentile of the distance between each simulation and the aggregated center.