Transform a GeoLocator Data Package to Darwin Core

Transforms a GeoLocator Data Package (GLDP) 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(pkg, directory)

pkg: 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().

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

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

The following terms are set from normalized package metadata (sourced from top-level package fields):

datasetName: Package title.
datasetID: Package identifier (DOI/ID).
rightsHolder: Rights holder as provided in contributors (contributor with "rightsHolder" role). If no rightsHolder role is found, this field will be NA.
license: License name.

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 most_likely path reconstruction.
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$scientific_name.
organismID is set to ring_number to track individual birds across multiple observations and deployments.
organismName is set to ring_number as the available label for the tracked individual.
occurrenceID is a unique identifier combining tag_id and stap_id.
occurrenceStatus is set to "present".
sex, lifeStage, and eventRemarks are included from matching observations when available.
minimumElevationInMeters and maximumElevationInMeters are estimated from pressurepaths$altitude when available.
coordinateUncertaintyInMeters is calculated as the 50th percentile of the distance between simulation paths and the most_likely position for each stationary period.