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Transform Movebank data to a Darwin Core Archive

Source: R/write_dwc.R
write_dwc.Rd

Transforms a Movebank dataset (formatted as a Frictionless Data Package) to a Darwin Core Archive.

Usage

write_dwc(
  package,
  directory,
  dataset_id = package$id,
  dataset_name = package$title,
  license = NULL,
  rights_holder = NULL
)

Arguments

package

A Frictionless Data Package of Movebank data, as returned by read_package(). It is expected to contain a reference-data and gps resource.

directory

Path to local directory to write files to.

dataset_id

Identifier for the dataset.

dataset_name

Title of the dataset.

license

License of the dataset.

rights_holder

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

Value

CSV and meta.xml files written to disk. And invisibly, a list of data frames with the transformed data.

Details

The resulting files can be uploaded to an IPT for publication to GBIF and/or OBIS. A corresponding eml.xml metadata file can be created with write_eml(). See vignette("movepub") for an example.

Transformation details

This function follows recommendations suggested by Peter Desmet, Sarah Davidson, John Wieczorek and others and transforms data to:

Key features of the Darwin Core transformation:

  • Deployments (animal+tag associations) are parent events, with tag attachment (a human observation) and GPS positions (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 tag attachment event often contains metadata about the animal (sex, life stage, comments) and deployment as a whole. The sex and life stage are additionally provided in an Extended Measurement Or Facts extension, where values are mapped to a controlled vocabulary recommended by OBIS.

  • No event/occurrence is created for the deployment end, since the end date is often undefined, unreliable and/or does not represent an animal occurrence.

  • Only visible (non-outlier) GPS records that fall within a deployment are included.

  • GPS positions are downsampled to the first GPS position per hour, to reduce the size of high-frequency data. It is possible for a deployment to contain no GPS positions, e.g. if the tag malfunctioned right after deployment.

  • Parameters or metadata are used to set the following record-level terms:

    • dwc:datasetID: dataset_id, defaulting to package$id.

    • dwc:datasetName: dataset_name, defaulting to package$title.

    • dcterms:license: license, defaulting to the first license name (e.g. CC0-1.0) in package$licenses.

    • dcterms:rightsHolder: rights_holder, defaulting to the first contributor in package$contributors with role rightsHolder.

See also

Other dwc functions: write_eml()

Examples

write_dwc(o_assen, directory = "my_directory")
#> 
#> ── Reading data ──
#> 
#> ℹ Taxa found in reference data and their WoRMS AphiaID:
#> Haematopus ostralegus: 147436
#> (<https://www.marinespecies.org/aphia.php?p=taxdetails&id=147436>)
#> 
#> ── Transforming data to Darwin Core ──
#> 
#> ── Writing files ──
#> 
#> • my_directory/occurrence.csv
#> • my_directory/meta.xml
#> • my_directory/emof.csv

# Clean up (don't do this if you want to keep your files)
unlink("my_directory", recursive = TRUE)