Build shareable biodiversity datasets

corella is for data preparation, editing and checking of data to follow the Darwin Core Standard, a global data standard to store, document, and share biodiversity information. The package provides tools to manipulate data to conform with, and check validity against, the Darwin Core Standard. Using corella will allow users to verify that their data can be used to build 'Darwin Core Archives' using the galaxias package.

The package is named for a genus of Australian birds. The logo image is of the Little Corella (Cacatua sanguinea), and was designed by Dax Kellie.

Functions

Suggest where to start

• suggest_workflow() for a summary of what column names match Darwin Core terms in your data, and a workflow for adding or editing more.

Add Darwin Core Terms

The following functions add single DwC fields, or collections of related fields, to an existing tibble.

• set_events() basic information on observation events (eventID, parentEventID, eventType)

• set_occurrences() basic information on observations (occurrenceID, basisOfRecord, occurrencesStatus)

• set_scientific_name() record the highest level of taxonomic specificity in the dataset (scientificName, scientificNameAuthorship, taxonRank)

• set_taxonomy() to specify higher taxonomic columns (kingdom, phylum, class, order, family, genus, species, specificEpithet, vernacularName)

• set_coordinates() for spatial data (decimalLatitude, decimalLongitude, geodeticDatum, coordinateUncertaintyInMeters, coordinatePrecision)

• set_coordinates_sf() for spatial data in sf format

• set_locality() for spatial descriptions (continent, country, countryCode, stateProvince, locality)

• set_datetime() for temporal data (eventDate, year, month, day, eventTime)

• set_collection() to give museum- or collection- specific information (datasetID, datasetName, catalogNumber)

• set_observer() to specify who made the observation (recordedByID, recordedBy)

• set_abundance() to state how many animals were seen during the observation (individualCount, organismQuantity, organismQuantityType)

• set_individual_traits() attributes of individuals measured (individualID, lifeStage, sex, vitality, reproductiveCondition)

• set_license() to specify license and rights information (license, rightsHolder, accessRights)

• set_measurements() for measurement columns, i.e. 'Measurement or Fact' data (optional)

Check data for Darwin Core compliance

The wrapper function for checking tibbles for Darwin Core compliance is check_dataset(). It calls all internal check functions for checking data in columns with matching Darwin Core terms.

Helper functions

These functions are called within use_ (or mutate() functions), and assist in common problems.

• composite_id() Supply a combination of variables to concatenate into a unique identifier, optionally incorporating sequential_id() or random_id().

• occurrence_terms() and event_terms() return a vector of accepted terms for different use cases.

• basisOfRecord_values() and countryCode_values() return a vector of accepted values for basisOfRecord and countryCode (respectively)

Data

Datasets to support usage of Darwin Core.

• darwin_core_terms A tibble of accepted terms, including URIs and usage notes

• country_codes A tibble of codes accepted by countryCode

References

If you have any questions, comments or suggestions, please email support@ala.org.au.

See also

Useful links:

• https://corella.ala.org.au

• Report bugs at https://github.com/AtlasOfLivingAustralia/corella/issues

Author

Maintainer: Dax Kellie dax.kellie@csiro.au

Authors:

• Shandiya Balasubramanium shandiya.balasubramanium@csiro.au

• Martin Westgate martin.westgate@csiro.au