elodea - R package to validate checklists of alien species from GBIF

Presentation given during the OneSTOP datathon in Brussels on 27 November 2025.

Transcript

1. Sanne Govaert 0000-0002-8939-1305 elodea OneSTOP Datathon - Brussels, Belgium R package to validate checklists of alien species from GBIF 27 November 2025
2. https://github.com/onestop-project/elodea remotes::install_github(“onestop-projec t/elodea”) To clean and standardise published GBIF checklists. Named after invasive Elodea (waterweed) species. elodea Photo by Christian Fischer - CC BY-SA 3.0
3. 1) get_taxa() Usage get_taxa(datasetKey) Taxa details get_taxa() returns a tibble with 8 variables. Example output
4. 2) get_distributions() Usage get_distributions(datasetKey, taxa = get_taxa(datasetKey)) Distributions details get_distributions() returns a tibble with 8 variables. Example output
5. 3) filter_data() Usage filter_data(taxa, distributions) Output A list with three data frames: • taxa: Filtered taxa data frame. • distributions: Filtered distributions data frame, with extra column nubKey (GBIF backbone taxon key). • notes: Data frame with notes on taxa that were not included or replaced in the filtered data.
6. 3) filter_data() Filter details Taxa are removed if • they are not matched with the GBIF backbone (i.e., nubKey is NA), • they do not have a matching distribution (i.e., taxonKey is not in distributions$taxonKey), • they are synonyms of accepted taxa (i.e., acceptedKey is not NA), • they do not have a matching distribution with establishmentMeans == introduced. scientificName is replaced with the scientific name matching the GBIF backbone.
7. notes.csv
8. notes.csv nubkey was missing: not_matched_with_backbone
9. notes.csv synonym of accepted taxa: merged_with_accepted
10. notes.csv Different scientific name matching the GBIF backbone: scientficName_replaced_by_backbone_name
11. unified-europe https://github.com/onestop-project/unified-europe 1) Download data 2) Filter data 3) Unify (merge) data Processed data: https://github.com/onestop-project/unified-europe/tree/initiation/data/processed
12. unified-europe Current result: - taxon.csv with 9.977 rows - distributions.csv with 18.319 rows
13. Questions, ideas, remarks?
14. Sanne Govaert sanne.govaert@inbo.be https://bit.ly/onestop-elodea Photo by Sanne Govaert Thank you!