Generate taxon keys for LIFE RIPARIAS early alert tool

Rationale

This repository contains the functionality to get the GBIF taxon keys to be used by the LIFE RIPARIAS early alert tool. The source taxa are retrieved from the followin GBIF checklists:

1. the LIFE RIPARIAS target species list

Upcoming lists to be added:

• the List of Invasive Alien Species of Union concern
• the DVW (De Vlaamse Waterweg) target species list (still to be published)

Workflow

1. read species list as exported from the LIFE RIPARIAS early alert tool: typically the most recent export is used
2. read and combine taxonomic information from both checklists and GBIF Backbone
3. Save the names and the GBIF taxon keys we should use in the early alert tool
4. Check that the exported names and taxon keys in 1 are identical the ones in 3

Repo structure

The repository structure is based on Cookiecutter Data Science and the Checklist recipe. Files and directories indicated with GENERATED should not be edited manually.

├── README.md              : Description of this repository
├── LICENSE                : Repository license
├── taxon-keys-early-alert.Rproj : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
├── .github
│   └── workflows          : GitHub actions to periodically run the check in ./src
│
├── src
│   └── retrieve_compare_taxon_keys.Rmd   : Check taxonomic info script
│
└── data
    ├── reference          : LIFE RIPARIAS early alert species list export
    └── processed          : names and GBIF taxon keys to be used in early alert tool GENERATED

Installation

1. Click on Use this template to create a new repository on your account
2. Open the RStudio project file
3. Open the dwc_mapping.Rmd R Markdown file in RStudio
4. Install any required packages
5. Click Run > Run All to generate the processed data
6. Alternatively, click Build > Build website to generate the processed data and build the website in docs/ (advanced)

Contributors

List of contributors

License

MIT License for the code and documentation in this repository. The included data is released under another license.