Red lists of Flanders, Belgium

Rationale

This repository contains the functionality to standardize two checklists - the Validated red lists of Flanders, Belgium and the Non-validated red lists of Flanders, Belgium - to Darwin Core checklists that can be harvested by GBIF. The repository also contains some miscellaneous scripts.

Workflow

The source data is an Access database managed by Dirk Maes containing all published red lists for Flanders (see included validated and non-validated red lists). A taxon can appear on multiple red lists. The data are split into two datasets, depending on the type of red list:

  • Validated red lists: Contains information from red lists that are considered validated, i.e. which used quantitative criteria and a representative sample of occurrences across all ecological regions in Flanders for red list assessment. The database also contains life-history traits for these (biome, biotope, cuddliness, lifespan, mobility, nutrient level, spine) which have been included in the description extension.

    source data (exported from Access) → Darwin Core mapping script → generated Darwin Core files

  • Non-validated red lists: Contains information from red lists that are considered non-validated, i.e. which did not use the above criteria.

    source data (exported from Access, same file) → Darwin Core mapping script → generated Darwin Core files

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
├── rl-flanders-checklist.Rproj : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
│
├── data
│   ├── raw                : Source data, input for mapping scripts 1 and 2
│   └── processed
│       ├── validated      : Darwin Core output of mapping script 1 GENERATED
│       └── nonvalidated   : Darwin Core output of mapping script 2 GENERATED
│
├── docs                   : Repository website GENERATED
│
└── src
    ├── dwc_mapping_validated.Rmd : Darwin Core mapping script 1 (for validated red lists)
    ├── dwc_mapping_nonvalidated.Rmd : Darwin Core mapping script 2 (for non-validated red lists)
    ├── _site.yml          : Settings to build website in docs/
    └── index.Rmd          : Template for website homepage

Installation

  1. Clone this repository to your computer
  2. Open the RStudio project file
  3. Open the dwc_mapping_validated.Rmd or dwc_mapping_nonvalidated.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/

Contributors

List of contributors

License

MIT License