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https://github.com/inbo/rl-flanders-checklist
Red lists of Flanders, Belgium
https://github.com/inbo/rl-flanders-checklist
dataset gbif open-data oscibio r rstats
Last synced: 3 months ago
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Red lists of Flanders, Belgium
- Host: GitHub
- URL: https://github.com/inbo/rl-flanders-checklist
- Owner: inbo
- License: mit
- Created: 2018-05-24T07:22:57.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-08-22T13:13:27.000Z (6 months ago)
- Last Synced: 2024-08-23T14:29:00.048Z (6 months ago)
- Topics: dataset, gbif, open-data, oscibio, r, rstats
- Language: R
- Homepage: https://inbo.github.io/rl-flanders-checklist/
- Size: 6.54 MB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](https://www.gbif.org/dataset-classes) that can be harvested by [GBIF](http://www.gbif.org). The repository also contains some miscellaneous scripts.
## Workflow
The source data is an Access database managed by [Dirk Maes](https://orcid.org/0000-0002-7947-3788) containing **all published red lists for Flanders** (see included [validated](https://inbo.github.io/rl-flanders-checklist/dwc_mapping_validated.html#35_preview_data) and [non-validated](https://inbo.github.io/rl-flanders-checklist/dwc_mapping_nonvalidated.html#35_preview_data) 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](https://github.com/inbo/rl-flanders-checklist/blob/master/data/raw) (exported from Access) → Darwin Core [mapping script](https://inbo.github.io/rl-flanders-checklist/dwc_mapping_validated.html) → generated [Darwin Core files](https://github.com/inbo/rl-flanders-checklist/blob/master/data/processed/validated)
* **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](https://github.com/inbo/rl-flanders-checklist/blob/master/data/raw) (exported from Access, same file) → Darwin Core [mapping script](https://inbo.github.io/rl-flanders-checklist/dwc_mapping_nonvalidated.html) → generated [Darwin Core files](https://github.com/inbo/rl-flanders-checklist/blob/master/data/processed/nonvalidated)
## Published datasets
* [Validated red lists on the IPT](https://ipt.inbo.be/resource?r=rl-flanders-validated-checklist)
* [Validated red lists on GBIF](https://doi.org/10.15468/8tk3tk)
---
* [Non-validated red list on the IPT](https://ipt.inbo.be/resource?r=rl-flanders-nonvalidated-checklist)
* [Non-validated red lists on GBIF](https://doi.org/10.15468/54nwog)
## Repo structure
The repository structure is based on [Cookiecutter Data Science](http://drivendata.github.io/cookiecutter-data-science/) and the [Checklist recipe](https://github.com/trias-project/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](https://rmarkdown.rstudio.com/) 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](https://github.com/inbo/rl-flanders-checklist/contributors)
## License
[MIT License](https://github.com/inbo/rl-flanders-checklist/blob/master/LICENSE)