Alien macroinvertebrates

Rationale

This repository contains the functionality to standardize the data of Boets et al. (2016) to both a Darwin Core checklist and Darwin Core occurrence dataset that can be harvested by GBIF. The repository also contains the code for a website to explore the occurrence data. It was developed for the TrIAS project.

Workflow

• Checklist dataset: source data → Darwin Core mapping script → generated Darwin Core files
• Occurrence dataset: source data → Darwin Core mapping script → generated Darwin Core files

Published datasets

• Checklist dataset on the IPT
• Checklist dataset on GBIF

---

• Occurrence dataset on the IPT
• Occurrence dataset on GBIF

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
├── alien-macroinvertebrates.Rproj : RStudio project file
├── .gitignore        : Files and directories to be ignored by git
│
├── data
│   ├── raw           : Source data, input for mapping script
│   └── processed     : Darwin Core output of mapping script GENERATED
│
├── docs              : Repository website GENERATED
│
├── specifications    : Data specifications for the Darwin Core files
│
└── src
    ├── dwc_checklist.Rmd  : Darwin Core mapping script for checklist dataset
    ├── dwc_occurrence.Rmd : Darwin Core mapping script for occurrence dataset
    ├── _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_checklist.Rmd or dwc_occurrence.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