melecoq / checklist-recipe

Template repository for standardizing thematic species checklist data to Darwin Core using R

Checklist recipe

👩🏻‍🍳 This is a template repository for standardizing thematic species checklist data to Darwin Core using R. As a result, the rest of the README is a template as well. To use this repository for your own checklist data, read the recipe. Happy cooking!

Rationale

This repository contains the functionality to standardize the data of to a Darwin Core checklist that can be harvested by GBIF.

Workflow

source data → Darwin Core mapping script → generated Darwin Core files

Published dataset

• Dataset on the IPT
• 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
├── checklist-recipe.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
│
└── src
    ├── dwc_mapping.Rmd    : Darwin Core mapping script, core functionality of this repository
    ├── _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.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.