trias-project / 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 Archive 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
│
├── src
│   ├── dwc_mapping.Rmd    : Darwin Core mapping script
│   ├── _site.yml          : Settings to build website in docs/
│   └── index.Rmd          : Template for website homepage
│
├── docs                   : Repository website GENERATED
│
└── data
    ├── raw                : Source data, input for mapping script
    └── processed          : Darwin Core output of mapping script 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.