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Standardizing biodiversity data to Darwin Core can be hard. 😅 Templates and the GBIF Integrated Publishing Toolkit facilitates standardization, but only caters for the most basic use cases.
To solve this, we have developed a template GitHub repository for standardizing thematic species checklist data to Darwin Core using R. This checklist recipe contains all the ingredients to make your data standardization open, repeatable, customizable and documented. The core functionality is an R Markdown file that makes use of the widely adopted tidyverse R packages to automatically transform a source data file to a Darwin Core checklist. Any user with a basic knowledge of R can customize the code to their own needs and explain specific data mapping decisions. In combination this makes the standardization process repeatable and transparent.
Our recipe is based on experience we gained by publishing checklist data for the TrIAS project. We hope it helps you standardize and publish your own checklist. Happy cooking!
- Introduction video created for the 2018 Ebbe Nielsen Challenge.
- Announcement of the checklist recipe winning the 2018 Ebbe Nielsen Challenge.
- Blog post written for the rOpenSci blog, highlighting some of the techniques and tools we used for the recipe.
Reyserhove L, Oldoni D, Desmet P (2018) Checklist recipe: a template for reproducible standardization of species checklist data. https://github.com/trias-project/checklist-recipe/wiki
Content in this wiki is licensed under the Creative Commons Attribution 4.0 International License.
- Home
- Getting started
- Basics
- Ingredients: Source data
- Instructions: R Markdown
- Utensils: Tidyverse functions
- Dinner: Darwin Core data
- Mapping script
- Data preparation
- Mapping
- GitHub
- Publishing data
- Examples