Reproducible Research in Computational Ecology
FRB-CESAB & RT EcoStat Training Course
Welcome
Registrations open each spring and the training course takes place during the fall.
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The objective of this five-day training course, co-organized by the FRB-CESAB and the RT EcoStat, is to train researchers in reproducibility, software development and version control tools (e.g. git, GitHub, Quarto, renv & Docker), applied to biodiversity research.
Program
MONDAY - Open science, Research compendium, Functions & Packages
Welcome & Opening remarks
Open science & Reproducible research
Coffee break
Introduction to Positron IDE
Organizing your project as a Research compendium
Hands-on session: Building my first research compendium
Lunch break
Refactoring scripts into R Functions
Hands-on session: Refactoring the research compendium scripts into functions
The DESCRIPTION file
Hands-on session: Adding a DESCRIPTION file to your research compendium
Coffee break
Developing an R Package
TUESDAY - Version control & targets
Introduction to git – Part 1: Initialization & Commits
Hands-on session: Initializing and using git in your research compendium
Coffee break
Introduction to git – Part 2: Pushing to GitHub
Hands-on session: Publishing your research compendium on GitHub
Lunch break
Optimizing your workflow with {targets}
Coffee break
Hands-on session: Integrating {targets} into your research compendium
WEDNESDAY - Version control, GitHub & Quarto
Introduction to git – Part 3: Collaboration and Conflict resolution
Coffee break
Hands-on session: Collaborating on the same project
Lunch break
Code hosting platforms: GitHub, GitLab & Codeberg
Literate programming with Quarto
Coffee break
Hands-on session: Adding Quarto to your research compendium
THURSDAY - renv, Docker & Group projects
Managing packages and their versions with {renv}
Hands-on session: Adding {renv} to your research compendium
Coffee break
Containerizing your project with Docker
Week recap and formation of project groups
Lunch break
Group projects
FRIDAY - Group projects
Group projects
Lunch break
Group project presentations
Prerequisites
Please follow this tutorial to install your working environment before attending the training course.
You also need to create an account on GitHub (please edit your profile and enter your name).
Material
All the material used in this training course (slides, data, exercises) is available at: https://github.com/rdatatoolbox/
Citation
Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2026) FRB-CESAB & RT EcoStat Training Course: Reproducible Research in Computational Ecology. Zenodo. URL: http://doi.org/10.5281/zenodo.4262978
Contributions
If you see mistakes or want to suggest changes, please create an issue on the source repository.
Reuse
Text and figures are licensed under Creative Commons Attribution CC BY 4.0, unless otherwise noted.
See also
Discover the other training courses provided by the FRB-CESAB and its partners: https://frbcesab.github.io/training-courses/