Data Toolbox for Reproducible Research in Ecology

FRB-CESAB & GdR EcoStat Workshop

Nicolas Casajus (FRB-CESAB) , Iago Bonnici (CNRS ISEM) , Stéphane Dray (CNRS LBBE) , Olivier Gimenez (CNRS CEFE) , Loreleï Guéry (CIRAD PHIM) , François Guilhaumon (IRD ENTROPIE) , Nina Schiettekatte (EPHE CRIOBE) , Aurélie Siberchicot (UCBL LBBE)

The objective of this five-day workshop, co-organized by the FRB-CESAB and the GdR EcoStat, is to train young researchers in reproducibility, software development and version management tools (e.g. Git, GitHub, R Markdown, Quarto, renv, Docker), applied to biodiversity research.

More information available here


Day 1

       Icebreaker and introduction of the week
       Open science and Reproducible research
       Research compendium & Good practices
       Version control with Git & GitHub

Day 2

       Basics of R Markdown
       Extending R Markdown: websites, slides and dashboards
       Introduction to Quarto
       Pipeline toolkit with targets

Day 3

       Dealing with R package versions with renv
       Containerization with Docker
       Building an R package

Day 4

       Subgroups projects

Day 5

       Subgroups projects
       Projects presentation


The following software must be installed before the workshop: R (latest version), RStudio et Git. Follow this tutorial to install your working environment.

You also need to create an account (free) on GitHub.


If you see mistakes or want to suggest changes, please Create an issue on the source repository.


The material of this website is licensed under Creative Commons Attribution CC BY 4.0. Source code is available at


Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2022) Workshop FRB-CESAB & GdR EcoStat: Data Toolbox for Reproducible Research in Computational Ecology. Zenodo.