Reproducible Research in Computational Ecology

FRB-CESAB & GdR EcoStat training course


November 24, 2023


Registrations for the 2024 session are not yet open

Registrations open each spring and the training course takes place during winter.

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The objective of this five-day training course, 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.


  • Open science & Reproducible research
  • Project organization & Good practices
  • Version control w/ Git (Part I)
  • Version control w/ Git (Part II)
  • Collaboration & sharing w/ GitHub
  • Literate programming w/ Quarto
  • Pipeline optimization w/ targets
  • Developing an package
  • Freezing package versions w/ renv
  • Containerization w/ Docker
  • Subgroups projects
  • Subgroups projects


  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).


All the material used in this training course (slides, data, exercises) is available at:


Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2023) FRB-CESAB & GdR EcoStat training course: Reproducible Research in Computational Ecology. Zenodo. URL:


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


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: