Reproducible Research in Computational Ecology

FRB-CESAB & GdR EcoStat training course

Published

November 20, 2024

Welcome

Registrations for the 2024 session are closed

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

  Subscribe to the FRB-CESAB newsletter to stay informed. More information is available on the FRB-CESAB website.

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.

Program

Monday

  • Open science & Reproducible research
  • Project organization & Good practices
  • Version control w/ Git (Part I)

Tuesday

  • Version control w/ Git (Part II)
  • Collaboration & sharing w/ GitHub

Wednesday

  • Literate programming w/ Quarto
  • Pipeline optimization w/ targets
  • Developing an package

Thursday

  • Freezing package versions w/ renv
  • Containerization w/ Docker
  • Subgroups projects

Friday

  • Subgroups projects

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 (2024) FRB-CESAB & GdR 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/