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 (2023) 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.

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