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The FRB in action
Since 2019
Best practice for reproducible research in computational ecology
Version control, reproducibility, research compendium and containerization
The objective of this five-day course, co-organized with the GDR EcoStat, is to train young researchers in reproducibility, software development and version management tools (Git, GitHub, Quarto, renv and Docker), applied to biodiversity research.
This course is delivered in French and takes place in December at CESAB’s premises in Montpellier. The fee is 250 € for the week, including lunch. Travel, accommodation, and evening meal costs are the responsibility of the participants.
Proficiency in R software is required.
List of speakers:
- Iago BONNICI (CNRS ISEM)
- Nicolas CASAJUS (FRB-Cesab)
- François GUILHAUMON (IRD Entropie)
- Aurélie SIBERCHICOT (UCBL LBBE)
Former speakers:
- Stéphane DRAY (CNRS LBBE)
- Olivier GIMENEZ (CNRS CEFE)
- Loreleï GUERY (CIRAD PHIM)
- Nina SCHIETTEKATTE (EPHE CRIOBE)
Sample program
The training will focus on lessons and exercises during the first three and a half days, with small-group projects scheduled for the final day and a half.
Monday
- Icebreaker & presentation of the week
- Open science & Reproducible research
- Project organization & Good practices
- Version control with git
Tuesday
- Version control with git (continued)
- Collaboration & sharing with GitHub
Wednesday
- Literate programming with Quarto
- Pipeline optimization with targets
- Developing an R package
Thursday
- Freezing package versions with renv
- Containerization with Docker
- Subgroup projects
Friday
- Subgroup projects
- Subgroup projects presentation
Training course history
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