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index.qmd
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index.qmd
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---
toc: true
---
# Welcome {.unnumbered}
::: {.callout-note}
## Registrations for the 2024 session are not yet open
Registrations open each spring and the training course takes place during winter.
{{< fa hand-point-right >}} Subscribe to the
[FRB-CESAB newsletter](https://www.fondationbiodiversite.fr/en/newsletter/)
to stay informed. More information is available on the [FRB-CESAB website](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/develop-skills/best-practice-for-reproducible-research-in-computational-ecology/).
:::
The objective of this five-day training course, co-organized by the
[FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/)
and the
[GdR EcoStat](https://sites.google.com/site/gdrecostat/),
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 {.unnumbered}
+---------------+-----------------------------------------------------+
| **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 {{< fa brands r-project >}} package |
+---------------+-----------------------------------------------------+
| **Thursday** | - Freezing package versions w/ `renv` |
| | - Containerization w/ `Docker` |
| | - Subgroups projects |
+---------------+-----------------------------------------------------+
| **Friday** | - Subgroups projects |
+---------------+-----------------------------------------------------+
## Prerequisites {.unnumbered}
{{< fa hand-point-right >}} Please follow this [tutorial](https://frbcesab.github.io/rsetup/) to install
your working environment **before attending the training course**.
{{< fa hand-point-right >}} You also need to create an account on [GitHub](https://github.com/signup/) (please edit your profile and enter your name).
## Material {.unnumbered}
All the material used in this training course (slides, data, exercises) is available at: <https://github.com/rdatatoolbox/>
## Citation {.unnumbered}
> 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 {.unnumbered}
If you see mistakes or want to suggest changes, please [create an issue](https://github.com/rdatatoolbox/rdatatoolbox.github.io/issues/new) on the source repository.
## Reuse {.unnumbered}
Text and figures are licensed under Creative Commons Attribution [CC By 4.0](https://creativecommons.org/licenses/by/4.0/), unless otherwise noted.
## See also {.unnumbered}
Discover the other training courses provided by the FRB-CESAB and its partners: <https://frbcesab.github.io/training-courses/>