rdatatoolbox.github.io/index.qmd at main · rdatatoolbox/rdatatoolbox.github.io · GitHub

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---
toc: true
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# Welcome {.unnumbered}

::: {.callout-note}
## Registrations to the training course

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

{{< fa hand-point-right >}}&nbsp; 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 researchers in reproducibility, software development and
version control tools (e.g. `git`, `GitHub`, `Quarto`, `renv` & `Docker`),
applied to biodiversity research.


## Program {.unnumbered}

**Monday**

- Open science & Reproducible research
- **_Research compendium_** (i.e. project organisation)
- Writing & documenting {{< fa brands r-project >}} functions
- The `DESCRIPTION` file

**Tuesday**

- Version control w/ `git`
- Collaboration & sharing w/ `GitHub`

**Wednesday**

- Literate programming w/ `Quarto`
- Pipeline optimisation 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 >}}&nbsp; Please follow this [tutorial](https://frbcesab.github.io/rsetup/) to install
your working environment **before attending the training course**.

{{< fa hand-point-right >}}&nbsp; 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 (2025)
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/>