update date & add new chapters

ahasverus · ahasverus · commit b2f13f3cc1d8 · 2025-11-29T09:25:07.000+01:00
diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ and the
 ### Citation
 
 > Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD 
-& Siberchicot A (2023) 
+& Siberchicot A (2025) 
 FRB-CESAB & GdR EcoStat training course: Reproducible Research in Computational Ecology. 
 Zenodo. URL: <http://doi.org/10.5281/zenodo.4262978>
 
@@ -27,4 +27,4 @@ Zenodo. URL: <http://doi.org/10.5281/zenodo.4262978>
 
 Website built with :heart: with 
 [`Quarto`](https://quarto.org/) & 
-[`GitHub Actions`](https://github.com/features/actions).
+[`GitHub Actions`](https://github.com/features/actions).
diff --git a/_quarto.yml b/_quarto.yml
@@ -69,7 +69,7 @@ book:
     collapse-level: 1
 
   page-footer: 
-    left: "&copy; CC-By [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/)"
+    left: "&copy; CC BY 4.0 [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/)"
     center: "Code source available on [{{< fa brands github >}}](https://github.com/rdatatoolbox/rdatatoolbox.github.io/)"
     right: "Built with [Quarto](https://quarto.org/)"
     border: true
@@ -79,11 +79,13 @@ book:
   
   chapters:
     - index.qmd
-    - chapters/setting-up-r.qmd
+    # - chapters/setting-up-r.qmd
     - part: "Courses"
       chapters: 
         - chapters/course-opensci.qmd
         - chapters/course-compendium.qmd
+        - chapters/course-functions.qmd
+        - chapters/course-description.qmd
         - chapters/course-git.qmd
         - chapters/course-github.qmd
         - chapters/course-quarto.qmd
diff --git a/chapters/course-compendium.qmd b/chapters/course-compendium.qmd
@@ -1,4 +1,4 @@
-## Research compendium {.unnumbered}
+## Research compendium
 
 
 ::: {.callout-note icon=true appearance="simple"}
diff --git a/chapters/course-description.qmd b/chapters/course-description.qmd
@@ -0,0 +1,18 @@
+## The `DESCRIPTION` file
+
+
+::: {.callout-note icon=true appearance="simple"}
+## The `DESCRIPTION` file
+
+<br />
+{{< fa user >}} &nbsp;**Author:** [Nicolas Casajus](https://nicolascasajus.fr/)<br/>
+{{< fa brands github >}} &nbsp;**Source:** <https://github.com/rdatatoolbox/description-file/><br/>
+{{< fa globe >}} &nbsp;**Slides:** <https://rdatatoolbox.github.io/description-file/>
+:::
+
+
+<br />
+
+<div class="container">
+  <iframe class="responsive-iframe" src="https://rdatatoolbox.github.io/description-file"></iframe>
+</div> 
diff --git a/chapters/course-docker.qmd b/chapters/course-docker.qmd
@@ -1,4 +1,4 @@
-## Containerization w/ `Docker` {.unnumbered}
+## Containerization
 
 
 ::: {.callout-note icon=true appearance="simple"}
diff --git a/chapters/course-functions.qmd b/chapters/course-functions.qmd
@@ -0,0 +1,18 @@
+## Writing **R** functions
+
+
+::: {.callout-note icon=true appearance="simple"}
+## Writing & documenting {{< fa brands r-project >}}&nbsp; functions
+
+<br />
+{{< fa user >}} &nbsp;**Author:** [Nicolas Casajus](https://nicolascasajus.fr/)<br/>
+{{< fa brands github >}} &nbsp;**Source:** <https://github.com/rdatatoolbox/r-functions/><br/>
+{{< fa globe >}} &nbsp;**Slides:** <https://rdatatoolbox.github.io/r-functions/>
+:::
+
+
+<br />
+
+<div class="container">
+  <iframe class="responsive-iframe" src="https://rdatatoolbox.github.io/r-functions"></iframe>
+</div> 
diff --git a/chapters/course-git.qmd b/chapters/course-git.qmd
@@ -1,4 +1,4 @@
-## Version control w/ `git` {.unnumbered}
+## Version control w/ `git`
 
 
 ::: {.callout-note icon=true appearance="simple"}
diff --git a/chapters/course-github.qmd b/chapters/course-github.qmd
@@ -1,4 +1,4 @@
-## Introduction to `GitHub` {.unnumbered}
+## Introduction to `GitHub`
 
 
 ::: {.callout-note icon=true appearance="simple"}
diff --git a/chapters/course-opensci.qmd b/chapters/course-opensci.qmd
@@ -1,4 +1,4 @@
-## Reproducible research {.unnumbered}
+## Reproducible research
 
 
 ::: {.callout-note icon=true appearance="simple"}
diff --git a/chapters/course-package.qmd b/chapters/course-package.qmd
@@ -1,8 +1,8 @@
-## Building an R package {.unnumbered}
+## Building an **R** package
 
 
 ::: {.callout-note icon=true appearance="simple"}
-## An introduction how on to create an R package
+## An introduction how on to create an {{< fa brands r-project >}}&nbsp; package
 
 <br />
 {{< fa user >}} &nbsp;**Authors:** [Aurélie Siberchicot](https://lbbe.univ-lyon1.fr/fr/annuaires-des-membres/siberchicot-aurelie) & [Nicolas Casajus](https://nicolascasajus.fr/)<br/>
diff --git a/chapters/course-quarto.qmd b/chapters/course-quarto.qmd
@@ -1,8 +1,8 @@
-## Literate programming w/ `Quarto` {.unnumbered}
+## Literate programming
 
 
 ::: {.callout-note icon=true appearance="simple"}
-## An introduction to literate programming w/ `Quarto` (and `R Markdown`)
+## An introduction to literate programming w/ `Quarto`
 
 <br />
 {{< fa user >}} &nbsp;**Authors:** [François Guillaumon](https://fguilhaumon.gitlab.io/)<br/>
diff --git a/chapters/course-renv.qmd b/chapters/course-renv.qmd
@@ -1,8 +1,8 @@
-## Virtual environments w/ `renv` {.unnumbered}
+## Virtual environments
 
 
 ::: {.callout-note icon=true appearance="simple"}
-## An introduction to `renv`: dealing with R package versions
+## An introduction to `renv`: Dealing with {{< fa brands r-project >}}&nbsp; package versions
 
 <br />
 {{< fa user >}} &nbsp;**Author:** [Nicolas Casajus](https://nicolascasajus.fr/)<br/>
diff --git a/chapters/course-targets.qmd b/chapters/course-targets.qmd
@@ -1,4 +1,4 @@
-## Pipeline toolkits w/ `targets` {.unnumbered}
+## Introduction to `targets`
 
 
 ::: {.callout-note icon=true appearance="simple"}
diff --git a/index.qmd b/index.qmd
@@ -5,7 +5,7 @@ toc: true
 # Welcome {.unnumbered}
 
 ::: {.callout-note}
-## Registrations for the 2024 session are closed
+## Registrations to the training course
 
 Registrations open each spring and the training course takes place during the fall. 
 
@@ -20,8 +20,8 @@ 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`), 
+is to train researchers in reproducibility, software development and 
+version control tools (e.g. `git`, `GitHub`, `Quarto`, `renv` & `Docker`), 
 applied to biodiversity research.
 
 
@@ -30,18 +30,19 @@ applied to biodiversity research.
 **Monday**
 
 - Open science & Reproducible research
-- Project organization & Good practices
-- Version control w/ `Git` (Part I)
+- **_Research compendium_** (i.e. project organisation)
+- Writing & documenting {{< fa brands r-project >}} functions
+- The `DESCRIPTION` file
 
 **Tuesday**
 
-- Version control w/ `Git` (Part II)
+- Version control w/ `git`
 - Collaboration & sharing w/ `GitHub`
 
 **Wednesday**
 
 - Literate programming w/ `Quarto`
-- Pipeline optimization w/ `targets`
+- Pipeline optimisation w/ `targets`
 - Developing an {{< fa brands r-project >}} package
 
 **Thursday**
@@ -73,7 +74,7 @@ All the material used in this training course (slides, data, exercises) is avail
 ## Citation {.unnumbered}
 
 > Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD 
-& Siberchicot A (2024) 
+& Siberchicot A (2025) 
 FRB-CESAB & GdR EcoStat training course: Reproducible Research in Computational Ecology. 
 Zenodo. URL: <http://doi.org/10.5281/zenodo.4262978>
 
@@ -85,7 +86,7 @@ If you see mistakes or want to suggest changes, please [create an issue](https:/
 
 ## 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.
+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}

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-## Research compendium {.unnumbered}`
	`1`	`+## Research compendium`
`2`	`2`
`3`	`3`
`4`	`4`	`::: {.callout-note icon=true appearance="simple"}`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		-## Containerization w/ `Docker` {.unnumbered}
	`1`	`+## Containerization`
`2`	`2`
`3`	`3`
`4`	`4`	`::: {.callout-note icon=true appearance="simple"}`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		-## Version control w/ `git` {.unnumbered}
	`1`	+## Version control w/ `git`
`2`	`2`
`3`	`3`
`4`	`4`	`::: {.callout-note icon=true appearance="simple"}`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		-## Introduction to `GitHub` {.unnumbered}
	`1`	+## Introduction to `GitHub`
`2`	`2`
`3`	`3`
`4`	`4`	`::: {.callout-note icon=true appearance="simple"}`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-## Reproducible research {.unnumbered}`
	`1`	`+## Reproducible research`
`2`	`2`
`3`	`3`
`4`	`4`	`::: {.callout-note icon=true appearance="simple"}`