add bibliography

Author: ahasverus

_quarto.yml

@@ -64,6 +64,10 @@ book:
 
   favicon: images/favicon.png
 
+  sidebar: 
+    style: "docked"
+    collapse-level: 1
+
   page-footer: 
     left: "© CC-By [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/)"
@@ -75,10 +79,10 @@ book:
 
   chapters:
     - index.qmd
-    - part: "PREREQUISITES"
+    - part: "Prerequisites"
       chapters: 
         - chapters/setting-up-r.qmd
-    - part: "COURSES"
+    - part: "Courses"
       chapters: 
         - chapters/course-opensci.qmd
         - chapters/course-compendium.qmd
@@ -89,7 +93,7 @@ book:
         - chapters/course-renv.qmd
         - chapters/course-docker.qmd
         - chapters/course-package.qmd
-    - part: "EXERCISES"
+    - part: "Exercises"
       chapters: 
         - chapters/ex-compendium.qmd
         - chapters/ex-github.qmd
@@ -98,14 +102,10 @@ book:
         - chapters/ex-renv.qmd
         - chapters/ex-docker.qmd
         - chapters/ex-package.qmd
-    - part: "RESOURCES"
-      chapters: 
-        - chapters/degrees-repro.qmd
-    - part: "ARCHIVES"
+    - part: "Resources"
       chapters: 
-        - chapters/course-api.qmd
-        - chapters/course-rspatial.qmd
-        - chapters/course-tidyverse.qmd
+        - chapters/biblio.qmd
+        - chapters/wrap-up.qmd
 
 format:
   html:

chapters/biblio.qmd

@@ -0,0 +1,50 @@
+## Bibliography {.unnumbered}
+
+### Articles
+
+Alston JA & Rick JM (2021) **A Beginner's Guide to Conducting Reproducible Research**. _The Bulletin of the Ecological Society of America_, 102, e01801. DOI: [10.1002/bes2.1801](https://doi.org/10.1002/bes2.1801).
+
+Barba LA (2018) **Terminologies for Reproducible Research**. _arXiv_. arXix: [ 	arXiv:1802.03311](https://arxiv.org/abs/1802.03311v1).
+
+Blischak JD, Davenport ER & Wilson G (2016) **A Quick Introduction to Version Control with Git and GitHub**. _PLoS Computational Biology_, 12, e1004668. DOI: [10.1371/journal.pcbi.1004668](https://doi.org/10.1371/journal.pcbi.1004668).
+
+Braga PHP, Hébert K, Hudgins EJ, _et al._ (2023) **Not Just for Programmers: How GitHub Can Accelerate Collaborative and Reproducible Research in Ecology and Evolution**. _Methods in Ecology and Evolution_, 14, 1364-1380. DOI: [10.1111/2041-210x.14108](https://doi.org/10.1111/2041-210x.14108).
+
+Brousil MR, Filazzola A, Meyer MF, _et al._ (2023) **Improving Ecological Data Science with Workflow Management Software**, 14, 1381-1388. DOI: [10.1111/2041-210X.14113](https://doi.org/10.1111/2041-210X.14113).
+
+Bryan J (2017) **Excuse Me, Do You Have a Moment to Talk About Version Control?** _PeerJ Preprints_, 5, e3159v2. DOI: [10.7287/peerj.preprints.3159v2](https://doi.org/10.7287/peerj.preprints.3159v2).
+
+
+Lee BD (2018) **Ten Simple Rules for Documenting Scientific Software**. _PLoS Computational Biology_, 12, e1006561. DOI: [10.1371/journal.pcbi.1006561](https://doi.org/10.1371/journal.pcbi.1006561).
+
+Marwick B, Boettiger C & Mullen L (2018) **Packaging Data Analytical Work Reproducibly Using R (and Friends)**. _The American Statistician_, 72, 80-88. DOI: [10.1080/00031305.2017.1375986](https://doi.org/10.1080/00031305.2017.1375986).
+
+Nüst D, Sochat V, Marwick Ben _et al._ (2020) **Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science**. _PLoS Computational Biology_, 16, e1008316 DOI: [10.1371/journal.pcbi.1008316](https://doi.org/10.1371/journal.pcbi.1008316).
+
+Peng RD & Hicks SC (2021) **Reproducible Research: A Retrospective**. _Annual Review of Public Health_, 42, 79-93. DOI: [10.1146/annurev-publhealth-012420-105110](https://doi.org/10.1146/annurev-publhealth-012420-105110)
+
+Perez-Riverol Y, Gatto L, Wang R _et al._ (2016) **Ten Simple Rules for Taking Advantage of Git and GitHub**. _PLoS Computational Biology_, 12, e1004947. DOI: [10.1371/journal.pcbi.1004947](https://doi.org/10.1371/journal.pcbi.1004947).
+
+Romano JD & Moore JH (2020) **Ten Simple Rules for Writing a Paper about Scientific Software**. _PLoS Computational Biology_, 16, e1008390 DOI: [10.1371/journal.pcbi.1008390](https://doi.org/10.1371/journal.pcbi.1008390).
+
+Sandve GK, Nekrutenko A, Taylor J _et al._ (2013) **Ten Simple Rules for Reproducible Computational Research**. _PLoS Computational Biology_, 9, e1003285. DOI: [10.1371/journal.pcbi.1003285](https://doi.org/10.1371/journal.pcbi.1003285).
+
+Wilson G & Bryan J & Cranston K _et al._ (2017) **Good Enough Practices in Scientific Computing**. _PLoS Computational Biology_, 13, e1005510. DOI: [10.1371/journal.pcbi.1005510](https://doi.org/10.1371/journal.pcbi.1005510).
+
+
+
+
+### Online books
+
+Bryan J (2023) **Happy Git and GitHub for the useR**. URL: <https://happygitwithr.com/>.
+
+Landau W (2023) **The targets R package user manual**. URL: <https://books.ropensci.org/targets/>.
+
+Wickham H (2019) **Advanced R**. URL: <https://adv-r.hadley.nz/>.
+
+Wickham H (2023) **R for Data Science**. URL: <https://r4ds.had.co.nz/>.
+
+Wickham H & Bryan J (2023) **R Packages: Organize, Test, Document, and Share Your Code**. URL: <https://r-pkgs.org/>.
+
+Yihui X, Allaire JJ & Grolemund G (2023) **R Markdown: The Definitive Guide**. URL: <https://bookdown.org/yihui/rmarkdown/>.
+

chapters/degrees-repro.qmd renamed to chapters/wrap-up.qmd

@@ -1,4 +1,4 @@
-# The degrees of reproducibility {.unnumbered}
+# Wrap up {.unnumbered}
 
 [![](../images/degrees.png)](the_degrees_of_reproductibility.pdf)
 

index.qmd

@@ -5,14 +5,13 @@ toc: true
 # Welcome {.unnumbered}
 
 ::: {.callout-note}
-## Registrations for the 2023 session are closed
+## 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 >}}&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/).
+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/).
 :::
 
 
@@ -28,30 +27,32 @@ applied to biodiversity research.
 
 ## Program {.unnumbered}
 
-+---------------+-------------------------------------------------+
-| **Monday**    | - Open science & Reproducible research          |
-|               | - Research compendium & Good practices          |
-|               | - Version control with `Git` & `GitHub`         |
-+---------------+-------------------------------------------------+
-| **Tuesday**   | - Literate programming: `R Markdown` & `Quarto` |
-|               | - Pipeline toolkit with `targets`               |
-+---------------+-------------------------------------------------+
-| **Wednesday** | - Dealing with R package versions with `renv`   |
-|               | - Containerization with `Docker`                |
-|               | - Building an R package                         |
-+---------------+-------------------------------------------------+
-| **Thursday**  | - Subgroups projects                            |
-+---------------+-------------------------------------------------+
-| **Friday**    | - Subgroups projects                            |
-+---------------+-------------------------------------------------+
++---------------+-----------------------------------------------------+
+| **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 >}}&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/).
+{{< 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}