Objectifs :
Using R for data analysis efficiently, and discovering a set of useful R packages. Using R and Quarto to write a reproducible research paper.
Note that this teaching unit is more geared towards good pratices in R programming (in a broad sense) than towards advanced statistical methods, or statistical theory per se.
Another, distinct teaching unit is proposed to that end.

Programme :
1) Good practices for R programming and reproducible research
Using Quarto notebooks instead of R scripts, using Quarto templates to write a research article and export it to a PDF, controlling the R environment (by setting packages versions, etc.) for a better reproducibility, discovering some basic features of Git for versionning scripts, managing bibliographical references through Rstudio.

2) Cleaning, reshaping and summarising data
Using a set of packages (mainly from the ‘tidyverse’) to import, check, reshape and summarise data easily.

3) Producing advanced, publication-ready plots
Using {ggplot2} and several of its natural extensions to create elegant and informative figures.

4) Easier modeling and iterations through the ‘tidyverse’
Depending on the interests of the audience, some more advanced topics could be addressed during the last half-day, such as:
- Using for getting better summaries and more structured information from your models
- Using for producing automatically a large number of models or plots
- Using {FactoMineR} & friends to do exploratory multivariate analyses (PCA, clustering, etc.).

Pré-requis :
- Having completed the “Introduction to R: from the basics to the first steps of data manipulation and representation” teaching unit, proposed by the Graduate Research Shgool of the University of Bordeaux.
- Otherwise, at least a very basic knowledge of the R langage is required (this teaching unit is not a general introduction to R for newcomers).
- Regarding Quarto, no previous knowledge is required.

Equipe pédagogique :
Frédéric Santos, ingénieur d’études en statistiques, laboratoire « De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie » (PACEA)-UMR 5199, Centre national de la recherche scientifique (CNRS), Université de Bordeaux

Méthode pédagogique :
All the “theoretical” content will be available on a dedicated website.
The practical part will consist in replicating exactly the PDF of a (fictive but credible!) research article, provided by the teacher (along with the corresponding dataset). To this end, PhD students will have to use both R programming (to reproduce the results, tables and figures) and Quarto (for composing the final PDF).
This format will allow each PhD student to progress with relative autonomy, at a pace that suits them.

Compétences acquises à l'issue de la formation :
- Develop a transparent and reproducible workflow for data analysis
- Discovering best practices for an efficient R programming
- Using literate programming (Quarto) for writing a research article

Les Compétences et capacités visées à l'issue de la formation (fiches RNCP)

Arrêté du 22 février 2019 définissant les compétences des diplômés du doctorat et inscrivant le doctorat au répertoire national de la certification professionnelle. https://www.legifrance.gouv.fr/loda/id/JORFTEXT000038200990/

Bloc 2 : Mise en œuvre d’une démarche de recherche et développement, d’études et prospective

- Mettre en œuvre les méthodes et les outils de la recherche en lien avec l’innovation