Data Toolbox for Reproducible Research in Ecology

FRB-CESAB & GdR EcoStat Workshop

Nicolas Casajus https://nicolascasajus.fr (FRB-CESAB)https://www.fondationbiodiversite.fr/la-fondation/le-cesab/ , Iago Bonnici https://isem-evolution.fr/en/membre/bonnici/ (CNRS ISEM)https://isem-evolution.fr/en/ , Stéphane Dray https://lbbe.univ-lyon1.fr/fr/annuaires-des-membres/dray-stephane (CNRS LBBE)https://lbbe.univ-lyon1.fr/fr , Olivier Gimenez https://oliviergimenez.github.io (CNRS CEFE)https://www.cefe.cnrs.fr/fr/ , Loreleï Guéry https://orcid.org/0000-0003-3004-8462 (CIRAD PHIM)https://umr-phim.cirad.fr/ , François Guilhaumon https://fguilhaumon.gitlab.io/ (IRD ENTROPIE)https://www.ird.fr/umr/entropie , Nina Schiettekatte http://www.criobe.pf/pro/personnel/doctorants/nina-schiettekatte/ (EPHE CRIOBE)http://www.criobe.pf/ , Aurélie Siberchicot https://lbbe.univ-lyon1.fr/fr/annuaires-des-membres/siberchicot-aurelie (UCBL LBBE)https://lbbe.univ-lyon1.fr/en
12-05-2022


The objective of this five-day workshop, co-organized by the FRB-CESAB and the GdR EcoStat, 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.

More information available here


Program

Day 1

       Icebreaker and introduction of the week
       Open science and Reproducible research
       Research compendium & Good practices
       Version control with Git & GitHub

Day 2

       Basics of R Markdown
       Extending R Markdown: websites, slides and dashboards
       Introduction to Quarto
       Pipeline toolkit with targets

Day 3

       Dealing with R package versions with renv
       Containerization with Docker
       Building an R package

Day 4

       Subgroups projects

Day 5

       Subgroups projects
       Projects presentation


Prerequisites

The following software must be installed before the workshop: R (latest version), RStudio et Git. Follow this tutorial to install your working environment.

You also need to create an account (free) on GitHub.

Corrections

If you see mistakes or want to suggest changes, please Create an issue on the source repository.

Reuse

The material of this website is licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/rdatatoolbox/rdatatoolbox.github.io/.

Citation

Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2022) Workshop FRB-CESAB & GdR EcoStat: Data Toolbox for Reproducible Research in Computational Ecology. Zenodo. http://doi.org/10.5281/zenodo.4262978.