Reproducible Research in Computational Ecology

FRB-CESAB & GdR EcoStat training course

Nicolas Casajus https://nicolascasajus.fr (FRB-CESAB)https://www.fondationbiodiversite.fr/en/about-the-foundation/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
06-15-2023

  Pre-registrations for the 2023 training course session are closed.


The objective of this five-day training course, 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.

N.B. This training course is in French, but some slides are available in English in the tab Courses/.


Program

Monday Icebreaker & Introduction to the week
Open science & Reproducible research SLIDES
Research compendium & Good practices SLIDES
Version control with Git & GitHub SLIDESSLIDES
Tuesday Basics of R Markdown SLIDES
Extending R Markdown: websites, slides and dashboards
Introduction to Quarto
Pipeline toolkit with targets SLIDES
Wednesday Dealing with R package versions with renv SLIDES
Containerization with Docker SLIDES
Building an R package SLIDES
Thursday Subgroups projects
Friday Subgroups projects


Prerequisites

Please follow this tutorial to install your working environment before attending the training course.

You also need to create an account on GitHub.


See also

Discover the other training courses provided by the FRB-CESAB and its partners: https://frbcesab.github.io/training-courses/

Citation

Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2023) FRB-CESAB & GdR EcoStat training course: Reproducible Research in Computational Ecology. Zenodo. http://doi.org/10.5281/zenodo.4262978.

Corrections

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

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/rdatatoolbox/rdatatoolbox.github.io, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".