Bibliography

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.

Barba LA (2018) Terminologies for Reproducible Research. arXiv. arXix: arXiv:1802.03311.

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.

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.

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.

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.

Lee BD (2018) Ten Simple Rules for Documenting Scientific Software. PLoS Computational Biology, 12, e1006561. DOI: 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.

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.

Peng RD & Hicks SC (2021) Reproducible Research: A Retrospective. Annual Review of Public Health, 42, 79-93. DOI: 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.

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.

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.

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.

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/.