Further reading

Author

Ellis Franklin

Published

February 6, 2025


1 Some resources for learning more about Quarto

  • Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2024) FRB-CESAB & GdR EcoStat training course: Reproducible Research in Computational Ecology. Zenodo. URL: http://doi.org/10.5281/zenodo.4262978 (link to workshop)

  • “Introduction to Quarto” by Andrew Bray at posit::conf(2024) (link)

  • “With Quarto Coming, is R Markdwon Going Away? No” blog post by Yihui Xie (link)

  • “Introduction to Quarto” by Eric Delmelle (link)


2 Some resources for understanding Reproducible Research

  • Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2024) FRB-CESAB & GdR EcoStat training course: Reproducible Research in Computational Ecology. Zenodo. (http://doi.org/10.5281/zenodo.4262978) (link to workshop)

  • Repro4Everyone. (n.d.). Introduction to Reproducibility. Repro4Everyone. (link)

  • “Guide for Reproducible Research” by The Turing Way Community. DOI: 10.5281/zenodo.3332807 (link to the guide)

  • “A conside guide to reproducible research using secondary data” by Katharina Blankart, Maryna Ivets, Eva Goetjes and Kai Miele (link)


3 Literature on Reproducible Research

  • Claerbout and Karrenbach (1992)
  • Loscalzo (2012)
  • Freedman, Cockburn, and Simcoe (2015)
  • Baker (2016)
  • This (2017)
  • Plesser (2018)
  • Marwick, Boettiger, and Mullen (2018)
  • Plesser (2018)
  • Schloss (2018)
  • Reproducibility and Replicability in Science (2019)
  • Desquilbet et al. (2019)
  • Gundersen (2021)
  • Alston and Rick (2021)
  • Ziemann, Poulain, and Bora (2023)
  • Calnan et al. (2024)
  • Casajus et al. (2024)
  • “Reproducibility: Why It Matters and How It Can Be Nurtured | Elsevier” (n.d.)
  • “Six Factors Affecting Reproducibility in Life Science Research and How to Handle Them” (n.d.)

References

Alston, Jesse M., and Jessica A. Rick. 2021. “A Beginner’s Guide to Conducting Reproducible Research.” The Bulletin of the Ecological Society of America 102 (2): e01801. https://doi.org/10.1002/bes2.1801.
Baker, Monya. 2016. “1,500 Scientists Lift the Lid on Reproducibility.” Nature 533 (7604): 452–54. https://doi.org/10.1038/533452a.
Calnan, Michael, Simon Kirchin, David L. Roberts, Mark N. Wass, and Martin Michaelis. 2024. “Understanding and Tackling the Reproducibility Crisis Why We Need to Study Scientists’ Trust in Data.” Pharmacological Research 199 (January): 107043. https://doi.org/10.1016/j.phrs.2023.107043.
Casajus, Nicolas, Iago Bonnici, Stéphane Dray, Olivier Gimenez, Loreleï Guéry, François Guilhaumon, Nina Schiettekatte, and Aurélie Siberchicot. 2024. “Reproducible Research in Computational Ecology.” https://rdatatoolbox.github.io/.
Claerbout, Jon F., and Martin Karrenbach. 1992. “Electronic Documents Give Reproducible Research a New Meaning.” In, 601–4. SEG Technical Program Expanded Abstracts. Society of Exploration Geophysicists. https://doi.org/10.1190/1.1822162.
Desquilbet, Loic, Sabrina Granger, Boris Hejblum, Arnaud Legrand, Pascal Pernot, Nicolas P. Rougier, Elisa de Castro Guerra, et al. 2019. Vers Une Recherche Reproductible. Edited by Unité régionale de formation à l’information scientifique et technique de Bordeaux. Unité régionale de formation à l’information scientifique et technique de Bordeaux. https://hal.science/hal-02144142.
Freedman, Leonard P., Iain M. Cockburn, and Timothy S. Simcoe. 2015. “The Economics of Reproducibility in Preclinical Research.” PLOS Biology 13 (6): e1002165. https://doi.org/10.1371/journal.pbio.1002165.
Gundersen, Odd Erik. 2021. “The Fundamental Principles of Reproducibility.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379 (2197): 20200210. https://doi.org/10.1098/rsta.2020.0210.
Loscalzo, Joseph. 2012. “Experimental Irreproducibility: Causes, (Mis)interpretations, and Consequences.” Circulation 125 (10): 1211–14. https://doi.org/10.1161/CIRCULATIONAHA.112.098244.
Marwick, Ben, Carl Boettiger, and Lincoln Mullen. 2018. “Packaging Data Analytical Work Reproducibly Using r (and Friends).” The American Statistician 72 (1): 80–88. https://doi.org/10.1080/00031305.2017.1375986.
Plesser, Hans E. 2018. “Reproducibility Vs. Replicability: A Brief History of a Confused Terminology.” Frontiers in Neuroinformatics 11 (January). https://doi.org/10.3389/fninf.2017.00076.
Reproducibility and Replicability in Science. 2019. Washington, D.C.: National Academies Press. https://doi.org/10.17226/25303.
“Reproducibility: Why It Matters and How It Can Be Nurtured | Elsevier.” n.d. https://www.elsevier.com/connect/reproducibility-why-it-matters-and-how-it-can-be-nurtured.
Schloss, Patrick D. 2018. “Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.” mBio 9 (3): 10.1128/mbio.00525–18. https://doi.org/10.1128/mbio.00525-18.
“Six Factors Affecting Reproducibility in Life Science Research and How to Handle Them.” n.d. https://www.nature.com/articles/d42473-019-00004-y.
This, Hervé. 2017. “La Question de La Reproductibilité Des Expériences Scientifiques.” Notes Académiques de l’Académie d’agriculture de France, no. 2: 1–8. https://hal.science/hal-01466964.
Ziemann, Mark, Pierre Poulain, and Anusuiya Bora. 2023. “The Five Pillars of Computational Reproducibility: Bioinformatics and Beyond.” Briefings in Bioinformatics 24 (6): bbad375. https://doi.org/10.1093/bib/bbad375.