Want to help out or contribute?
If you find any typos, errors, or places where the text may be improved, please let us know by providing feedback either in the feedback survey (given during class) or by using GitHub.
On GitHub open an issue or submit a pull request by clicking the " Edit this page" link at the side of this page.
References
1.
Kim Y-M, Poline J-B, Dumas G. Experimenting with reproducibility: A case study of robustness in bioinformatics. GigaScience. 2018 Jun;7(7).
2.
Plesser HE. Reproducibility vs. Replicability: A brief history of a confused terminology. Frontiers in Neuroinformatics. 2018 Jan;11.
3.
Ram K. Git can facilitate greater reproducibility and increased transparency in science. Source Code for Biology and Medicine. 2013;8(1):7.
4.
Wilson G, Aruliah DA, Brown CT, Hong NPC, Davis M, Guy RT, et al. Best practices for scientific computing. Eisen JA, editor. PLoS Biology. 2014 Jan;12(1):e1001745.
5.
Eglen S, Marwick B, Halchenko Y, Hanke M, Sufi S, Gleeson P, et al. Towards standard practices for sharing computer code and programs in neuroscience. bioRxiv. 2016 Mar;
6.
Vandewalle P. Code sharing is associated with research impact in image processing. Computing in Science & Engineering. 2012 Jul;14(4):42–7.
7.
Perkel JM. A toolkit for data transparency takes shape. Nature. 2018 Aug;560(7719):513–5.
8.
Peng RD, Dominici F, Zeger SL. Reproducible epidemiologic research. American Journal of Epidemiology. 2006 Mar;163(9):783–9.
9.
Leek JT, Jager LR. Is most published research really false? Annual Review of Statistics and Its Application. 2017 Mar;4(1):109–22.
10.
Stodden V, Guo P, Ma Z. Toward reproducible computational research: An empirical analysis of data and code policy adoption by journals. Zaykin D, editor. PLoS ONE. 2013 Jun;8(6):e67111.
11.
Considine EC, Thomas G, Boulesteix AL, Khashan AS, Kenny LC. Critical review of reporting of the data analysis step in metabolomics. Metabolomics. 2017 Dec;14(1).
12.
Tellioglu H. Collaboration life cycle. In: 2008 international symposium on collaborative technologies and systems. IEEE; 2008.
13.
Bosman J, Bruno I, Chapman C, Tzovaras BG, Jacobs N, Kramer B, et al. The scholarly commons - principles and practices to guide research communication. OSF Preprints. 2017 Sep;
14.
Peng RD. Reproducible research in computational science. Science. 2011 Dec;334(6060):1226–7.
15.
Seibold H, Czerny S, Decke S, Dieterle R, Eder T, Fohr S, et al. A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses. Wicherts JM, editor. PLOS ONE. 2021 Jun;16(6):e0251194.
16.
Trisovic A, Lau MK, Pasquier T, Crosas M. A large-scale study on research code quality and execution. Scientific Data. 2022 Feb;9(1).
17.
Lewis LM, Edwards MC, Meyers ZR, Talbot CC, Hao H, Blum D, et al. Replication study: Transcriptional amplification in tumor cells with elevated c-myc. eLife. 2018 Jan;7.
18.
Wickham H. Downlit: Syntax highlighting and automatic linking [Internet]. 2023. Available from: https://downlit.r-lib.org/
19.
Wickham H, François R, Henry L, Müller K, Vaughan D. Dplyr: A grammar of data manipulation [Internet]. 2023. Available from: https://dplyr.tidyverse.org
20.
Hester J, Wickham H, Csárdi G. Fs: Cross-platform file system operations based on libuv [Internet]. 2024. Available from: https://fs.r-lib.org
21.
Wickham H, Chang W, Henry L, Pedersen TL, Takahashi K, Wilke C, et al. ggplot2: Create elegant data visualisations using the grammar of graphics [Internet]. 2024. Available from: https://ggplot2.tidyverse.org
22.
Müller K. Here: A simpler way to find your files [Internet]. 2020. Available from: https://here.r-lib.org/
23.
Carr D, Lewin-Koh N, Maechler M. Hexbin: Hexagonal binning routines [Internet]. 2023. Available from: https://github.com/edzer/hexbin
24.
Xie Y. Knitr: A general-purpose package for dynamic report generation in r [Internet]. 2024. Available from: https://yihui.org/knitr/
25.
Xie Y, Allaire J, Horner J. Markdown: Render markdown with commonmark [Internet]. 2023. Available from: https://github.com/rstudio/markdown
26.
Pruim R. NHANES: Data from the US national health and nutrition examination study [Internet]. 2015. Available from: https://CRAN.R-project.org/package=NHANES
27.
Johnston L. Prodigenr: Research project directory generator [Internet]. 2022. Available from: https://github.com/rostools/prodigenr
28.
Wickham H, Henry L. Purrr: Functional programming tools [Internet]. 2023. Available from: https://purrr.tidyverse.org/
29.
Allaire J, Dervieux C. Quarto: R interface to quarto markdown publishing system [Internet]. 2024. Available from: https://github.com/quarto-dev/quarto-r
30.
Johnston L. r3: Companion package for the R3 courses [Internet]. 2024. Available from: https://github.com/rostools/r3
31.
Johnston L. r3admin: R-cubed teaching helper functions. [Internet]. 2024. Available from: https://github.com/rostools/r3admin
32.
Allaire J, Xie Y, Dervieux C, McPherson J, Luraschi J, Ushey K, et al. Rmarkdown: Dynamic documents for r [Internet]. 2024. Available from: https://github.com/rstudio/rmarkdown
33.
Grosser M. Snakecase: Convert strings into any case [Internet]. 2023. Available from: https://github.com/Tazinho/snakecase
34.
Müller K, Walthert L. Styler: Non-invasive pretty printing of r code [Internet]. 2024. Available from: https://github.com/r-lib/styler
35.
Wickham H, Vaughan D, Girlich M. Tidyr: Tidy messy data [Internet]. 2024. Available from: https://tidyr.tidyverse.org
36.
Wickham H. Tidyverse: Easily install and load the tidyverse [Internet]. 2023. Available from: https://tidyverse.tidyverse.org
37.
Wickham H, Bryan J, Barrett M, Teucher A. Usethis: Automate package and project setup [Internet]. 2024. Available from: https://usethis.r-lib.org
38.
Wickham H. ggplot2: Elegant graphics for data analysis [Internet]. Springer-Verlag New York; 2016. Available from: https://ggplot2.tidyverse.org
39.
Xie Y. Dynamic documents with R and knitr [Internet]. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC; 2015. Available from: https://yihui.org/knitr/
40.
Xie Y. Knitr: A comprehensive tool for reproducible research in R. In: Stodden V, Leisch F, Peng RD, editors. Implementing reproducible computational research. Chapman; Hall/CRC; 2014.
41.
Xie Y, Allaire JJ, Grolemund G. R markdown: The definitive guide [Internet]. Boca Raton, Florida: Chapman; Hall/CRC; 2018. Available from: https://bookdown.org/yihui/rmarkdown
42.
Xie Y, Dervieux C, Riederer E. R markdown cookbook [Internet]. Boca Raton, Florida: Chapman; Hall/CRC; 2020. Available from: https://bookdown.org/yihui/rmarkdown-cookbook
43.
Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the tidyverse. Journal of Open Source Software. 2019;4(43):1686.