Reproducibility Guide

Scholarly literature on reproducible research

Barnes, N. Publish your computer code: it is good enough. Nature. 467, (2010), 753.(http://www.nature.com/news/2010/101013/full/467753a.html) pdf

Baumer, B. et al. R Markdown: Integrating a Reproducible Analysis Tool in Introductory Statistics. (2014) Technology Innovations in Statistics Education. 8(1). 1-29. pdf

Birney, E. et al. Prepublication data sharing. Nature. 461, (2009), 168-170.](http://www.nature.com/nature/journal/v461/n7261/full/461168a.html) pdf

Buckheit, J.B. and Donoho, D.L. Wavelab and reproducible research. (1995). pdf

Bray, A., Çetinkaya-Rundel, M., & Stangl, D. (2014). Taking a Chance in the Classroom: Five Concrete Reasons Your Students Should Be Learning to Analyze Data in the Reproducible Paradigm. CHANCE, 27(3), 53–56. doi:10.1080/09332480.2014.965635 link

Drummond, C. Reproducible Research: a Dissenting Opinion. (2012), 1-10. pdf

Fehr, J., Heiland, J., Himpe, C. and Saak, J. Best practices for replicability, reproducibility and reusability of computer-based experiments exemplified by model reduction software. AIMS Mathematics 1(3): 261-281, 2016. doi:10.3934/Math.2016.3.261 link.

Freire, J. et al. Computational reproducibility: state-of-the-art, challenges, and database research opportunities. SIGMOD2012 (2012), 593-596. pdf

Gandrud C 2013 Reproducible Research with R and RStudio. CRC Press Florida. link

Gentleman, R. and Temple Lang, D. (2007). Statistical analyses and reproducible research. Journal of Computational and Graphical Statistics 16, 1–23. pdf

Healy, K. (2011). Choosing Your Workflow Applications. The Political Methodologist, 18(2), 9–18. pdf

Hothorn T and Leisch F 2011. Case studies in reproducibility. Briefings in Bioinformatics 12(3), 288-300. pdf

Ioannidis, J.P. a et al. Repeatability of published microarray gene expression analyses. Nature genetics. 41, (2009), 149-55. pdf

King, G. Replication, Replication. PS: Political Science and Politics. (1995).pdf

Leek, J.T. and Peng, R.D. 2015 Opinion: Reproducible research can still be wrong: Adopting a prevention approach. PNAS vol. 112 no. 6 1645–1646, doi: 10.1073/pnas.1421412111 link

Leisch F, Eugster M and Hothorn T 2011. Executable Papers for the R Community: The R2 Platform for Reproducible Research. Procedia Computer Science 4(0), 618-626. pdf

LeVeque, R.J. Python tools for reproducible research on hyperbolic problems. Computing in Science & Engineering. (2009),19-27. pdf

LeVeque, R.J. Wave propagation software, computational science, and reproducible research. Proceedings of the International Congress of Mathematicians (Madrid, Spain, 2006), 1-27. pdf

LeVeque, R, Stodden, V., & Mitchell, I. (2012). Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture. Computing in Science and Engineering, 14(4), 13–17 pdf

McCullough, B.D. Got Replicability? The Journal of Money, Credit and Banking Archive. Econ Journal Watch. 4, (2007),326-337 pdf

McCullough, B.D. Do economics journal archives promote replicable research?. Economics Journal Archives. (2008). pdf

Manolescu, I. et al. Repeatability & Workability Evaluation of SIGMOD 2009. SIGMOD 2009 (2009), 2-4. pdf

McCullough BD, Heiser DA (2008). “On the Accuracy of Statistical Procedures in Microsoft Excel 2007.” Computational Statistics & Data Analysis, 52, 4570–4578. pdf

Merali, Z. Error: Why scientific programming does not compute. Nature. (2010), 6-8. pdf

Morin, A. et al. Shining light into black boxes. Science. 336, (2012), 159-160. pdf

Peng, R.D. Reproducible research and Biostatistics. Biostatistics (Oxford, England). 10, (2009), 405-408. link

Price, K. Anything You Can Do, I Can Do Better (No You Can’t)… Computer Vision, Graphics, and Image Processing. (1986), 387-391. pdf

Piwowar, H. a et al. Sharing detailed research data is associated with increased citation rate. PloS one. 2, (2007), 308. link

Quirk, J. Computational Science “Same Old Silence, Same Old Mistakes” “Something More Is Needed…” Adaptive Mesh Reenement-Theory and Applications. (2005), 4-28. link

Rossini, Anthony and Leisch, Friedrich, “Literate Statistical Practice” (March 2003). UW Biostatistics Working Paper Series. Working Paper 194. link

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285 link

Savage, C.J. and Vickers, A.J. Empirical study of data sharing by authors publishing in PLoS journals. PloS one. 4, (2009),7078. link

Schofield, P.N. et al. Post-publication sharing of data and tools. Nature. 461, (2009), 171-173. pdf

Stodden, V. 2014 What scientific idea is ready for retirement? Reproducibility. Edge.org link

Stodden, V. 2013 Resolving Irreproducibility in Empirical and Computational Research. IMS Bulletin Online, Nov 2013. link

Stodden, V. 2011 “Trust Your Science? Open Your Data and Code,” Amstat News, 1 July 2011. link

Stodden V 2010 The Scientific Method in Practice: Reproducibility in the Computational Sciences. MIT Sloan School Working Paper 4773-10. link

Stodden, V. 2009 The Legal Framework for Reproducible Scientific Research: Licensing and Copyright. Computing in Science &Engineering. 11, (2009), 35-40. pdf link

Stodden, V and Miguez, S 2014. Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research. Journal of Open Research Software 2(1):e21, DOI: http://dx.doi.org/10.5334/jors.ay

Stodden, V., Borwein, J., & Bailey, D. H. (2013). Setting the default to reproducible. computational science research. SIAM News, 46, 4-6. pdf

Stodden V, Guo P, Ma Z (2013) Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals. PLoS ONE 8(6): e67111. doi:10.1371/journal.pone.0067111 link

Vandewalle, P. et al. 2009 Reproducible research in signal processing - What, why, and how. IEEE Signal Processing Magazine.26, (2009), 37-47. pdf

Wilson, G. et al. Best Practices for Scientific Computing. 1-6. link

Xie Y 2013 Dynamic Documents with R and knitr. CRC Press Florida link repo

http://www.nature.com/nature/focus/reproducibility/

http://www.mendeley.com/groups/1142301/reproducible-research/papers/