[ ] Sandve, G. K., Nekrutenko, A., Taylor, J. & Hovig, E. Ten simple rules for reproducible computational research. PLoS Comput. Biol. 9, e1003285 (2013).https://doi.org/10.1371/journal.pcbi.1003285
All above references found in:
Lowndes, Julia S Stewart, Benjamin D Best, Courtney Scarborough, Jamie C Afflerbach, Melanie R Frazier, Casey C O’Hara, Ning Jiang, and Benjamin S Halpern. 2017. “Our Path to Better Science in Less Time Using Open Data Science Tools.” Nature Ecology & Evolution 1 (6). Nature Publishing Group
https://www.nature.com/articles/s41559-017-0160
In addition add new R Markdown Book (https://bookdown.org/yihui/rmarkdown/) nd Link to R package rticles, which provides templates for writing journal articles in R markdown.
Reminder to myself to add the following references in the relevant chapters of the report, e.g.:
Why to share Code?
[ ]
Baker, M. Why scientists must share their research code. Nature Newshttp://dx.doi.org/10.1038/nature.2016.20504 (2016).[ ]
Barnes, N. Publish your computer code: it is good enough. Nature 467, 753 (2010).http://dx.doi.org/10.1038/467753aUncategorized
[ ]
McKiernan, E. C. et al. How open science helps researchers succeed. eLife 5, e16800 (2016).https://elifesciences.org/articles/16800#[ ]
Baker, M. Scientific computing: Code alert. Nature 541, 563–565 (2017).https://dx.doi.org/10.1038/nj7638-563a[ ]
Broman, K. Initial steps toward reproducible research.http://kbroman.org/steps2rr/ (2016).[ ]
Martinez, C. et al. Reproducibility in Science: A Guide to Enhancing Reproducibility in Scientific Results and Writinghttps://ropensci.github.io/reproducibility-guide/ (See also https://github.com/ropensci/reproducibility-guide/issues/86)[ ]
Michener, W. K. Ten simple rules for creating a good data management plan. PLoS Comput. Biol. 11, e1004525 (2015).https://doi.org/10.1371/journal.pcbi.1004525[ ]
Goodman, A. et al. Ten simple rules for the care and feeding of scientific data. PLoS Comput. Biol. 10, e1003542 (2014).https://doi.org/10.1371/journal.pcbi.1003542Best practices scientific computing
[ ]
Sandve, G. K., Nekrutenko, A., Taylor, J. & Hovig, E. Ten simple rules for reproducible computational research. PLoS Comput. Biol. 9, e1003285 (2013).https://doi.org/10.1371/journal.pcbi.1003285[ ]
Wilson, G. et al. Best practices for scientific computing. PLoS Biol. 12, e1001745 (2014).https://doi.org/10.1371/journal.pbio.1001745Why GitHub?
Perkel, J. Democratic databases: Science on GitHub. Nature 538, 127–128 (2016).https://www.nature.com/news/democratic-databases-science-on-github-1.20719All above references found in: Lowndes, Julia S Stewart, Benjamin D Best, Courtney Scarborough, Jamie C Afflerbach, Melanie R Frazier, Casey C O’Hara, Ning Jiang, and Benjamin S Halpern. 2017. “Our Path to Better Science in Less Time Using Open Data Science Tools.” Nature Ecology & Evolution 1 (6). Nature Publishing Group https://www.nature.com/articles/s41559-017-0160
In addition add new R Markdown Book (https://bookdown.org/yihui/rmarkdown/) nd Link to R package rticles, which provides templates for writing journal articles in R markdown.
[ ]
Practical Data Science for Stats - a PeerJ Collection 2018https://peerj.com/collections/50-practicaldatascistats/[ ]
Broman KW, Woo KH. (2017) Data organization in spreadsheets. PeerJ Preprints 5:e3183v1https://doi.org/10.7287/peerj.preprints.3183v1[ ]
Nüst et al 2018 Reproducible research and GIScience: an evaluation using AGILE conference papershttps://peerj.com/articles/5072/[ ]
Reproducible research: Strategies, tools, and workflowshttp://www.helsinki.fi/varieng/series/volumes/19/flanagan/#sect1[ ]
Leek and Peng 2015: Opinion: Reproducible research can still be wrong: Adopting a prevention approachhttps://doi.org/10.1073/pnas.1421412111Sackler Colloquium on Improving the Reproducibility of Scientific Research (Free Online) http://www.pnas.org/content/115/11 , e.g.:
An empirical analysis of journal policy effectiveness for computational reproducibilityhttps://doi.org/10.1073/pnas.1708290115Scientific progress despite irreproducibility: A seeming paradoxhttps://doi.org/10.1073/pnas.1711786114