12 Software options

rOpenSci is a non-profit initiative founded in 2011 by Karthik Ram, Scott Chamberlain, and Carl Boettiger to make scientific data retrieval reproducible. Over the past seven years we have developed an ecosystem of open source tools, we run annual unconferences, and review community developed software.

They have produced a great interface for reproducible packages in R with documentation. The key software and packages I use for my workflow are:

12.1 File building

Im not sure what this is actually meant to represent but I see these options as packages making packages

12.1.1 packrat

In mid-August of 2016, Eric Nantz of the R-Podcast converted me to packrat (by Kevin Ushey and others at RStudio), a package that lengthens the shelf life of R projects. Packrat maintains local snapshots of dependencies so that your project won’t break when external packages are updated. Just be sure your current working directory is the root directory of your project when you run remake::make() or the Makefile. Also, if you use a shell.sh with your Makefile, be sure to modify module load R so that it points to the version of R corresponding to your packrat library. You can learn more about packrat with the hands-on walkthrough.

12.1.2 ProjectTemplate

12.2 Packages

Hadley wickham book on R Packages.

12.2.1 R

12.3 Version control

12.4 Markdown

Xie, Yihui. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. http://yihui.org/knitr/.
———. 2021. Bookdown: Authoring Books and Technical Documents with r Markdown. https://CRAN.R-project.org/package=bookdown.

  1. This is a footnote.↩︎