Reproducible Research, R, R Studio, and You!

A long long time ago, in a galaxy far far away, I was asked to give a talk about reproducible research in the R ecosystem during the University of Illinois at Urbana-Champaign’s Department of Statistics Friday Brownbag series. The talk was a long time coming. In fact, it was rescheduled twice since a guest economics professor appeared for a lecture and I was struck with the worst cold of my life.

Last Friday, the stars aligned and I was able to give the presentation. I really focused the presentation on removing point and click data modification, copy and paste transference of tables and graphs, and documentation duplication through advocating for an automated approach when it comes to data cleaning, data analysis, and generating a presentation. Since the standard at UIUC is to use R and R Studio, the presentation really focuses in on using these two tools to create a successful workflow that enables reproducible research. Other software packages that I talk about are git for version control + GitHub and pandoc for documentation conversion. I extend out on the R platform by recommending the following packages: knitr for dynamic documents, rmarkdown for an agnostic file format, xtable for transferring R data to LaTeX or HTML graphs, and roxygen2 for taking inline document comments and generating .Rd documentation.

If this is interesting, I recommend checking out the slides and R code used to create the presentation here: Reproducible Research via R, LaTeX, and knitr (R Code).

During the course of preparing the last two talks I gave, I was a bit disappointed that UIUC lacked a beamer color theme. Previously, I had obtained a UIUC-oriented theme from a professor, but I thought I could do it better. I modified the theme a bit so that it looks like: UIUC Beamer Theme (sample). If you are interested in using the theme, download: Illinois I Logo and .Rnw File. For those of you who are googling “UIUC Beamer Theme” and are going “why is there no .tex?” Please note that .Rnw is a form of .tex. The main difference is .Rnw allows for r code to be embedded in it. Removing code chunks like «name»=@ will revert the file to a normal .tex file.

Till next time….

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