R Markdown for Scholarly Communication?

Open question: how much longer will researchers be limited to submitting manuscripts in formats like Word or LaTeX to STM journals?

I caught a glimpse of a potential alternative at a recent Software Carpentry Bootcamp hosted by UC Davis.

Software Carpentry is a volunteer organization that teaches basic computing skills to researchers. Instruction typically takes the form of 2 to 3 day hands-on workshops aimed at helping researchers, typically graduate students, work more effectively with data.

The event was a blast. Topics can vary from bootcamp to bootcamp and included the following in the session I attended:

  • Basic UNIX Shell Functions
  • Data Munging
  • Basic Version Control using Git
  • Data Sharing with GitHub
  • Intro to Programming in R for data manipulation and visualization
  • Markdown and R Markdown for creating text documents that run R code
  • Intro to ggplot2, a plotting system for R that make creating beautiful plots easy

Thanks in large part to Software Carpentry’s patient and capable volunteers, after two full days I was able to write short scripts, post them to GitHub, and create simple visualizations using sample data.

countries.png GDP per capita from 1950 through 2010

After the first day of instruction (and over drinks) a discussion popped up over the relative merits of R Markdown and IPython Notebook – two potential alternatives to Word and LaTeX. What makes the formats compelling is their ability to leverage R or Python code to create dynamic documents.

Both R Markdown documents and IPython Notebooks can easily be converted to HTML, PDF and even Word – formats that scholarly publishers are generally familiar with. While these conversions make it easy for researchers to produce traditional research outputs, I wonder if there is a better way for publishers to leverage these formats. It also makes me curious to hear from the research community directly. How can publishers leverage formats like R Markdown and IPython Notebook to facilitate enhanced scholarly communication? Any and all suggestions are welcome.

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2 Responses to R Markdown for Scholarly Communication?

  1. Yes please, journals need to support this, we need something like Markdown or Ipython to make research more reproducible. I’d love to submit a paper in Markdown. See Martin Fenner on Scholarly Markdown http://blog.martinfenner.org/2013/06/17/what-is-scholarly-markdown/

  2. Pingback: FunFunFun: Our Software carpentry bootcamp @UCDavis | lushgreengrassatafridayafternoon

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