Notebooks with R Markdown

Presented by:

JJ Allaire, RStudio


R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. R Markdown has some similarities with notebook user interfaces like Jupyter, Beaker, and Apache Zeppelin however has some important distinguishing characteristics, including: Its base representation is plain-text (markdown with embedded R code chunks) which creates a clean separation between source code and output, makes it authorable in the same tools used for creating R scripts (there are R Markdown modes for Emacs, Vim, Sublime, Eclipse, and RStudio), and works well with version control. It includes a system of extensible output formats that enable creation of high-quality, production-level output in many formats including HTML, PDF, MS Word, ODT, HTML5 slides, Beamer, LaTeX-based journal articles, and even full length books. In this talk we'll describe a new notebook user-interface for R that works seamlessly with existing R Markdown documents. Notebook output is displayed inline within the standard RStudio .Rmd editing mode. Building a notebook on top of .Rmd preserves the traditional benefits of R Markdown (plain text, reproducible workflow, extensible output formats, etc.) while at the same time enabling a richer, more literate REPL for data analysis. While R Markdown Notebooks are based on traditional .Rmd files, they are also capable of producing a rendered notebook file (.Rnb) that includes both code and output. This file can be shared as a standalone artifact which (unlike traditional R Markdown documents) contains all the source code for optional modification and direct execution by readers.


  • A set of accounts have been created on a series of RStudio servers for the duration of eCOTS 2016. See for an editable google drive file with login information.


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Teaching with R