knitr/RMarkdown

Pro tips
RMarkdown Tips
Customizing pandoc
Tables
Editor support
Citations

knitr is the R-based entrant in the scientific workbook race, combining the code that creates your data analysis with the text, keeping them in sync in perpetuity.

It is frequently used in the form of RMarkdown which supports the markdown input format instead of e.g. LaTeX. I most often use it in the form of blogdown, which is the engine that drives this blog. There are several pieces in this toolchain with a complicated relationship, but the user can ignore most of this complexity. The result is such fanciness as automatically rendering and caching graphs, an interactive notebook UI, nearly first-class support for python and julia plus mediocre support for other languages. Here are some guides:

Interactive reports with R and knitr
(Original author) Yihui Xie’s examples gallery has great material for learning-by-cut-and-paste
His draft knitr manual is free online.

For an intro to the various way to build this into a full reproducible research workflow, via, say, a scientific workbook see the excellent reproducible analysis workshop.

Pro tips

Multi-part documents are supported, even for LaTeX. The keyword is ‘child’ documents.

You can add custom classes to output graphics via chunk options, specifically class.output=c("myclass").

RMarkdown Tips

To execute it from the command-line you do

R -e "rmarkdown::render('script.Rmd', output_file='output.html')"

There are quirks depending on what markup format you use. LaTeX is just LaTeX. Markdown (Via the RMarkdown package) does not have a unified standard for all the bells and whistles you might want. You can include graphics via native markdown or via R itself. The latter is more powerful if more circuitous, doing e.g. automatic resizing.

RMarkdown equation references are supported but weird.

See equation \@ref(eq:linear)

\begin{equation}
a + bx = c  (\#eq:linear)
\end{equation}

Some miscellaneous tips:

I constantly need the chunk options docs
How to customise the rmarkdown pandoc output by e.g. adding extensions? There are two ways, Markdown variants and md_extensions option.
Might stargazer be useful? It generates marked-up and formatted tables for tabular data, but seems not be generic about output formats.
tufte is an Edward-Tufte-compliant stylesheet. (cran link) tint is an alternate version.
For online web-friendly (e.g. teaching) purposes, there is literate interactive coding using shiny and LaTeX via shinyTex.

Customizing pandoc

Tables

kable (plus possibly kableExtra) is recommended as a multiple-backend table creator.
pander is recommended for the same purpose; It targets pandoc.

Editor support

RStudio has intimate RMarkdown integration. AFAICT nothing else supports interactive editing nearly as well, though, but Yihui shows you how to make it work.

AFAICT stencila is a hosted GUI for reproducible research in RMarkdown. USD39/month.

Citations

Citations are laundered through either biblatex or pandoc-citeproc. Configuration is via blogdown header.