knitr is the R-based entrant in the scientific workbook race.
It is frequently used with 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.
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.
knitr::include_graphics("../images/oesterreich_karte.jpg")
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
pandocoutput 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.
tufteis 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.
Tables
- kable (plus possibly kableExtra) is recommended as a multiple-backend table creator.
panderis recommended for the same purpose; It targetspandoc.
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.