rmarkdown: compile_notebook – R documentation

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compile_notebook

Compiling R scripts to a notebook

Description

R Markdown can also compile R scripts to a notebook which includes commentary, source code, and script output. Notebooks can be compiled to any output format including HTML, PDF, and MS Word.

Overview

To compile a notebook from an R script you simply pass the script to render. For example:

rmarkdown::render("analysis.R")
rmarkdown::render("analysis.R", "pdf_document")

The first call to render creates an HTML document, whereas the second creates a PDF document.

By default the name of the script, username, and current date and time are included in the header of the generated notebook. You can override this default behavior by including explicit metadata in a specially formatted R comment:

#' ---
#' title: "Crop Analysis Q3 2013"
#' author: "John Smith"
#' date: "May 3rd, 2014"
#' ---

Including Markdown

Note that the R comment used above to add a title, author, and date includes a single-quote as a special prefix character. This is a roxygen2 style comment, and it's actually possible to include many such comments in an R script, all of which will be converted to markdown content within the generated notebook. For example:

#' A script comment that includes **markdown** formatting.

Rather than displaying as an R comment in the compiled notebook any roxygen2 style comment will be treated as markdown and rendered accordingly.

knitr Spin

Including markdown within R comments is possible because render calls the knitr spin function to convert the R script to an Rmd file. The spin function also enables you to add knitr chunk options with another special comment prefix (#+).

Here's an example of a script that uses the various features of spin:

https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R

For more details on knitr::spin see the following documentation:

https://yihui.org/knitr/demo/stitch/

rmarkdown

Dynamic Documents for R

v2.10

GPL-3

Authors

JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>), Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>, Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (<https://orcid.org/0000-0002-4958-2844>), Christophe Dervieux [ctb], Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>), Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], RStudio, PBC [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)

Initial release