R Markdown templates

R Notebook
Document
- HTML
- Markdown
- PDF
- Word
Presentation
- HTML (ioslides)
- HTML (Slidy)
- PDF (Beamer)
- reveal.js
Shiny
- Document
- Presentation (ioslides)
Template
- Lightweight and Pretty Document & Vignette¹ (HTML)
- GitHub Document (Markdown)
- HTML clean & HTML clean ProjectTemplate report templates
- HTML docco & HTML docco ProjectTemplate report templates
- HTML readthedown & HTML readthedown ProjectTemplate report templates
- Tufte Handout (HTML or PDF)
- Journal Articles…

Most of these templates are showcased in a gallery.

Beyond the basics settings (code & plot chunks, code & languages, parameters, tables), we have specific settings and options for HTML documents.

This post is a wrap-up of templates. It covers the prettydoc package, the rmarkdown package (GitHub), the rmdformats package (clear, docco, readthedocs), and the tufte package.

R Notebook

This is similar to Jupyter Notebook.

Documents

The document default settings…

output: document

…can be changed; see the appearance and style.

output:
  html_document:
    theme: default
    highlight: default

Presentations

output: ioslides_presentation creates simple HTML slides with smooth transitions in the browser.
output: slidy_presentation creates contrasted HTML slides in the browser.
output: beamer_presentation creates simple PDF slides.

Shiny

The difference between a Document and a Shiny document…

output: html_document
runtime: shiny

… or a Presentation and a Shiny presentation…

output: ioslides_presentation
runtime: shiny

…is the interactivity.

Templates

They have standard settings for theme and highlight.

The Lightweight and Pretty Document & Vignette templates

Install the prettydoc package.

# Document
output:
  prettydoc::html_pretty:
    theme: architect
    highlight: github

# Vignette
output:
  prettydoc::html_pretty:
    theme: cayman
    highlight: github

The GitHub Document & Vignette templates

Install the rmarkdown package.

# Document
output: github_document

# Vignette
output: rmarkdown::html_vignette

The rmdformat templates

Install the rmdformats package.

output:
  rmdformats::readthedown:
    highlight: kate

…rmdformats::html_clean: and rmdformats::html_docco:.

The Tufte templates

Install the tufte package.

output:
  tufte::tufte_handout: default
  ...

The Journal Articles templates

Install the rticles package.

Appearance and style

output:
  html_document:
    toc: true
    toc_depth: 2 # 2 shows levels # and ##
    toc_float: true # always visible on the left
      collapsed: false # sub-section are displayed
      smooth_scroll: true
      number_sections: true # add numbers

Tabbed sections

Add {.tabset .tabset-fade .tabset-pills} following a ## Title.

By product

(Content ABC)
(Content DEF)
(Content GHI)

By region

(Tab content XYZ)
(Tab content 789)

Figure options

output:
  html_document:
    fig_width: 7
    fig_height: 6
    fig_caption: true

Data Frame printing

# Markdown
knitr::kable(mtcars[1:3,])

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108	93	3.85	2.320	18.61	1	1	4	1

# HTML
library(tibble)

print(as_tibble(mtcars[1:3,]))

## # A tibble: 3 × 11
##     mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
##   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1  21       6   160   110  3.9   2.62  16.5     0     1     4     4
## 2  21       6   160   110  3.9   2.88  17.0     0     1     4     4
## 3  22.8     4   108    93  3.85  2.32  18.6     1     1     4     1

For long tables, set the heading…

output:
  html_document:
    df_print: paged

…and set the code chunk.

{r, cols.print=6, rows.print=3}

mtcars

Code folding

code_folding: hide displays the code with the Code button

output:
  html_document:
    code_folding: hide

code_folding: show displays the code with the Hide button

code_folding: hide:

code_folding: code:

Document dependencies

By default, R Markdown produces standalone HTML files with no external dependencies, using data: URIs to incorporate the contents of linked scripts, stylesheets, images, and videos. For dependencies on external files.

output:
  html_document:
    self_contained: false

For self-contained documents, MathJax is still loaded externally. We can serve MathJax locally: mathjax: local and self_contained: false.

Keeping markdown

Creates a Markdown file with HTML. Or replace html_document with md_document. Consult the documentation for Markdown options.

output:
  html_document:
    keep_md: true

Shared options

We can specify a set of default options to be shared by multiple documents within a directory. Include a file named _output.yaml within the directory:

html_document:
  self_contained: false
  theme: united
  highlight: textmate
...

All documents located in the same directory will inherit the yaml options.

HTML fragments

HTML fragments are not complete HTML documents. Rather, they are intended for inclusion within other web pages or content management systems (like blogs). As such, they don’t support features like embedded images, themes, or code highlighting (it’s expected that the environment they are ultimately published within handles these things).

title: "Optional"
output:
  html_fragment:
    number_sections: true
    smart: true
    keep_md: true
    fig_width: 7
    fig_height: 6
    fig_caption: true
    fig_retina: 2

A vignette is a long-form guide to a package.↩︎

Themes