To create an HTML document from R Markdown you specify the html_document
output format in the front-matter of your document:
---
title: "Habits"
author: John Doe
date: March 22, 2005
output: html_document
---
You can add a table of contents using the toc
option and specify the depth of headers that it applies to using the toc_depth
option. For example:
---
title: "Habits"
output:
html_document:
toc: true
toc_depth: 2
---
If the table of contents depth isn’t explicitly specified then it defaults to 3 (meaning that all level 1, 2, and 3 headers will be included in the table of contents).
You can specify the toc_float
option to float the table of contents to the left of the main document content. The floating table of contents will always be visible even when the document is scrolled. For example:
---
title: "Habits"
output:
html_document:
toc: true
toc_float: true
---
You may optionally specify a list of options for the toc_float
parameter which control it’s behavior. Options include:
collapsed
(defaults to TRUE
) controls whether the table of contents appers with only the top-level (e.g. H2) headers. When collapsed the table of contents is automatically expanded inline when necessary.
smooth_scroll
(defaults to TRUE
) controls whether page scrolls are animated when table of contents items are navigated to via mouse clicks.
For example:
---
title: "Habits"
output:
html_document:
toc: true
toc_float:
collapsed: false
smooth_scroll: false
---
Support for floating table of contents is only available in very recent versions of the rmarkdown package. You can install the most current version as follows:
install.packages("rmarkdown")
You can add section numbering to headers using the number_sections
option:
---
title: "Habits"
output:
html_document:
toc: true
number_sections: true
---
Note that if you do choose to use the number_sections
option you will likely also want to use #
(H1) headers in your document as ##
(H2) headers will include a decimal point.
You can organize content using tabs by applying the .tabset
class attribute to headers within a document. This will cause all sub-headers of the header with the .tabset
attribute to appear within tabs rather than as standalone sections. For example:
## Quarterly Results {.tabset}
### By Product
(tab content)
### By Region
(tab content)
You can also specify two additional attributes to control the appearance and behavior of the tabs. The .tabset-fade
attribute causes the tabs to fade in and out when switching. The .tabset-pills
attribute causes the visual appearance of the tabs to be “pill” rather than traditional tabs. For example:
## Quarterly Results {.tabset .tabset-fade .tabset-pills}
Support for tabsets is only available in very recent versions of the rmarkdown package. You can install the most current version as follows:
install.packages("rmarkdown")
There are several options that control the appearance of HTML documents:
theme
specifies the Bootstrap theme to use for the page (themes are drawn from the Bootswatch theme library). Valid themes include "default"
, "cerulean"
, "journal"
, "flatly"
, "darkly"
, "readable"
, "spacelab"
, "united"
, "cosmo"
, "lumen"
, "paper"
, "sandstone"
, "simplex"
, and "yeti"
. Pass null for no theme (in this case you can use the css
parameter to add your own styles).
highlight
specifies the syntax highlighting style. Supported styles include "default"
, "tango"
, "pygments"
, "kate"
, "monochrome"
, "espresso"
, "zenburn"
, "haddock"
, and "textmate"
. Pass null to prevent syntax highlighting.
smart
indicates whether to produce typographically correct output, converting straight quotes to curly quotes, ---
to em-dashes, --
to en-dashes, and ...
to ellipses. Note that smart
is enabled by default.
For example:
---
title: "Habits"
output:
html_document:
theme: united
highlight: tango
---
You can add your own CSS to an HTML document using the css
option:
---
title: "Habits"
output:
html_document:
css: styles.css
---
If you want to provide all of the styles for the document from your own CSS you set the theme
(and potentially highlight
) to null:
---
title: "Habits"
output:
html_document:
theme: null
highlight: null
css: styles.css
---
You can also target specific sections of documents with custom CSS by adding ids or classes to section headers within your document. For example the following section header:
## Next Steps {#nextsteps .emphasized}
Would enable you to apply CSS to all of its content using either of the following CSS selectors:
#nextsteps {
color: blue;
}
.emphasized {
font-size: 1.2em;
}
There are a number of options that affect the output of figures within HTML documents:
fig_width
and fig_height
can be used to control the default figure width and height (7x5 is used by default)
fig_retina
Specifies the scaling to perform for retina displays (defaults to 2, which currently works for all widely used retina displays). Note that this only takes effect if you are using knitr >= 1.5.21. Set to null
to prevent retina scaling.
fig_caption
controls whether figures are rendered with captions
dev
controls the graphics device used to render figures (defaults to png)
For example:
---
title: "Habits"
output:
html_document:
fig_width: 7
fig_height: 6
fig_caption: true
---
You can enhance the default display of data frames via the df_print
option. Valid values include:
Option | Description |
---|---|
default | Call the print.data.frame generic method |
kable | Use the knitr::kable function. |
tibble | Use the tibble::print.tbl_df function. |
paged | Use the rmarkdown::print.paged_df function which creates a pageable HTML table. |
When the df_print
option is set to paged
, tables are printed as an html table with support for pagination over rows and columns. For instance,
---
title: "Motor Trend Car Road Tests"
output:
html_document:
df_print: paged
---
```{r}
mtcars
```
The following options are avaialble:
Option | Description |
---|---|
max.print | The number of rows to print. |
rows.print | The number of rows to display. |
cols.print | The number of columns to display. |
cols.min.print | The minimum number of columns to display. |
pages.print | The number of pages to display under page navigation. |
paged.print | When set to FALSE turns off paged tables. |
rownames.print | When set to FALSE turns off row names. |
These options are specified under each chunk as follows:
```{r cols.print=3, rows.print=3}
mtcars
```
When the knitr chunk option echo = TRUE
is specified (the default behavior) the R source code within chunks is included within the rendered document. In some cases it may be appropriate to exclude code entirely (echo = FALSE
) but in other cases you might want the code available but not visible by default.
The code_folding: hide
option enables you to include R code but have it hidden by default. Users can then choose to show hidden R code chunks either indvidually or document wide. For example:
---
title: "Habits"
output:
html_document:
code_folding: hide
---
You can specify code_folding: show
to still show all R code by default but then allow users to hide the code if they wish.
Support for code folding is only available in very recent versions of the rmarkdown package. You can install the most current version as follows:
install.packages("rmarkdown")
By default MathJax scripts are included in HTML documents for rendering LaTeX and MathML equations. You can use the mathjax
option to control how MathJax is included:
Specify “default” to use an https URL from the official MathJax CDN.
Specify “local” to use a local version of MathJax (which is copied into the output directory). Note that when using “local” you also need to set the self_contained
option to false.
Specify an alternate URL to load MathJax from another location.
Specify null to exclude MathJax entirely.
For example, to use a local copy of MathJax:
---
title: "Habits"
output:
html_document:
mathjax: local
self_contained: false
---
To use a self-hosted copy of MathJax:
---
title: "Habits"
output:
html_document:
mathjax: "http://example.com/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
---
To exclude MathJax entirely:
---
title: "Habits"
output:
html_document:
mathjax: null
---
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. This means you can share or publish the file just like you share Office documents or PDFs. If you’d rather have keep depenencies in external files you can specify self_contained: false
. For example:
---
title: "Habits"
output:
html_document:
self_contained: false
---
Note that even for self contained documents MathJax is still loaded externally (this is necessary because of it’s size). If you want to serve MathJax locally then you should specify mathjax: local
and self_contained: false
.
One common reason keep dependencies external is for serving R Markdown documents from a website (external dependencies can be cached separately by browsers leading to faster page load times). In the case of serving multiple R Markdown documents you may also want to consolidate dependent library files (e.g. Bootstrap, MathJax, etc.) into a single directory shared by multiple documents. You can use the lib_dir
option to do this, for example:
---
title: "Habits"
output:
html_document:
self_contained: false
lib_dir: libs
---
When knitr processes an R Markdown input file it creates a markdown (md) file which is subsequently tranformed into HTML by pandoc. If you want to keep a copy of the markdown file after rendering you can do so using the keep_md
option:
---
title: "Habits"
output:
html_document:
keep_md: true
---
You can do more advanced customization of output by including additional HTML content or by replacing the core pandoc template entirely. To include content in the document header or before/after the document body you use the includes
option as follows:
---
title: "Habits"
output:
html_document:
includes:
in_header: header.html
before_body: doc_prefix.html
after_body: doc_suffix.html
---
You can also replace the underlying pandoc template using the template
option:
---
title: "Habits"
output:
html_document:
template: quarterly_report.html
---
Consult the documentation on pandoc templates for additional details on templates. You can also study the default HTML template default.html5
as an example.
By default R Markdown is defined as all pandoc markdown extensions with the following tweaks for backward compatibility with the markdown package:
+autolink_bare_uris
+ascii_identifier
+tex_math_single_backslash
You can enable or disable markdown extensions using the md_extensions
option (you preface an option with -
to disable and +
to enable it). For example:
---
title: "Habits"
output:
html_document:
md_extensions: -autolink_bare_uris+hard_line_breaks
---
The above would disable the autolink_bare_uris
extension and enable the hard_line_breaks
extension.
For more on available markdown extensions see the pandoc markdown specification.
If there are pandoc features you want to use that lack equivilants in the YAML options described above you can still use them by passing custom pandoc_args
. For example:
---
title: "Habits"
output:
html_document:
pandoc_args: [
"--title-prefix", "Foo",
"--id-prefix", "Bar"
]
---
Documentation on all available pandoc arguments can be found in the pandoc user guide.
If want to create an HTML fragment rather than a full HTML document you can use the html_fragment
format. For example:
---
output: html_fragment
---
Note that there is no title or author because fragments don’t contain the standard header content that HTML documents do. HTML fragments are typically used for including snippets of HTML within larger web sites (e.g. blogs).
For additional information see the article on HTML Fragments. Note that another good option for generating content to be included in larger websites is the md_document
format, which generates markdown. For more information on this format see the article on Markdown Documents.
You can render collections of R Markdown documents as a website using the rmarkdown::render_site
function. See the article on R Markdown Websites for additional details.