Overview

To create an HTML fragment from R Markdown you specify the html_fragment output format in the front-matter of your document:

---
output: html_fragment
---

Note that 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).

Figure Options

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_fragment:
    fig_width: 7
    fig_height: 6
    fig_caption: true
---

Additional Options

There are several other options that can be used to customized HTML fragment generation:

  • You can add section numbering to headers using the number_sections option.

  • You can specify smart 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).

  • If you want to keep a copy of the markdown file after rendering you can do so using the keep_md option.

For example:

---
output:
  html_fragment:
    number_sections: true
    smart: true
    keep_md: true
---

Markdown Extensions

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.

Pandoc Arguments

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.

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