Overview

To create a PDF document from R Markdown you specify the pdf_document output format in the front-matter of your document:

---
title: "Habits"
author: John Doe
date: March 22, 2005
output: pdf_document
---

Within R Markdown documents that generate PDF output you can use raw LaTeX and even define LaTeX macros. See the documentation on Raw TeX for details.

Note that PDF output (including Beamer slides) requires a full installation of TeX.

Table of Contents

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:
  pdf_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 add section numbering to headers using the number_sections option:

---
title: "Habits"
output:
  pdf_document:
    toc: true
    number_sections: true
---

Figure Options

There are a number of options that affect the output of figures within PDF documents:

  • fig_width and fig_height can be used to control the default figure width and height (6 x 4.5 is used by default)

  • fig_crop controls whether the the pdfcrop utility (if available) is automatically applied to pdf figures (this is true by default). If your graphics device is postscript, you are recommended to disable this feature (see more info here).

  • fig_caption controls whether figures are rendered with captions (this is false by default).

  • dev controls the graphics device used to render figures (defaults to pdf)

For example:

---
title: "Habits"
output:
  pdf_document:
    fig_width: 7
    fig_height: 6
    fig_caption: true
---

Data Frame Printing

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.

For example:

---
title: "Habits"
output:
  pdf_document:
    df_print: kable
---

Syntax Highlighting

The highlight option specifies the syntax highlighting style. Supported styles include “default”, “tango”, “pygments”, “kate”, “monochrome”, “espresso”, “zenburn”, and “haddock” (specify null to prevent syntax highlighting):

For example:

---
title: "Habits"
output:
  pdf_document:
    highlight: tango
---

LaTeX Options

Many aspects of the LaTeX template used to create PDF documents can be customized using top-level YAML metadata (note that these options do not appear underneath the output section but rather appear at the top level along with title, author, etc.). For example:

---
title: "Crop Analysis Q3 2013"
output: pdf_document
fontsize: 11pt
geometry: margin=1in
---

Available metadata variables include:

Variable Description
lang Document language code
fontsize Font size (e.g. 10pt, 11pt, 12pt)
documentclass LaTeX document class (e.g. article)
classoption Option for documentclass (e.g. oneside); may be repeated
geometry Options for geometry class (e.g. margin=1in); may be repeated
mainfont, sansfont, monofont, mathfont Document fonts (works only with xelatex and lualatex, see the latex_engine option)
linkcolor, urlcolor, citecolor Color for internal, external, and citation links (red, green, magenta, cyan, blue, black)

LaTeX Packages for Citations

By default, citations are processed through pandoc-citeproc, which works for all output formats. For PDF output, sometimes it is better to use LaTeX packages to process citations, such as natbib or biblatex. To use one of these packages, just set the option citation_package to be natbib or biblatex, e.g.

---
output:
  pdf_document:
    citation_package: natbib
---

Advanced Customization

LaTeX Engine

By default PDF documents are rendered using pdflatex. You can specify an alternate engine using the latex_engine option. Available engines are “pdflatex”, “xelatex”, and “lualatex”. For example:

---
title: "Habits"
output:
  pdf_document:
    latex_engine: xelatex
---

Keeping Intermediate TeX

R Markdown documents are converted to PDF by first converting to a TeX file and then calling the LaTeX engine to convert to PDF. By default this TeX file is removed, however if you want to keep it (e.g. for an article submission) you can specify the keep_tex option. For example:

---
title: "Habits"
output:
  pdf_document:
    keep_tex: true
---

Includes

You can do more advanced customization of PDF output by including additional LaTeX directives and/or 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:
  pdf_document:
    includes:
      in_header: header.tex
      before_body: doc_prefix.tex
      after_body: doc_suffix.tex
---

Custom Templates

You can also replace the underlying pandoc template using the template option:

---
title: "Habits"
output:
  pdf_document:
    template: quarterly_report.tex
---

Consult the documentation on pandoc templates for additional details on templates. You can also study the default LaTeX template as an example.

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:
  pdf_document:
    pandoc_args: [
      "--no-tex-ligatures"
    ]
---

Documentation on all available pandoc arguments can be found in the pandoc user guide.

Shared Options

If you want to specify a set of default options to be shared by multiple documents within a directory you can include a file named _output.yaml within the directory. Note that no YAML delimeters or enclosing output object are used in this file. For example:

_output.yaml

pdf_document:
  toc: true
  highlight: zenburn

All documents located in the same directory as _output.yaml will inherit it’s options. Options defined explicitly within documents will override those specified in the shared options file.

comments powered by Disqus