R Markdown: The Definitive Guide

To create a PDF document from R Markdown, you specify the pdf_document output format in the YAML metadata:

 --- 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 Pandoc’s documentation on the raw_tex extension for details.

Note that PDF output (including Beamer slides) requires an installation of LaTeX (see Chapter 1).

3.3.1 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 TOC depth is not explicitly specified, it defaults to 2 (meaning that all level 1 and 2 headers will be included in the TOC), while it defaults to 3 in html_document .

You can add section numbering to headers using the number_sections option:

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

If you are familiar with LaTeX, number_sections: true means \section<> , and number_sections: false means \section*<> for sections in LaTeX (it also applies to other levels of “sections” such as \chapter<> , and \subsection<> ).

3.3.2 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 (6.5x4.5 is used by default).
• fig_crop controls whether the pdfcrop utility, if available in your system, is automatically applied to PDF figures (this is true by default).
  • If you are using TinyTeX as your LaTeX distribution, we recommend that you run tinytex::tlmgr_install("pdfcrop") to install the LaTeX package pdfcrop . You also have to make sure the system package ghostscript is available in your system for pdfcrop to work. For macOS users who have installed Homebrew, ghostscript can be installed via brew install ghostscript .
  • If your graphics device is postscript , we recommend that you disable this feature (see more info in the knitr issue #1365).

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

  3.3.3 Data frame printing

  You can enhance the default display of data frames via the df_print option. Valid values are presented in Table 3.3.

  TABLE 3.3: The possible values of the df_print option for the pdf_document format.

  Option	Description
  default	Call the print.data.frame generic method
  kable	Use the knitr::kable() function
  tibble	Use the tibble::print.tbl_df() function
  A custom function	Use the function to create the table. See 3.1.6.2

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

  3.3.4 Syntax highlighting

  The highlight option specifies the syntax highlighting style. Its usage in pdf_document is the same as html_document (Section 3.1.4). For example:

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

  3.3.5 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 , and so on). For example:

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

  A few available metadata variables are displayed in Table 3.4 (consult the Pandoc manual for the full list):

  TABLE 3.4: Available top-level YAML metadata variables for LaTeX output.

  Variable	Description
  lang	Document language code
  fontsize	Font size (e.g., 10pt , 11pt , or 12pt )
  documentclass	LaTeX document class (e.g., article )
  classoption	Options for documentclass (e.g., oneside )
  geometry	Options for geometry class (e.g., margin=1in )
  mainfont, sansfont, monofont, mathfont	Document fonts (works only with xelatex and lualatex )
  linkcolor, urlcolor, citecolor	Color for internal, external, and citation links

  3.3.6 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 ---

  3.3.7 Advanced customization

  3.3.7.1 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 ---

  The main reasons you may want to use xelatex or lualatex are: (1) They support Unicode better; (2) It is easier to make use of system fonts. See some posts on Stack Overflow for more detailed explanations, e.g., https://tex.stackexchange.com/q/3393/9128 and https://tex.stackexchange.com/q/36/9128.

  3.3.7.2 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 ---

  3.3.7.3 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: preamble.tex before_body: doc-prefix.tex after_body: doc-suffix.tex ---

  3.3.7.4 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.

  3.3.8 Other features

  Similar to HTML documents, you can enable or disable certain Markdown extensions for generating PDF documents. See Section 3.1.10.4 for details. You can also pass more custom Pandoc arguments through the pandoc_args option (Section 3.1.10.5), and define shared options in _output.yml (Section 3.1.11).