3.3 PDF document
To create a PDF document from R Markdown, you specify the pdf_document output format in the YAML metadata:
---title: "Habits"author: John Doedate: March 22, 2005output: 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_widthandfig_heightcan be used to control the default figure width and height (6.5x4.5 is used by default).fig_cropcontrols whether thepdfcroputility, if available in your system, is automatically applied to PDF figures (this istrueby default).If you are using TinyTeX as your LaTeX distribution, we recommend that you run
tinytex::tlmgr_install("pdfcrop")to install the LaTeX packagepdfcrop. You also have to make sure the system packageghostscriptis available in your system forpdfcropto work. For macOS users who have installed Homebrew,ghostscriptcan be installed viabrew install ghostscript.If your graphics device is
postscript, we recommend that you disable this feature (see more info in the knitr issue #1365).
fig_captioncontrols whether figures are rendered with captions (this istrueby default).devcontrols the graphics device used to render figures (defaults topdf).
For example:
---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.
| 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 |
For example:
---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_documentfontsize: 11ptgeometry: margin=1in---A few available metadata variables are displayed in Table 3.4 (consult the Pandoc manual for the full list):
| 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).
