rmarkdown :: Cheatsheet
Surround code chunks with ``` and ``` or use the Insert Code Chunk button. Add a chunk label and/or chunk options inside the curly braces after r .
Set Global Options
Set options for the entire document in the first chunk.
``` knitr::opts_chunk$set(message = FALSE) ```
Inline Code
Insert `r ` into text sections. Code is evaluated at render and results appear as text.
The markdown text
Built with `r getRversion()`
will render as “Built with 4.4.0” in the output file.
Chunk Options
Table of chunk options. The first column is the option name, the second column is the option’s default value, the third column describes what the option does. | Option | Default | Effects |
|---|
| echo | TRUE | display code in output document |
| error | FALSE | TRUE (display error messages in doc), FALSE (stop render when error occurs) |
| eval | TRUE | run code in chunk |
| include | TRUE | include chunk in doc after running |
| message | TRUE | display code messages in document |
| warning | TRUE | display code warnings in document |
| results | "markup" | "asis" (pass through results), "hide" (don’t display results), "hold" (put all results below all code) |
| fig.align | "default" | "left" , "right" , or "center" |
| fig.alt | NULL | alt text for a figure |
| fig.cap | NULL | figure caption as a character string |
| fig.path | "figure/" | prefix for generating file paths |
| fig.width & fig.height | 7 | plot dimensions in inches |
| out.width | rescales output width, e.g. "75%" , "300px" |
| collapse | FALSE | collapse all sources & output into a single block |
| comment | "##" | prefix for each line of results |
| child | NULL | file(s) to knit and then include |
| purl | TRUE | include or exclude a code chunk when extracting source code with knitr::purl() |
See more options and defaults by running str(knitr::opts_chunk$get()) .
Insert Citations
Create citations from a bibliography file, a Zotero library, or from DOI references.
- Add BibTex or CSL bibliographies to the YAML header.
--- title: "My Document" bibliography: references.bib link-citations: TRUE ---
Insert Citations
- Access the Insert Citations dialog in the Visual Editor by clicking the @ symbol in the toolbar or by clicking Insert > Citation.
- Add citations with markdown syntax by typing [@cite] or @cite .
Insert Tables
Output data frames as tables using kable(data, caption) .
``` data knitr::kable(data, caption = "Tables with kable") ```
Other table packages include flextable, gt, and kableExtra.
Write With Markdown
The syntax on the left renders as the output on the right.
Markdown Syntax
Plain text.
Rendered Output
End a line with two spaces to start a new paragraph.
End a line with two spaces to
start a new paragraph.
Also end a line with a backslash\ to make a new line.
Also end a line with a backslash
to make a new line.
*italics* and **bold**
superscript^2^/subscript~2~
~~strike through~~
escaped: \* \_ \\
en dash: --, em dash: ---
# Header 1
Header 1
## Header 2
Header 2
###### Header 6
Header 6
- unordered list - item 2 - item 2a (indent 1 tab) - item 2b
1. ordered list 2. item 2 - item 2a (indent 1 tab) - item 2b
[This is a link.](link url)
[This is another link.][id]. At the end of the document: [id]: link url
 or  At the end of the document include: [id2]: image.png
`verbatim code`
``` multiple lines of verbatim code ```
multiple lines of verbatim code
> block quotes
equation: $e^ + 1 = 0$
equation block: $$E = mc^$$
horizontal rule: ---
|Right|Left|Default|Center| |----:|:---|-------|:----:| |12 |12 |12 |12 | |123 |123 |123 |123 | |1 |1 |1 |1 | Table: Caption text, example rendered table
Caption text, example rendered table. | Right | Left | Default | Center |
|---|
| 12 | 12 | 12 | 12 |
| 123 | 123 | 123 | 123 |
| 1 | 1 | 1 | 1 |
## Results ### Plots text ### Tables more text
Results
Set Output Formats and Their Options in YAML
Use the document’s YAML header to set an output format and customize it with output options. Indent format 2 characters, indent options 4 characters.
--- title: "My Document" author: "Author Name" output: html_document: toc: true toc-location: left ---
Output Format Table
Table of output formats. The output format in the first column creates the file type in the second column. | Output Format | Creates |
|---|
| html_document | .html |
| pdf_document 1 | .pdf |
| word_document | Microsoft Word (.docx) |
| powerpoint_presentation | Microsoft PowerPoint (.pptx) |
| odt_document | OpenDocument Text |
| rtf_document | Rich Text Format |
| md_document | Markdown |
| github_document | Markdown for Github |
| ioslides_presentations | ioslides HTML slides |
| slidy_presentation | Slidy HTML slides |
| beamer_presentation 2 | Beamer slides |
Also see flexdashboard, bookdown, distill, and blogdown.
Output Options Table
Table of output options. The first column is the option name, the second column is the description and possible values, and then remaining columns show what file types each option can be applied to. | Important Options | Description | HTML | PDF | MS Word | MS PPT |
|---|
| anchor_sections | Show section anchors on mouse hover (TRUE or FALSE) | X |
| citation_package | The LaTeX package to process citations (“default”, “natbib”, biblatex”) |
| code_download | Give readers an option to download the .Rmd source code (TRUE or FALSE) | X |
| code_folding | Let readers toggle the display of R code (“none”, “hide”, or “show”) | X |
| css | CSS or SCSS file to use to style the document (e.g. “style.css”) | X |
| dev | Graphics device to use for figure output (e.g. “png”, “pdf”) | X | X |
| df_print | Method for printing data frames (“default”, “kable”, “tibble”, “paged”) | X | X | X | X |
| fig_caption | Should figures be rendered with captions (TRUE or FALSE) | X | X | X | X |
| highlight | Syntax highlighting (“tango”, “pygments”, “kate”, “zenburn”, “textmate”) | X | X | X |
| includes | File of content to place in doc (“in_header”, “before_body”, “after_body”) | X | X |
| keep_md | Keep the Markdown .md file generated by knitting (TRUE or FALSE) | X | X | X | X |
| keep_tex | Keep the intermediate TEX file used to convert to PDF (TRUE or FALSE) | X |
| latex_engine | LaTeX engine for producing PDF output (“pdflatex”, “xelatex”, or “lualatex”) | X |
| reference_docx/_doc | docx/pptx file containing styles to copy in the output (e.g. “file.docx”, “file.pptx”) | X | X |
| theme | Theme options (see Bootswatch and Custom Themes below) | X |
| toc | Add a table of contents at start of document (TRUE or FALSE) | X | X | X | X |
| toc_depth | The lowest level of headings to add to table of contents (e.g. 2, 3) | X | X | X | X |
| toc_float | Float the table of contents to the left of the main document content (TRUE or FALSE) | X |
Use ? to see all of a format’s options, e.g. ?html_document
More Header Options
Parameters
Parameterize your documents to ruse with new inputs (e.g. data, values, etc.).
Add parameters in the header as sub-values of params .
--- params: state: "hawaii" ---
``` data summary(data) ```
Reusable Templates
- Create a new package with an inst/rmarkdown/templates directory.
- Add a folder containing template.yaml (below) and skeleton.Rmd (template contents).
--- name: "My Template" ---
Bootswatch Themes
Customize HTML documents with Bootswatch themes from the bslib package using the theme output option. Use bslib::bootswatch_themes() to list available themes.
--- title: "My Document" author: "Author Name" output: html_document: theme: bootswatch: solar ---
Custom Themes
Customize individual HTML elements using bslib variables. Use ?bs_theme to see more variables.
--- output: html_document: theme: bg: "#121212" fg: "#E4E4E4" base_font: google: "Prompt" ---
Styling With CSS and SCSS
Add CSS and SCSS to your documents by adding a path to a file with the css option in the YAML header.
--- title: "My Document" author: "Author Name" output: html_document: css: "style.css" ---
Apply CSS styling by writing HTML tags directly or:
- Use markdown to apply style attributes inline.
- Bracketed Span
A [green] word. will render as “A green word.”
- Fenced Div
. All of these words are green .
will render as
All of these words are green.
Interactivity
Turn your report into an interactive Shiny document in 4 steps:
Add runtime: shiny to the YAML header.
--- output: html_document runtime: shiny ---
``` numericInput("n", "How many cars?", 5) renderTable( head(cars, input$n) >) ```
Embed a complete Shiny app into your document with shiny::shinyAppDir() . More at https://bookdown.org/yihui/rmarkdown/shiny-embedded.html.
Render
When you render a document, rmarkdown:
- Runs the code and embeds results and text into an .md file with knitr.
- Converts the .md file into the output format with Pandoc.
Save, then Knit to preview the document output. The resulting HTML/PDF/MS Word/etc. document will be created and saved in the same directory as the .Rmd file.
Use rmarkdown::render() to render/knit in the R console. See ?render for available options.
Share
Publish on Posit Connect to share R Markdown documents securely, schedule automatic updates, and interact with parameters in real-time. https://posit.co/products/enterprise/connect/.
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packageVersion("rmarkdown")
[1] '2.27'
