rmarkdown :: Cheatsheet (2024)

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What is rmarkdown?

.Rmd files: Develop your code and ideas side-by-side in a single document. Run code as individual chunks or as an entire document.
Dynamic Documents: Knit together plots, tables, and results with narrative text. Render to a variety of formats like HTML, PDF, MS Word, or MS PowerPoint.
Reproducible Research: Upload, link to, or attach your report to share. Anyone can read or run your code to reproduce your work.

Workflow

Open a new .Rmd file in the RStudio IDE by going to File > New File > R Markdown.
Embed code in chunks. Run code by line, by chunk, or all at once.
Write text and add tables, figures, images, and citations. Format with Markdown syntax or the RStudio Visual Markdown Editor.
Set output format(s) and options in the YAML header. Customize themes or add parameters to execute or add interactivity with Shiny.
Save and render the whole document. Knit periodically to preview your work as you write.
Share your work!

Source Editor

Expand to read about the features in the Source Editor

Features within the Source Editor

New File
Embed Code
Write Text
Set Output Format(s) and Options
Save and Render
Share

Set preview location
Insert code chunk
Go to code chunk
Run code chunk(s)
Show outline
Modify chunk options
Run all previous chunks
Run current chunk
Switch to visual editor

Visual Editor

Expand to read about the features in the Visual Editor

Features within the Visual Editor

Insert citations
Style options
Add/edit attributes
Switch to source editor

Rendered Output

Expand to read about the features in the Rendered Output Window

Features within the Rendered Output Window

File path to output document
Find in document
Publish to rpubs.com, shinyapps.io, Posit Connect
Reload document

Embed Code With knitr

Code Chunks

Surround code chunks with ```{r} and ``` or use the Insert Code Chunk button. Add a chunk label and/or chunk options inside the curly braces after r.

```{r chunk-label, include = FALSE}```

Set Global Options

Set options for the entire document in the first chunk.

```{r include = FALSE}knitr::opts_chunk$set(message = FALSE)```

Inline Code

Insert `r <code>` 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.

Build Your Bibliography

Add BibTex or CSL bibliographies to the YAML header.

---title: "My Document"bibliography: references.biblink-citations: TRUE---

If Zotero is installed locally, your main library will automatically be available.
Add citations by DOI by searching “from DOI” in the Insert Citation dialog.

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).

```{r}data <- faithful[1:4,]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.

Plain text.

Plain text.

End a line with two spaces tostart 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**

italics and bold

superscript^2^/subscript~2~

superscript² /subscript₂

~~strike through~~

~~strike through~~

escaped: \* \_ \\

escaped: * _ \

en dash: --, em dash: ---

en dash: –, em dash: —

# Header 1

## Header 2

Header 2

...

…

###### Header 6

Header 6

- unordered list- item 2 - item 2a (indent 1 tab) - item 2b

unordered list
item 2
- item 2a (indent 1 tab)
- item 2b

1. ordered list2. item 2 - item 2a (indent 1 tab) - item 2b

ordered list
item 2
- item 2a
- item 2b

<link url>

https://posit.co/

[This is a link.](link url)

This is a link.

[This is another link.][id].At the end of the document:[id]: link url

This is another link.

![Caption](image.png)or![Caption](id2)At the end of the document include:[id2]: image.png

`verbatim code`

verbatim code

```multiple linesof verbatim code```

multiple linesof verbatim code

> block quotes

block quotes

equation: $e^{i \pi} + 1 = 0$

equation: $e^{i \pi} + 1 = 0$

equation block:$$E = mc^{2}$$

equation block:

\[E = mc^{2}\]

horizontal rule:---

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

HTML Tabsets

## Results {.tabset}### Plotstext### Tablesmore text

text

more text

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 ?<output_format> 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"---
```

Call parameters in code using params$name.

```{r}data <- df[,params$state]summary(data)```

Set parameters with Knit with Parameters or the params argument of render().

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"---
```
Install the package to access template by going to File > New R Markdown > From 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"---

More on bslib at https://pkgs.rstudio.com/bslib/.

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]{.my-color} word. will render as “A green word.”
- Fenced Div
```
:::{.my-color}All of these wordsare green:::
```
  will render as
  All of these words
  are green.
Use the Visual Editor. Go to Format > Div/Span and add CSS styling directly with Edit Attributes.

Interactivity

Turn your report into an interactive Shiny document in 4 steps:

Add runtime: shiny to the YAML header.

---output: html_documentruntime: shiny---

Call Shiny input functions to embed input objects.

Call Shiny output functions to embed reactive output.

```{r echo = FALSE}numericInput("n", "How many cars?", 5)renderTable({ head(cars, input$n)})```

Render with rmarkdown::run() or click Run Document in RStudio IDE.

Also see Shiny Prerendered for better performance. https://rmarkdown.rstudio.com/authoring_shiny_prerendered.

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.

Footnotes

PDFs and Beamer slides require LaTeX, use tinytex::install_tinytex().↩︎
PDFs and Beamer slides require LaTeX, use tinytex::install_tinytex().↩︎

FAQs

What does the --- delimiter indicate in an R markdown notebook? ›

Rmd extension. The first four lines are a metadata header that indicate the title (printed at the top of your report) and the output format. The "---" delimiters indicate the start and end of the header, so you should leave them alone.

Get More Info Here ›

How to separate paragraphs in RMarkdown? ›

In order to start a new paragraph, you need to add white space between the two paragraphs: Here is an example of text with a line break and white space. You may expect this line to appear in a new paragraph and it does.

What does echo false do in r? ›

echo = FALSE prevents code, but not the results from appearing in the finished file. This is a useful way to embed figures.

Discover More ›

What does eval false do? ›

"eval = FALSE" ` will present your code without the associated output. For example: how to calculate two plus two… "echo = FALSE" will not present your code but will show the associated output.

See Details ›

What does the --- delimiter three hyphens indicate in an R Markdown notebook? ›

This header is established by a set of three dashes --- as delimiters (one starting set, and one ending set). This part of the file requires you to use YAML syntax (Yet Another Markup Language.) Within the delimiter sets of dashes, you specify settings (or metadata) that will apply to the entire document.

What delimiter should they type in their .RMD file? ›

The correct delimiter for marking the beginning of a code chunk in an R Markdown (. Rmd) file is ```{R }. This combination is essential for running R code within R Markdown documents, where backticks and braces are used to define code chunks, and the # symbol is used for comments in scripts.

Know More ›

What does this mean knitr :: opts_chunk set echo true? ›

```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` is used to specify any global settings to be applied to the R Markdown script. The example sets all code chunks as “echo=TRUE”, meaning they will be included in the final rendered version.

Explore More ›

What does unnamed chunk mean in R? ›

Chunk labels are mainly used in filenames of plots and cache. If the label of a chunk is missing, a default one of the form unnamed-chunk-i will be generated, where i is incremental.

Explore More ›

How to silence warnings in R Markdown? ›

We discussed three methods to remove warning messages in R Markdown documents: using suppressWarnings() function, setting the warnings option to FALSE in YAML metadata, and using the knitr::opts_chunk$set() function to set global options for all code chunks in the document.

Read The Full Story ›

Why eval is not recommended? ›

Malicious code : invoking eval can crash a computer. For example: if you use eval server-side and a mischievous user decides to use an infinite loop as their username. Terribly slow : the JavaScript language is designed to use the full gamut of JavaScript types (numbers, functions, objects, etc)… Not just strings!

How to hide code chunk in R Markdown? ›

To hide a specific code chunk set echo to “false” ( echo=false ). Include the code chunk in the rendered document with echo=true . Exclude the code chunk in the rendered document with echo=false .

What does "knit" mean in R? ›

There are two ways to render an R Markdown document into its final output format. If you are using RStudio, then the “Knit” button (Ctrl+Shift+K) will render the document and display a preview of it.

What does the r delimiter indicate? ›

Explanation: The "r delimiter (three backticks followed by an r contained inside curly brackets) in an R Markdown notebook indicates the start of a code chunk. This syntax is used to delineate where executable R code begins within the notebook.

Discover More Details ›

What is a delimiter in a data file? ›

Delimiters in the Data File. Delimiters are those characters in the data file that separate fields and mark the end of records.

Get More Info Here ›

What does the --- delimiter three hyphens indicate in an R Markdown notebook 1 point code chunk YAML metadata bold text italic text? ›

A YAML header (optional) at the top of the document:

The header is enclosed by two sets of three dashes --- . This block allows you to fine-tune the output of your document. It's a set of key:value pairs that describes the file that should be built from the R Markdown file.

Find Out More ›

What are the different types of delimiters in r? ›

Any character can be used as a delimiter; however, the comma, tab, and colon are the most widely used, and such data files can be read in R as follows.

Discover More Details ›