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#

1. Open a new .Rmd file in the RStudio IDE by going to File > New File > R Markdown.

2. Embed code in chunks. Run code by line, by chunk, or all at once.

3. Write text and add tables, figures, images, and citations. Format with Markdown syntax or the RStudio Visual Markdown Editor.

4. Set output format(s) and options in the YAML header. Customize themes or add parameters to execute or add interactivity with Shiny.

5. Save and render the whole document. Knit periodically to preview your work as you write.

6. Share your work!

Source Editor#

Visual Editor#

Rendered Output#

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 4.5.1” 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.

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.bib
  link-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.

Table of markdown syntax and rendered examples. The syntax in the first column renders to the output in the second column.

Markdown Syntax# Plain text.	Rendered Output# Plain text.
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**	italics and bold
superscript^2^/subscript~2~	superscript^2^ /subscript2
~~strike through~~	strike through
escaped: \* \_ \\	escaped: * _ \
en dash: --, em dash: ---	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	unordered list item 2 item 2a (indent 1 tab) item 2b
1. ordered list 2. 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.
 or  At the end of the document include: [id2]: image.png
`verbatim code`	verbatim code
``` multiple lines of verbatim code ```	multiple lines of 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	Right Left Default Center 12 12 12 12 123 123 123 123 1 1 1 1 : Caption text, example rendered table.
HTML Tabsets ## Results {.tabset} ### Plots text ### Tables more text	Results# Plots# text Tables# 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.

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.

Use ?<output_format> to see all of a format’s options, e.g. ?html_document

More Header Options#

Parameters#

Parameterize your documents to reuse with new inputs (e.g. data, values, etc.).

1. Add parameters in the header as sub-values of params.

   ---
   params:
     state: "hawaii"
   ---

2. Call parameters in code using params$name.

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

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

Reusable Templates#

1. Create a new package with an inst/rmarkdown/templates directory.

2. Add a folder containing template.yaml (below) and skeleton.Rmd (template contents).

   ---
   name: "My Template"
   ---

3. 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 word. will render as “A green word.”

  • Fenced Div

    :::{.my-color}
    All of these words
    are 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:

1. Add runtime: shiny to the YAML header.

   ---
   output: html_document
   runtime: shiny
   ---

2. Call Shiny input functions to embed input objects.

3. Call Shiny output functions to embed reactive output.

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

4. 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:

1. Runs the code and embeds results and text into an .md file with knitr.
2. 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/.

CC BY SA Posit Software, PBC • info@posit.co • posit.co

Learn more at rmarkdown.rstudio.com.

Updated: 2026-10.

packageVersion("rmarkdown")

[1] '2.29'