rmarkdown :: Cheatsheet (2024)

Source Editor

Visual Editor

Rendered Output

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

See more options and defaults by running str(knitr::opts_chunk$get()).

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.

Output Format Table

Also see flexdashboard, bookdown, distill, and blogdown.

Output Options Table

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

Parameters

Parameterize your documents to ruse 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]{.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:

1. Add runtime: shiny to the YAML header.

   ---output: html_documentruntime: 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.