litedown: R Markdown Reimagined (2024)

• Preface
  • The past journey
  • A question
  • Overview
  • Highlights
    • Small footprint
    • Live preview everything
    • Precise parser
    • Versioned CSS/JS assets
    • Chunk options management
    • Non-linear order of execution
    • Time code chunks
    • Table output for data frames by default
    • Relieved pain of paths
    • Output in memory or to disk
    • A new cache system
    • A book is a single HTML file
    • R scripts as first-class citizens
    • Clean HTML output
    • Features out of scope
• 1 Knitting, or Fusing
  • 1.1 Code chunks
  • 1.2 Inline code
  • 1.3 R scripts
  • 1.4 Comparison to knitr
• 2 Markdown Syntax
  • 2.1 Basic syntax
  • 2.2 Add-on features
    • 2.2.1 Raw LaTeX/HTML blocks
    • 2.2.2 LaTeX math
    • 2.2.3 Superscripts and subscripts
    • 2.2.4 Footnotes
    • 2.2.5 Attributes
    • 2.2.6 Appendices
    • 2.2.7 Fenced Divs
    • 2.2.8 Cross-references
    • 2.2.9 Smart HTML entities
  • 2.3 Comparison to Pandoc
• 3 Markdown Rendering
  • 3.1 Markdown options
    • 3.1.1 auto_identifiers
    • 3.1.2 embed_resources
    • 3.1.3 js_highlight
    • 3.1.4 js_math
    • 3.1.5 latex_math
    • 3.1.6 number_sections
    • 3.1.7 smartypants
    • 3.1.8 superscript
    • 3.1.9 subscript
    • 3.1.10 toc
    • 3.1.11 top_level
  • 3.2 Templates
  • 3.3 YAML metadata
• 4 CSS/JS assets
  • 4.1 HTML slides
  • 4.2 HTML articles
    • 4.2.1 The overall style
    • 4.2.2 Side elements
    • 4.2.3 Body elements
  • 4.3 Tabbed sections
  • 4.4 Code folding
  • 4.5 Callout blocks
  • 4.6 Right-align a quote footer
  • 4.7 Add anchor links to headings
  • 4.8 Style keyboard shortcuts
• 5 Authoring
  • 5.1 The Knit button
  • 5.2 Live preview
  • 5.3 Visual editor
• 6 Books and Websites
  • 6.1 Books
  • 6.2 Websites
• Appendix
• A For rmarkdown Users
• B Package vignettes
• C Technical Notes
  • C.1 Embedding resources
  • C.2 CSS for margin content

The litedown package is still new and experimental. The documentation isvery incomplete. Besides, litedown was designed for minimalists with alimited scope. Average users should perhaps consider using rmarkdown orQuarto instead.

You may say I’m a dreamer
But I’m not the only one
I hope someday you’ll join us
And the world will live as one

—John Lennon, Imagine

Imagine there’s no PDF. It’s easy if you try. No Word below us. Above us, onlyHTML.

I do not mean PDF and Word are bad. I only lament the time that human beingsspend on various document formats, given how much a static web page can do.

The past journey

Having worked on the development of R Markdown for nearly 12 years, I have toconfess that I have become a little perplexed about my work, although I clearlyremember the exciting moments. For example:

• The moment when I added syntax highlighting to R code in .Rnw documents.Beautiful!

• The moment when I managed to generate a base R plot and a ggplot in the samecode chunk and place them side by side in LaTeX. Magic! Not to mention thatggplot does not require an explicit print() call in a code chunk—youprobably do not even know what that means now.

• The moment when I saw the impossible-to-read diagram that shows all possibleconversions among numerous document formats on the Pandoc homepage.Incredible!

• The moment when I discovered DZSlides in Pandoc. Wow! So PowerPoint andLaTeX beamer were not the only choices for slides.

• The moment when some rstudio::conf attendees started applauding after I toldthem that the PowerPoint support had been added to the development versionof rmarkdown when one person asked about it.

• The moment when I came across remark.js. And tufte.css. And GitBook. AndHugo. And distill.pub. And htmlwidgets, reticulate, and so on.

• …

I think the work was largely meaningful. The only problem is I do not see anend. The list of exciting things to do goes on and on.

A question

“At forty, I had no more doubts.” Confucius said. Apparently, I’m not Confucius.On the contrary, as I’m turning forty, I’m having more doubts. I have beenreflecting on the things that have kept me busy.

If I were to summarize the 700+ episodes of Naruto in one sentence, I would usethe question that Gaara (the Fifth Kazekage) asked Onoki (the Third Tsuchikage):

When did you all forsake yourselves?

In my opinion, this question was the most critical turning point in the 700+episodes, reminding the 79-year-old Onoki and the rest of people of theiroriginal dreams. The shinobi world existed to put an end to wars, but it turnedout to bring even more and larger-scale wars.

When did we forsake simplicity? We create software to simplify things, butsoftware often ends up in feature wars.

Markdown was originally invented for simplicity. That is, to make it easier towrite HTML. I used to take out my wallet and tell people that if they are unableto learn the basics of Markdown in 5 minutes, I’d award them 20 dollars. I alsoused to say “In HTML I Trust”, which sounds like a joke, but I really love HTMLand web technologies. Again, I do not mean other document formats are bad atall. It is just that I feel HTML has the greatest potential, and I hope to takefull advantage of its power.¹

In other words, I do not expect that “the (software) world will live as one”. Ijust want to make the HTML world a little bit better.

Overview

The litedown package is an attempt to reimagine R Markdown with one primarygoal—do HTML, and do it well, with the minimalism principle. Before LaTeX fanswalk away in disappointment, let me quickly clarify that LaTeX output is alsosupported, but please do not expect anything fancy before you learn to customizeLaTeX templates. Most other output formats are not supported. No Word, RTF,PowerPoint, or EPUB.

R Markdown is rendered via litedown::fuse(), which is similar tormarkdown::render() and knitr::knit(). Markdown is rendered vialitedown::mark(), which uses commonmark instead of Pandoc.

The commonmark package follows the GFM (GitHub Flavored Markdown) spec,which can be seen as a subset of Pandoc’s Markdown. Therefore the litedownpackage can be viewed as a small subset of the current R Markdown ecosystem (thelatter is based on Pandoc). It aims at simplicity, lightweight, and speed, atthe cost of giving up some advanced features. This package is intended forminimalists. Most users may prefer using tools based on Pandoc instead, such asrmarkdown or Quarto, which offer richer features.

Is litedown really simple? From the developer’s perspective, yes, it is,largely due to the limited scope of the package. From the user’s perspective,some features are definitely not that simple. However, the point is that thecore is simple and small, and you can enable or disable most features. What’smore, you can implement features by yourself if you know CSS/JS.

Highlights

Small footprint

Almost everything in litedown was written from scratch. The package is verylightweight. Currently, it has two dependencies, commonmark andxfun.² It does not depend on knitr or Pandoc.

It is a deliberate design choice to keep this package lightweight, to make itrelatively easy to use and simple to maintain. The functions mark() andfuse() can be viewed as significantly trimmed-down versions of Pandoc andknitr, respectively.

It is absolutely not the goal for litedown to become a substitute of toolsbased on knitr and Pandoc, such as rmarkdown and Quarto. If you are notsure if you should choose litedown or rmarkdown/Quarto, you may want tochoose the latter (especially Quarto). Some litedown features may be portedinto knitr in the future.

Live preview everything

To get started, run litedown::roam() and it will launch a file browser to letyou preview everything that can be rendered to HTML, such as .md, .Rmd, and.R files. The rendering takes place in memory, which means it will not render.html files on your disk, unless you request so. The page will beautomatically updated as you edit and save a file. This update-on-save featurecan be turned off, and then you can manually refresh the page to re-render thefile whenever you want.

You can open any file in your editor or the default system application byclicking a button in the browser. You can also render a file or a project in anew R session by clicking a button in the browser.

Precise parser

The R Markdown parser stores the precise line and column numbers of codeelements. The location information is used in various places. For example, whenan error occurs, you will get a message that tells you the precise location inthe source. In editors that support ANSI links (such as the RStudio IDE), youcan even click on the message to go to a specific line/column in the sourcedocument, so you can quickly and easily know where the error occurred exactly.When previewing .Rmd documents with roam(), you will see line numbers on theleft side of code blocks. Clicking on these numbers will bring you to the linesin the source.

Due to the fact that the parser is based on commonmark (instead of solely onregular expressions like knitr’s parser), it can precisely recognize codechunks and inline code, which means code within other verbatim code blocks orcomments will be untouched. For example:

````mdBelow is not a code chunk but verbatim contentinside a fenced code block (with four backticks).```{r}1 + 1```Inline code expressions like `{r} 1+1` are notparsed, either.````

<!--Feel free to comment out anything, such as a code chunk:```{r}1 + 1```-->

Versioned CSS/JS assets

By default, litedown produces bare minimal HTML output, but many featurescan be enabled by adding CSS/JS assets (see 4). You can freely choosewhatever versions that work for you to avoid potential future breakage when theassets are upgraded. The assets are not bundled in the litedown package, buthosted on CDN, so updating litedown will not update your assets.

The CSS and JS code for commonly used features do not depend on any frameworkssuch as Bootstrap or jQuery. They are simply vanilla code written from scratch.No generator was used (such as SCSS). The code is often relatively short, so youcould just fork the code, modify it, publish your own version, and use it if youare not satisfied with the original version.

Chunk options management

Chunk options are managed by an environment, i.e., litedown::reactor(). Usingan environment (as compared to a list like knitr’s opts_chunk) means youcan access the up-to-date chunk options anywhere, because environments in R aremutable. I cannot explain how awkward knitr’s opts_current has been. It isbasically a lie—chunk options that you get from opts_current are notnecessarily “current”.

Non-linear order of execution

A document does not have to be compiled in the linear order. With the chunkoption order, you can specify code chunks and inline code expressions to beexecuted in an arbitrary order. For example, if you have an abstract in thebeginning of a document, and the abstract needs to use a number calculated atthe end of the document, you can let the abstract be compiled in the end,although it appears earlier in the document.

I guess some users may want to kill me upon knowing this feature, and some maysend me flowers (although I’m not sure if they want to thank me or prepare theflowers for my funeral). For those who want to kill me, please note that thisfeature does not mean litedown is as awful as Jupyter notebooks. It meansyou can specify a fixed order to execute code in the document. The order doesnot have to be from beginning to end, but it is deterministic. In other words,it does not mean you run code chunks in an arbitrary or random order that candetriment reproducibility.

Time code chunks

If you want to figure out which code chunks are time-consuming, simply set thechunk option litedown::reactor(time = TRUE) in the beginning, and putlitedown::timing_data() in the last code chunk. It will tell you detailedinformation. In the roam() preview, the data will also contain links tospecific lines of code chunks, so you click to jump to a specific code chunk.

Table output for data frames by default

Rectangular objects such as data frames (including tibbles) and matrices areprinted as tables by default, and the number of rows is limited to 10 by defaultto avoid generating huge tables by accident.

Relieved pain of paths

File paths (such as image paths) have been a mess in knitr. My deepestapologies for that. I have worked much harder in litedown in this regard.

Output in memory or to disk

Functions such as mark(), fuse(), and fuse_book() can operate in memorywithout writing to disk. By default, if you pass a file input, you get a fileoutput; if you pass text input, you get text output.

A new cache system

You can feel more confident with using the chunk option cache = TRUE inlitedown than in knitr. The new cache system is more robust andintelligent.

A book is a single HTML file

Unlike bookdown and Quarto, litedown::fuse_book() renders multiple inputfiles to a single output file. Yes, your whole precious book is in a single(HTML or PDF) file. Grab and go.

The assumption of single-file output for books has made several things a loteasier. For example, if you want to search within the book, just pressCtrl + F or Command + F in your browser as you usually do on any other webpage. You do not need a client-side search library. It is also quicker to jumpbetween chapters because they are on the same page. If you want to print theHTML version of the book to PDF, just press Ctrl + P or Command + P.

I know you have a concern: wouldn’t the single HTML file be too heavy for thebrowser? The answer is: you should be fine if you do not have too many images.If you do, do not base64 encode them (which is the default), and you can alsolazy-load images to make the book load faster.

R scripts as first-class citizens

An R script has the same status as an R Markdown document. You can writeMarkdown in #' comments, and chunk options in #| comments (both areoptional). These are the only two rules to remember. Compared toknitr::spin(), the rules are much simpler. Besides, R scripts are alsocarefully parsed into “code chunks”, so their line numbers work as well as RMarkdown’s line numbers.

Any application that you can create with R Markdown can be created with Rscripts, such as books and websites.

Clean HTML output

The HTML output generated from litedown is very clean. For example, codeblocks in HTML output contain plain code, instead of full of <span> tags withrandom attributes. Clean HTML output means the output file size is smaller, andmore importantly, it is easier to inspect the differences between two versionsof output (e.g., in Git). Every time when you update the source document, youcan know more clearly what has changed in the output, which can help you avoidunexpected changes before publishing the output.

Features out of scope

Output formats besides HTML and LaTeX are unlikely to be supported.³ If otheroutput formats are desired, you may use Pandoc to do the conversion.

For tables, only pipe tables are supported. Other table formats are notrecognized.

At the moment, litedown mainly supports R as the computing language. Otherlanguages might be added in the future, but please keep your expectation low,because the support is unlikely to be as good as R.

HTML widgets are not supported yet, but may be reimagined in the future withsome minimal support.

R Markdown documents need to be knitted to Markdown before being rendered to atarget output format. The function litedown::fuse() plays a role similar toknitr::knit(). It “fuses” program code with narratives, i.e., it executes allcode in the source document and interweaves results with narratives in theoutput document. Similar to knitr, litedown supports code chunks andinline code.

1.1 Code chunks

A code chunk consists of the language name, chunk options (in the chunk headeror pipe comments), and the code:

```{lang}#| chunk optionscode```

Currently, a subset of knitr chunk options aresupported, which can be accessed in litedown::reactor(). To get an optionvalue, use reactor("NAME"), where NAME is the option name (e.g.,fig.width). To set an option globally, use reactor(NAME = VALUE).Alternatively, you can manipulate the value returned by reactor() directly,which is essentially an environment:

opts = litedown::reactor()opts$fig.width # get an optionopts$echo = FALSE # set an option

Code chunks inside other code blocks are not parsed or evaluated, which providesa way to write verbatim code chunks, e.g.,

````markdownSome verbatim content.```{r}1 + 1```````

Similarly, code in comments will not be recognized, either, e.g.,

<!--Do not run this chunk:```{r}1 + 1```or the inline code `{r} pi`.-->

If N + 1 pairs of curly braces are used in the opening fence, the chunk fences(with N pairs of curly braces) and chunk options will be shown in the output,which can be useful for telling readers the full source of a chunk, e.g.,

```{{r}}#| echo = TRUE, eval = FALSE1 + 1```

1.2 Inline code

The syntax for inline code expressions is `{lang} code`, where lang isthe language name, e.g., r. Spaces are allowed after the opening backtick andbefore the closing backtick. If the code happens to contain N backticks, youwill need to use at least N + 1 backticks outside, e.g.,``{r} paste("`", rnorm(1), "`")``. An inline code expression insideanother piece of inline code is not parsed or evaluated, which provides a way towrite verbatim inline code expressions, e.g., `` `{lang} code` ``.

Comma-separated chunk options can also be provided to inline code expressionsafter the language name, e.g., `{r, eval=FALSE} code`.

For knitr users, please note that the syntax `r code` is not supportedby default. You have to wrap the language name r in curly braces. As atemporary workaround, you may set options(litedown.enable.knitr_inline = TRUE)in your .Rprofile to make litedown recognize `r code`, but werecommend that you convert the document via litedown:::convert_knitr() insteadif you decide to stay with litedown in the long run.

1.3 R scripts

Besides R Markdown, you can also pass an R script to fuse(). You can writeMarkdown content in #' comments, and group lines of code into chunks by #|comments, e.g.,

#' ---#' title: An R script#' output:#' litedown::latex_format: null#' ---#' #' A _paragraph_.#| eval=FALSE1:101 + 1#| fig.width=10, dev='pdf'plot(cars)

Both #' and #| comments are optional.

1.4 Comparison to knitr

Major differences between knitr and litedown include:

If you feel any indispensable features are missing in litedown, please feelfree to suggest them in Github issues.However, please remember that the goal of litedown is not to fullyre-implement rmarkdown, knitr or Pandoc. Some features may never bere-implemented, especially when the implementation is not simple enough.

2.1 Basic syntax

For the full list of supported document elements, please read the GFM spec.Below is a quick summary:

• Headings start with a number of #’s, e.g., ## level-two heading.

• Inline elements: **strong**, _emphasis_, ~~strikethrough~~,[text](link), and ![alt](image/path).⁴

• Inline code is written in a pair of backticks, e.g., `code`. Codeblocks can be indented, or fenced by ```.

• List items start with -, +, or *, e.g., - item. A task list item isa regular list item with [ ] or [x] in the beginning, e.g.,- [ ] item.

• Block quotes start with >.

• Tables are created with | as the column separator (i.e., Pandoc’s pipetable, which can be generated by knitr::kable(x, "pipe") orxfun::md_table()).

2.2 Add-on features

In addition to GFM features, the litedown package also supports thefollowing features.

2.2.1 Raw LaTeX/HTML blocks

Raw LaTeX and HTML blocks can be written as fenced code blocks with languagenames =latex (or =tex) and =html, e.g.,

```{=tex}This only appears in \LaTeX{} output.```

Raw LaTeX blocks will only appear in LaTeX output, and will be ignored in otheroutput formats. Similarly, raw HTML blocks will only appear in HTML output. Oneexception is raw LaTeX blocks that are LaTeX math environments, which also workfor HTML output (see the next section).

2.2.2 LaTeX math

You can write both $inline$ and $$display$$ LaTeX math, e.g.,\(\sin^{2}(\theta)+\cos^{2}(\theta) = 1\)

$$\bar{X} = \frac{1}{n} \sum_{i=1}^n X_i$$

$$|x| = \begin{cases} x &\text{if } x \geq 0 \\ -x &\text{if } x < 0 \end{cases}$$

LaTeX math environments are also supported, e.g., below are an alignenvironment and an equation environment:

\begin{align}a^{2}+b^{2} & = c^{2}\\\sin^{2}(\theta)+\cos^{2}(\theta) & = 1\end{align}\begin{equation}\begin{split}(a+b)^2 &=(a+b)(a+b)\\ &=a^2+2ab+b^2\end{split}\end{equation}

These math environments can be written in raw LaTeX blocks, and they work forboth LaTeX and HTML output, e.g.,

```{=latex}\begin{align}a^{2}+b^{2} & = c^{2}\\\sin^{2}(\theta)+\cos^{2}(\theta) & = 1\end{align}```

For HTML output, it is up to the JavaScript library (MathJax or KaTeX) whether amath environment can be rendered.

2.2.3 Superscripts and subscripts

Write superscripts in ^text^ and subscripts in ~text~ (same syntax asPandoc’s Markdown), e.g., 2¹⁰ and H₂O. Currently only alphanumericcharacters, *, (, and ) are allowed in the scripts. For example, a^b c^will not be recognized as a superscript (because the space is not allowed). Notethat GFM supports striking out text via ~text~, but this feature has beendisabled and replaced by the feature of subscripts in litedown. To strikeout text, you must use a pair of double tildes.

2.2.4 Footnotes

Insert footnotes via [^n], where n is a footnote number (a uniqueidentifier). The footnote content should be defined in a separate block startingwith [^n]:. For example:

Insert a footnote here.[^1][^1]: This is the footnote.

The support is limited for LaTeX output at the moment,⁵ and thereare two caveats if the document is intended to be converted to LaTeX:

• The footnote content must be a single paragraph.

• Only numbers⁶ are supported as identifiers, and other types ofidentifiers are not recognized.

The two limitations do not apply to HTML output, e.g., you can write arbitraryelements in footnotes and not necessarily one paragraph.

2.2.5 Attributes

Attributes on images, fenced code blocks, and section headings can be written in{}. For example, ![text](path){.foo #bar width="50%"} will generate an<img> tag with attributes in HTML output:

<img src="path" alt="text" id="bar" class="foo" width="50%" />

and ## Heading {#baz} will generate:

<h2 id="baz">Heading</h2>

For fenced code blocks, a special rule is that the first class name will betreated as the language name for a block, and the class attribute of theresult <code> tag will have a language- prefix. For example, the followingcode block

```{.foo .bar #my-code style="color: red;"}```

will generate the HTML output below:

<pre> <code class="language-foo bar" id="my-code" style="color: red;"> </code></pre>

Most attributes in {} are ignored for LaTeX output except for:

• The width attribute for images, e.g., ![text](path){width="50%"} will beconverted to \includegraphics[width=.5\linewidth]{path}.

• The .unnumbered attribute, which will make a heading unnumbered, e.g.,# Hello {.unnumbered} will be converted to \section*{Hello}.

• The .appendix attribute on a heading, which will start the appendix, e.g.,# Appendix {.appendix} will be converted to \appendix.

2.2.6 Appendices

When a top-level heading has the attribute .appendix, the rest of the documentwill be treated as the appendix. If section numbering is enabled(3.1.6), the appendix section headings will be numbereddifferently.

2.2.7 Fenced Divs

A fenced Div can be written in ::: fences. Note that the opening fence musthave at least one attribute, such as the class name. For example:

::: fooThis is a fenced Div.:::::: {.foo}The syntax `::: foo` is equivalent to `::: {.foo}`.:::::: {.foo #bar style="color: red;"}This div has more attributes.It will be red in HTML output.:::

A fenced Div will be converted to <div> with attributes in HTML output,e.g.,

<div class="foo" id="bar" style="color: red;"></div>

For LaTeX output, it can be converted to a LaTeX environment if both the classname and an attribute data-latex are present. For example,

::: {.tiny data-latex=""}This is _tiny_ text.:::

will be converted to:

\begin{tiny}This is \emph{tiny} text.\end{tiny}

The data-latex attribute can be used to specify arguments to the environment(which can be an empty string if the environment doesn’t need an argument). Forexample,

::: {.minipage data-latex="{.5\linewidth}"}

will be converted to:

\begin{minipage}{.5\linewidth}

If a fenced Div doesn’t have the data-latex attribute, the fence will beignored, and its content will be written out normally without a surroundingenvironment. If a fenced Div has multiple class names (e.g., {.a .b .c}),only the first class name will be used as the LaTeX environment name. However,all class names will be used if the output format is HTML (e.g.,<div class="a b c">).

2.2.8 Cross-references

To cross-reference an element, it must be numberd first. For section headings,the numbers are automatically generated if the number_sections option is true.For other elements, they must contain empty anchors of the form [](#@ID),where ID is the ID of the element to be referenced. For figures, these anchorsare automatically generated if the chunk options fig.cap (figure caption) andfig.env are not empty, e.g.,

```{r}#| nice-plot, fig.cap="A nice caption", fig.env=".figure"plot(cars)```

To refer to an element in the text, use the syntax @ID, e.g.,

Please see @fig-nice-plot for an overview of the `cars` data.

2.2.9 Smart HTML entities

“Smart” HTML entities can be represented by ASCII characters, e.g., you canwrite fractions in the form n/m. Below are some example entities:

2.3 Comparison to Pandoc

As mentioned earlier, a lot of features in Pandoc’s Markdown are not supportedin the litedown package. Any feature that you find missing in previoussections is likely to be unavailable. In addition, a lot of R Markdown andQuarto (both are based on Pandoc) features are not supported, either. Some HTMLfeatures have been implemented via JavaScript and CSS.

Pandoc can convert Markdown to many output formats, such as Word, PowerPoint,LaTeX beamer, and EPUB. The litedown package is unlikely to support outputformats beyond HTML and LaTeX.

The main function to convert Markdown to other formats is litedown::mark().

You can either call litedown::mark() to render a Markdown documentprogrammatically, or click the Knit button in RStudio to render a (Markdown orR Markdown) document interactively. The latter requires you to specify theoutput format in the output field in YAML metadata (3.3), e.g.,

---output: litedown::html_format: options: js_math: package: "katex" version: "0.16.4" number_sections: true embed_resources: ["local", "https"] meta: css: "custom.css"---

3.1 Markdown options

The options argument of mark() can be used to enable/disable/set options tocontrol Markdown rendering. This argument can take either a list, e.g.,list(toc = TRUE, smart = FALSE), or a character vector, e.g.,c("+toc", "-smart"), or equivalently, +toc-smart, where + means to enablean option, and - means to disable an option. The options can also be set inYAML metadata in 3.3 (recommended). Available options are listedbelow.

3.1.1 auto_identifiers

Add automatic IDs to headings, e.g.,

# Hello world!

will be converted to

<h1 id="sec-hello-world">Hello world!</h1>

You can override the automatic ID by providing an ID manually via the IDattribute, e.g.,

# Hello world! {#hello}

An automatic ID is generated by substituting non-alphanumeric characters in theheading text with hyphens. If the result is empty, the ID will be section. Ifany ID is duplicated, a numeric suffix will be added to the ID, e.g.,example_1 and example_2. A prefix sec- will be added to the automatic IDs.

3.1.2 embed_resources

Embed resources (images, CSS, and JS) in the HTML output using theirbase64-encoded data (images) or raw content (CSS/JS). Possible values are:

• null or false: Do not embed any resources.

• "local" or true: Embed local image/CSS/JS files.

• "https": Embed web resources (links that start with https://).

• "all": An alias to the union of "local" and "https".

The default is "local", i.e., local resources are embedded, whereas httpsresources are not. This means the output document may not work offline. If youhave to view the output offline, you need to use the option value "https" (or"all") and render the document at least once before you go offline.

3.1.3 js_highlight

Specify the JavaScript library to syntax highlight code blocks. Possible valuesare highlight (highlight.js) and prism(Prism.js). The default is prism. This option can alsotake a list of the form list(package, version, style, languages), whichspecifies the package name (highlight or prism), version, CSS style/themename, and names of languages to be highlighted.

• You can find information about Prism.js from its CDN athttps://cdn.jsdelivr.net/npm/prismjs/. Available styles are under thethemes/ directory (e.g., prism-dark), and languages are under thecomponents/ directory (e.g., prism-c). You can omit the prefix prism-,e.g.,

  js_highlight: package: prism style: dark languages: [r, latex, yaml]

• The CDN of highlight.js is athttps://cdn.jsdelivr.net/gh/highlightjs/cdn-release/build/. Themes areunder the styles/ directory (e.g., github), and you can find demos ofthemes at https://highlightjs.org/static/demo/. Supported language areunder the languages/ directory (e.g., latex).

By default, languages are automatically detected and the required JS files areautomatically loaded. Normally you need to specify the languages array only ifthe automatic detection fails.

Technically this option is a shorthand for setting the metadata variables cssand js in 3.3. If you want full control, you may disable thisoption (set it to false or null) and use metadata variables directly, whichrequires more familiarity with the JS libraries and the jsdelivr CDN.

3.1.4 js_math

Specify the JavaScript library for rendering math expressions in HTML output.Possible values are "mathjax" and "katex" (the default). Like thejs_highlight option, this option is also essentially a shorthand for settingthe metadata variables css and js.

• For MathJax, the js variable isset to tex-mml-chtml.js.

• For KaTeX, the js variable is setto katex.min.js and the css variable is set to katex.min.css. KaTeX’sauto-render extension (auto-render.min.js) is also enabled by default,so math expressions can be immediately rendered when the page is loaded.

If you want finer control, you can provide a list of the formlist(package, version, css, js). This will allow you to specify the packagename, version, and css/js files. For example, if you want to use MathJax’stex-chtml.js instead, you may set:

js_math: package: mathjax version: 3 js: es5/tex-chtml.js

By default, MathJax version 3 is used. If you want to use the older v2, you mayset:

js_math: package: mathjax version: 2 js: MathJax.js?config=TeX-AMS-MML_CHTML

Please visit the MathJax CDN to knowwhich versions and JS files are available.

For KaTeX, the version is not specified by default, which means the latestversion from the CDN. Below is an exampleof specifying the version 0.16.4 and using the mhchem extension:

js_math: package: katex version: 0.16.4 js: [dist/katex.min.js, dist/contrib/mhchem.min.js]

Note that if you want the HTML output to be self-contained via theembed_resources option, KaTeX can be embedded and used offline, but MathJaxcannot be fully embedded due to its complexity. MathJax v3 can be partiallyembedded and used offline, but currently only its fonts can be embedded, andextensions cannot. If you must view HTML output offline, we recommend usingKaTeX, but please also note that KaTeX and MathJax do not fully cover eachother’s features.

3.1.5 latex_math

Whether to identify LaTeX math expressions in pairs of single ($ $) or doubledollar signs ($$ $$), and transform them so that they could be correctlyrendered by MathJax (HTML output) or LaTeX.

3.1.6 number_sections

Whether to number section headings. To skip numbering a specific heading, add anattribute {.unnumbered} to it.

3.1.7 smartypants

Whether to translate certain ASCII strings into smart typographic characters(see ?litedown::smartypants).

3.1.8 superscript

Whether to translate strings between two carets into superscripts, e.g.,text^foo^ to text<sup>foo</sup>.

3.1.9 subscript

Whether to translate strings between two tildes into subscripts, e.g.,text~foo~ to text<sub>foo</sub>.

3.1.10 toc

Whether to generate a table of contents (TOC) from section headings. If aheading has an id attribute, the corresponding TOC item will be a link to thisheading. You can also set a sub-option:

• depth: The number of section levels to include in the TOC (3 bydefault). Setting toc to true is equivalent to:

  toc: depth: 3

3.1.11 top_level

The desired type of the top-level headings in LaTeX output. Possible values are'chapter' and 'part'. For example, if top_level = 'chapter', # headingwill be rendered to \chapter{heading} instead of the default\section{heading}.

Options not described above can be found on the help pages of commonmark,e.g., the hardbreaks option is for the hardbreaks argument ofcommonmark::markdown_*() functions, and the table option is for the tableextension in commonmark’s extensions.

litedown::markdown_options()

#> [1] "-hardbreaks" "-number_sections" "-smartypants" #> [4] "-tagfilter" "-toc" "+auto_identifiers"#> [7] "+autolink" "+cross_refs" "+embed_resources" #> [10] "+js_highlight" "+js_math" "+latex_math" #> [13] "+smart" "+strikethrough" "+subscript" #> [16] "+superscript" "+table" "+tasklist" 

# commonmark's argumentsopts = formals(commonmark::markdown_html)opts = opts[setdiff(names(opts), c('text', 'extensions'))]unlist(opts)

#> hardbreaks smart normalize sourcepos footnotes #> FALSE FALSE FALSE FALSE FALSE 

# commonmark's extensionscommonmark::list_extensions()

#> [1] "table" "strikethrough" "autolink" "tagfilter" #> [5] "tasklist" 

3.2 Templates

By default, mark() generates a document fragment (i.e., the body) if the inputdoes not contain YAML metadata at the beginning. To generate a full document,you need to specify YAML metadata. A full document is generated with a template.Below is a simple HTML template example:

<html> <head> <title>$title$</title> </head> <body> $body$ </body></html>

It contains two variables, $title$ and $body$. All variables will besubstituted by metadata values, except for $body$, which is from the body ofthe input document (after conversion to a target output format).

The litedown has provided default templates forHTMLandLaTeXoutput. To pass metadata to templates, use the meta argument, e.g.,

litedown::mark(..., meta = list(title = "My Title"))

If you want to use a custom template file, you can either set the path in theglobal option litedown.FORMAT.template (where FORMAT is the output formatname (html or latex), e.g., in .Rprofile:

options(litedown.html.template = 'path/to/my/template.html')

The global option will be applied to all documents to be converted by mark().Alternatively, you can pass a template path to the template argument of theoutput format litedown::html_format or litedown::latex_format in anindividual document, e.g.,

---output: litedown::html_format: template: "path/to/my/template.html"---

The template path can also take a logical value: TRUE means to use the defaulttemplate, and FALSE means to generate only a fragment document without usingany template.

Alternatively, the meta argument can read YAML metadata in the Markdowndocument. The following variables can be set in the top-level fields in YAML:

• author: The document author(s).

• date: The date.

• title: The document title.

For example:

---title: "My Title"author: "[Frida Gomam](https://example.com)"date: "2023-01-09"---

Note that you can use Markdown syntax in them.

Other variables need to be specified underoutput -> litedown::*_format -> meta, where * can be html or latex,e.g.,

---title: "My Title"output: litedown::html_format: meta: css: "style.css" js: "script.js" litedown::latex_format: meta: documentclass: "book" header_includes: "\\usepackage{microtype}"---

The following metadata variables are supported for both HTML and LaTeXtemplates:

• header-includes, include-before, include-after: Either a vector of(HTML/LaTeX) code or a code file to be included in the header, before thebody, or after the body of the output.

Variables specific to the HTML template:

• css: A vector of CSS files to be included in the output. The default valueis litedown:::pkg_file('resources', 'default.css').

  If you want to use built-in CSS files in this package, you can only specifythe base name, e.g., default means default.css in this package.

  You can also use web resources, e.g., https://example.org/style.css. Onespecial case is jsdelivr resources: if a cssvalue starts with @, it will be recognized as a jsdelivr.com resource. ifyou are not familiar with jsdelivr, you may read its documentation tounderstand the following example URLs. The shorthand syntax is as follows(CDN stands for https://cdn.jsdelivr.net):

  • @foo (without a filename extension) will be converted toCDN/npm/@xiee/utils/css/foo.min.css, e.g., @default meansCDN/npm/@xiee/utils/css/default.min.css. If you prefer the .cssextension over .min.css, you can use @default.css.

  • @foo@version (a filename followed by a version number) will beconverted to CDN/npm/@xiee/utils@version/css/foo.min.css, e.g.,@[emailprotected] meansCDN/npm/@xiee/[emailprotected]/css/article.min.css.

  • @path/to/file (i.e., a value that contains slashes) will be convertedto CDN/path/to/file, e.g., @npm/@xiee/utils/js/center-img.js will beconverted to CDN/npm/@xiee/utils/js/center-img.min.js.

  • @path/to/file-1,file-2 (comma-separated values and later values do notcontain slashes) will be converted toCDN/combine/path/to/file-1,path/to/file-2 (this can be useful tocombinemultiple resources and load all at once).

  • @path-1/to/file-1,path-2/to/file-2 (comma-separated values and latervalues contain slashes) will be converted toCDN/combine/path-1/to/file-1,path-2/to/file-2.

  This provides a way to reduce the output HTML file size by loading CSS fromthe web instead of embedding inside HTML, at the cost of requiring Internetconnection when viewing the HTML file. If you need the external webresources to work after you go offline, you can enable "https" in theMarkdown option embed_resources in advance to embed the resources.

• js: A vector of JavaScript files to be included in the output. The syntaxis the same as the css variable, e.g., snap means snap.js in thispackage, and @snap means a “jsdelivr” resource.

• body-class: A class name for the main body (the default value is body).

Variables specific to the LaTeX template:

• classoption: A string containing options for the document class.

• documentclass: The document class (by default, article).

Note that you can use either underscores or hyphens in the variable names.Underscores will be normalized to hyphens internally, e.g., header_includeswill be converted to header-includes. This means if you use a custom template,you must use hyphens instead of underscores as separators in variable names inthe template.

The above are variables supported in the default templates. If you use a customtemplate, you can use arbitrary variable names consisting of alphanumericcharacters and hyphens, except for $body$ (which is a reserved name), and yourmetadata values will be passed to these variables in your template.

Besides metadata variables, the aforementioned Markdown options can also be setin YAML under output -> litedown::*_format -> options, e.g.,

output: litedown::html_format: options: toc: true js_highlight: package: highlight theme: github languages: [diff, latex]

See the help page ?litedown::html_format for possible fields in addiction tometa and options that can be specified under the format name, e.g.,

output: litedown::latex_format: latex_engine: xelatex keep_md: true template: custom-template.tex

The litedown package aims at lightweight with a minimal number of featuresat its core, but you can add more features by yourself. In this chapter, weintroduce some CSS/JS assets from the GitHub repositoryhttps://github.com/yihui/misc.js. You can load arbitrary external JS and CSSfiles via the js and css meta variables. There are numerous JS libraries andCSS frameworks on the web that you can use, and you do not have to use the onesmentioned in this chapter. You can also write CSS/JS by yourself to enhance yourHTML applications.

Remember that the CSS and JS are introduced under the output formatlitedown::html_format in YAML metadata, e.g.,

---output: litedown::html_format: meta: css: ["one.css", "two.css"] js: ["three.js", "four.js"]---

For the sake of brevity, we will omit the full YAML fields in examplesthroughout this chapter but only use the css and js fields. A file namefoo.js denotes the file under the js/ directory of the aforementionedyihui/misc.js repository. Similarly, foo.css is under the css/ directory.

All these CSS/JS resources can be used offline, and there are two ways to do it.One way is to clone the GitHub repo to your working directory, and use the filesyou need, e.g.,

js: ["repo/path/js/callout.js"]

Another way is to enable embedding resources:

output: litedown::html_format: meta: js: ["@callout"] options: embed_resources: ["https"]

After you have embedded CSS/JS resources once when you have Internet access,these resources will be cached locally and will not require an Internetconnection again. This solution works for any online resources, not limited tothe yihui/misc.js repository.

4.1 HTML slides

With snap.css and snap.js, you can create lightweight HTML slides:

css: ["@default", "@snap"]js: ["@snap"]

You can learn more in vignette('slides', package = 'litedown').

4.2 HTML articles

We can style an HTML page in an article format via the following CSS and JS:

css: ["@default", "@article"]js: ["@sidenotes", "@appendix"]

The article.css is mainly for styling the article frontmatter, body, and sidecontent.

• The sidenotes.js is required only if you want to place certain elements onthe left or right side, such as the table of contents (TOC), footnotes, andsidenotes.

• The appendix.js is required only if you have an appendix in the article.

The web version of this book is also based on the article format, so you knowwhat an article format looks like when you read the HTML version of the book.

4.2.1 The overall style

The maximum width of the article body is 800px. For larger screens, this meansthere will be extra space in the left/right margin, where we can place auxiliaryinformation, such as the TOC and footnotes. On smaller screens, the side contentwill be collapsed into the body.

The article frontmatter, body, and optionally the appendix are placed inseparate boxes.

The default typeface is sans-serif, and you can customize it by supplying anexternal CSS file (via the css meta variable) or just embedding CSS in thedocument body, e.g.,

```{css, echo=FALSE}body { font-family: Palatino, "Book Antiqua", Georgia, serif; font-size: 1em;}```

4.2.2 Side elements

The TOC and footnotes are automatically placed in the margin if space permits.You can also write arbitrary content in the margin via a fenced Div.

4.2.2.1 The TOC

The TOC is sticky on the left side as you scroll down the article. If you do notlike this behavior, you may cancel it via CSS:

#TOC { top: unset;}

4.2.2.2 Footnotes

Footnotes are moved to the right side. When you move your cursor over a footnotenumber in the body, the footnote will be moved next to your cursor. This can beconvenient when you have multiple footnotes on a line, since you do not need tolook for a specific footnote in the margin.

4.2.2.3 Arbitrary sidenotes

You can write anything in the margin by using a fenced Div with the classes.side and .side-left or .side-right.

And here is a note on the right side. Seriously, we should letcommonmark’s authors know that fenced Divs reallydeserve first-class support! They can make Markdown infinitely customizable.

::: {.side .side-left}**Anything** on the left.:::

::: {.side .side-right}_Anything_ on the right.:::

4.2.3 Body elements

Inside the article body, you can write a few special elements.

4.2.3.1 Full-width elements

When an element is wider than the article body, you can show it in its fullwidth by enclosing the element in a fenced Div with the class .fullwidth,e.g.,

::: {.fullwidth}![text](path/to/image):::

If you use R Markdown, you can generate a wide plot or table from an R codechunk, e.g.,

::: {.fullwidth}```{r}#| sunspots, echo=FALSE, fig.dim=c(14, 4),#| fig.cap='Monthly mean relative sunspot numbers from 1749 to 1983.'par(mar = c(4, 4, .1, .1), bg = 'lightgoldenrodyellow', fg = 'red', las = 1)plot(sunspots, col = 'red', panel.first = grid())```:::

If you want to show code (echo = TRUE) but do not want the code to be in thefull-width container, you can apply the .fullwidth class to the plot only,e.g.,

```{r}#| sunspots, fig.dim=c(14, 4), fig.env='.fullwidth .figure .box',#| fig.cap='Monthly mean relative sunspot numbers from 1749 to 1983.'par(mar = c(4, 4, .1, .1), bg = 'lightgoldenrodyellow', fg = 'red', las = 1)plot(sunspots, col = 'red', panel.first = grid())```

4.2.3.2 Left/right quotes

Sometimes you may want to add a quote but do not want it to take the full widthin the body. You may use a fenced Div with the class .quote-left or.quote-right.

Despite the class names, the content does not have to be a quote. If you do wanta quote, just use the blockquote syntax >, e.g.,

::: {.quote-right}> This is a boring quote.>> ---Someone:::

4.2.3.3 Margin embedding

You can embed elements on the left or right margin using a fenced Div with theclass .embed-left or .embed-right. These elements will float to the left orright and exceed the margin by about 200px, which can save some space in thearticle body. You can use the extra space to explain the embedded element withtext.

We have embedded a table of the first 4 rows of the mtcars data on the rightmargin, which you can see if the browser window is wide enough.

4.3 Tabbed sections

You can load the script tabsets.js and CSS tabsets.css to create tabsetsfrom sections (see documentationhere).

css: ["@tabsets"]js: ["@tabsets"]

4.4 Code folding

Code folding is supported by fold-details.js (see documentationhere).

js: ["@fold-details"]

4.5 Callout blocks

A callout block is a fenced Div with the class name callout-*. Calloutsrequire callout.css and callout.js:

css: ["@callout"]js: ["@callout"]

For example:

::: callout-tipThis is a tip.> You can write arbitrary content, such as a blockquote.::: callout-cautionEven another callout!:::Is that cool?:::

Output:

The stylesheet callout.css supports styling three types of callouts: tip,caution, and important. For example:

seq(0, 1, .2) == c(0, .2, .4, .6, .8, 1)

#> [1] TRUE TRUE TRUE FALSE TRUE TRUE

For the sake of reproducibility, please remember to render an R Markdowndocument in a new R session before publishing or submitting the outputdocument.

You do not have to use callout.css but can define your own CSS rules, e.g.,

.callout-important { background-color: red; color: yellow;}

Under the hood, callout.js turns the fenced Div into a <fieldset> for theform:

<fieldset class="callout-*"> <legend>Title</legend> Content.</fieldset>

The content comes from the original fenced Div. The title comes from the classname (converted to uppercase) by default. You can provide a custom title via thedata-legend attribute of the Div, e.g.,

::: {.callout-tip data-legend="Information"}:::

The icons before the callout titles can be defined via CSS, e.g., you can addtwo exclamation marks before the title of important callouts:

.callout-important legend::before { content: "!! ";}

The default icons defined in callout.css are essentially UTF-8characters. In theory,there are hundreds of thousands of characters that you can choose from. Eachcharacter is 1 to 4 bytes. For example, you can define a music callout withthe music note symbol ♫ in the CSS:

.callout-music { background-color: springgreen;}.callout-music legend::before { content: "♫ ";}

Then you can insert a music callout in your document:

::: callout-musicPlease listen to this lovely song.:::

You can use the script right-quote.js to right-align a blockquote footer if itstarts with an em-dash (---).

js: ["@right-quote"]

4.7 Add anchor links to headings

The CSS is necessary only if you want to hide the anchors by default and revealthem on hover.

css: ["@heading-anchor"]js: ["@heading-anchor"]

4.8 Style keyboard shortcuts

The script key-button.js identifies keys and the CSS styles them, which can beuseful for showing keyboardshortcuts.

css: ["@key-buttons"]js: ["@key-buttons"]

Of course, you can combine any number of JS scripts and CSS files if you wantmultiple features.

5.1 The Knit button

If you use the RStudio IDE, the Knit button can render R Markdown to alitedown output format specified in YAML (e.g., litedown::html_format orlitedown::latex_format). Please also remember to add a top-level settingknit: litedown:::knit in YAML, otherwise RStudio will use knitr::knit()instead of litedown::fuse() to compile R Markdown.

---output: litedown::html_format: null litedown::latex_format: nullknit: litedown:::knit---

5.2 Live preview

Unless it has become your muscle memory to click on the Knit button inRStudio, you may try to switch to litedown::roam() to preview your HTMLoutput. It also allows you to render a document or project in a new R session byclicking on the ↯ button at the top, which is similar to what the Knit buttondoes.

By default, the preview will automatically refresh the content after you editand save a file. If you prefer building the document only when you want to, youcan turn off the live preview via litedown::roam(live = FALSE). In this case,the document will be rebuilt only when you refresh the page by yourself.

In the preview mode, you can click on the ✎ button to open a plain-text file inyour editor. Code blocks in the preview mode will have line numbersautomatically added to their left. If you click on a line number, it will bringyou to the that line in the source document.

5.3 Visual editor

Since the Markdown syntax of litedown can be viewed as a subset of Pandoc’sMarkdown, you can use RStudio’s visual Markdown editor to author documents.Please bear in mind that most common, but not all, Markdown features aresupported.

Books and websites are usually based on multiple input files under a directory.For a directory to be recognized as a book or website project, it needs tocontain a configuration file named _litedown.yml.

If you want to customize the output formats html_format or latex_format forbooks or websites, you should do it in _litedown.yml, e.g.,

output: litedown::html_format: options: toc: depth: 4 litedown::latex_format: meta: documentclass: "book"

6.1 Books

The _litedown.yml file should contain a top-level field named book, whichcurrently supports these options:

book: new_session: false subdir: false pattern: "[.]R?md$" chapter_before: "Information before a chapter." chapter_after: "This chapter was generated from `$input$`."

You can choose whether to render each input file in a new R session, whether tosearch subdirectories for input files, the types of input files (e.g., you canuse .md or .R files if you want), and additional information to be includedbefore/after each chapter, in which you can use some variables such as$input$, which is the path of each input file.

6.2 Websites

The _litedown.yml file should contain a top-level field named site, and youare likely to customize the meta variables css, include_before, andinclude_after for the html_format, e.g.,

site: rebuild: "outdated" pattern: "[.]R?md$"output: litedown::html_format: meta: css: ["@default"] include_before: "[Home](/) [About](/about.html)" include_after: "© 2024 | [Edit]($input$)"

Basically, include_before can take a file or text input that will be used asthe header of each web page, and include_after will be the footer.

The litedown package has also provided two internal output formats forcompatibility with rmarkdown: litedown:::html_document andlitedown:::pdf_document.⁷ The purpose is to make it a littleeasier to switch from rmarkdown to litedown by mapping somermarkdown output format options to litedown.

For example, for an R Markdown document with the following output format:

output: html_document: toc: true number_sections: true anchor_sections: true self_contained: false

You can switch to litedown simply by changing the output format name fromhtml_document to litedown:::html_document. Internally, the above outputformat is transformed to:

output: litedown::html_format: options: toc: true number_sections: true embed_resources: false meta: css: ["default", "@heading-anchor"] js: ["@heading-anchor"]

Note that not all rmarkdown options are supported, and not even allsupported options have exactly the same effects in litedown. The supportedoptions include:toc, toc_depth, number_sections, anchor_sections, code_folding, self_contained, math_method, css, and includes.

To build package vignettes with litedown, first add this to the packageDESCRIPTION file:

VignetteBuilder: litedown

Then use the vignette engine litedown::vignette in the YAML metadata of a.Rmd or .md vignette file:

vignette: > %\VignetteEngine{litedown::vignette} %\VignetteIndexEntry{Your vignette title} %\VignetteEncoding{UTF-8}

The output format of a vignette can be specified in the output field of theYAML metadata, e.g., litedown::html_format (for HTML vignettes) orlitedown::latex_format (for PDF vignettes). If no output format is specified,the default is HTML.

The vignette file can be either .Rmd or .md. The former is processed bylitedown::fuse(), and the latter is converted by litedown::mark(). Pleaseavoid using the same base filename for two .Rmd and .md files, otherwisetheir output files will overwrite each other.

C.1 Embedding resources

When https resources needs to be embedded (via the embed_resources option),only these elements are considered:

<img src="..." /><link rel="stylesheet" href="..."><script src="..."></script>

Background images set in the attribute style="background-image: url(...)" arealso considered. If an external CSS file contains url() resources, theseresources will also be downloaded and embedded.

C.2 CSS for margin content

It’s quite simple to move an element into the margin using CSS. For example, the.side-right class in this article is roughly defined as:

.side-right { width: 200px; float: right; margin-right: -200px}

That basically means the width of the element is 200px and it floats to theright. Now its right side will touch the right margin of its parent element (thearticle body). What we need to do next is move it further to the right by 200px(i.e., its width), which is done by the -200px right margin. Remember, apositive right margin in CSS moves an element to the left, and a negative rightmargin moves it to the right.