Note: This book has been published by Chapman & Hall/CRC. The online version of this book is free to read here (thanks to Chapman & Hall/CRC), and licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
The document format 'R Markdown' was first introduced in the knitr package (Xie 2015, 2021b) in early 2012. The idea was to embed code chunks (of R or other languages) in Markdown documents. In fact, knitr supported several authoring languages from the beginning in addition to Markdown, including LaTeX, HTML, AsciiDoc, reStructuredText, and Textile. Looking back over the five years, it seems to be fair to say that Markdown has become the most popular document format, which is what we expected. The simplicity of Markdown clearly stands out among these document formats.
Markdown Quick Reference Cheat Sheet Note: The instructions from this guide are referring to the Classic Editor. If you are using the WordPress block editor, please see this guide. See the Markdown page for instructions on enabling Markdown for posts, pages and comments on your blog, and for more detailed information about using Markdown. Markdownis a way to style text on the web. You control the display of the document; forma˜ing words as bold or italic, adding images, and creating lists are just a few of the things we can do with Markdown. Mostly, Markdown is just regular text with a few non-alphabetic characters thrown in, like # or. Pandoc Markdown Quick Reference by Examples. GitHub Gist: instantly share code, notes, and snippets.
However, the original version of Markdown invented by John Gruber was often found overly simple and not suitable to write highly technical documents. For example, there was no syntax for tables, footnotes, math expressions, or citations. Fortunately, John MacFarlane created a wonderful package named Pandoc (http://pandoc.org) to convert Markdown documents (and many other types of documents) to a large variety of output formats. More importantly, the Markdown syntax was significantly enriched. Now we can write more types of elements with Markdown while still enjoying its simplicity.
In a nutshell, R Markdown stands on the shoulders of knitr and Pandoc. The former executes the computer code embedded in Markdown, and converts R Markdown to Markdown. The latter renders Markdown to the output format you want (such as PDF, HTML, Word, and so on).
The rmarkdown package (Allaire, Xie, McPherson, et al. 2021) was first created in early 2014. During the past four years, it has steadily evolved into a relatively complete ecosystem for authoring documents, so it is a good time for us to provide a definitive guide to this ecosystem now. At this point, there are a large number of tasks that you could do with R Markdown:
Compile a single R Markdown document to a report in different formats, such as PDF, HTML, or Word.
Create notebooks in which you can directly run code chunks interactively.
Make slides for presentations (HTML5, LaTeX Beamer, or PowerPoint).
Produce dashboards with flexible, interactive, and attractive layouts.
Build interactive applications based on Shiny.
Write journal articles.
Author books of multiple chapters.
Generate websites and blogs.
There is a fundamental assumption underneath R Markdown that users should be aware of: we assume it suffices that only a limited number of features are supported in Markdown. By 'features,' we mean the types of elements you can create with native Markdown. The limitation is a great feature, not a bug. R Markdown may not be the right format for you if you find these elements not enough for your writing: paragraphs, (section) headers, block quotations, code blocks, (numbered and unnumbered) lists, horizontal rules, tables, inline formatting (emphasis, strikeout, superscripts, subscripts, verbatim, and small caps text), LaTeX math expressions, equations, links, images, footnotes, citations, theorems, proofs, and examples. We believe this list of elements suffice for most technical and non-technical documents. It may not be impossible to support other types of elements in R Markdown, but you may start to lose the simplicity of Markdown if you wish to go that far.
Epictetus once said, 'Wealth consists not in having great possessions, but in having few wants.' The spirit is also reflected in Markdown. If you can control your preoccupation with pursuing typesetting features, you should be much more efficient in writing the content and can become a prolific author. It is entirely possible to succeed with simplicity. Jung Jae-sung was a legendary badminton player with a remarkably simple playing style: he did not look like a talented player and was very short compared to other players, so most of the time you would just see him jump three feet off the ground and smash like thunder over and over again in the back court until he beats his opponents.
Please do not underestimate the customizability of R Markdown because of the simplicity of its syntax. In particular, Pandoc templates can be surprisingly powerful, as long as you understand the underlying technologies such as LaTeX and CSS, and are willing to invest time in the appearance of your output documents (reports, books, presentations, and/or websites). As one example, you may check out the PDF report of the 2017 Employer Health Benefits Survey. It looks fairly sophisticated, but was actually produced via bookdown(Xie 2016), which is an R Markdown extension. A custom LaTeX template and a lot of LaTeX tricks were used to generate this report. Not surprisingly, this very book that you are reading right now was also written in R Markdown, and its full source is publicly available in the GitHub repository https://github.com/rstudio/rmarkdown-book.
R Markdown documents are often portable in the sense that they can be compiled to multiple types of output formats. Again, this is mainly due to the simplified syntax of the authoring language, Markdown. The simpler the elements in your document are, the more likely that the document can be converted to different formats. Similarly, if you heavily tailor R Markdown to a specific output format (e.g., LaTeX), you are likely to lose the portability, because not all features in one format work in another format.
Last but not least, your computing results will be more likely to be reproducible if you use R Markdown (or other knitr-based source documents), compared to the manual cut-and-paste approach. This is because the results are dynamically generated from computer source code. If anything goes wrong or needs to be updated, you can simply fix or update the source code, compile the document again, and the results will be automatically updated. You can enjoy reproducibility and convenience at the same time.
Markdown is a lightweight and easy-to-use syntax for styling all forms of writing on the GitHub platform.
What you will learn:
- How the Markdown format makes styled collaborative editing easy
- How Markdown differs from traditional formatting approaches
- How to use Markdown to format text
- How to leverage GitHub's automatic Markdown rendering
- How to apply GitHub's unique Markdown extensions
What is Markdown?
Markdown is a way to style text on the web. You control the display of the document; formatting words as bold or italic, adding images, and creating lists are just a few of the things we can do with Markdown. Mostly, Markdown is just regular text with a few non-alphabetic characters thrown in, like # or *.
You can use Markdown most places around GitHub:
- Comments in Issues and Pull Requests
- Files with the
.mdor.markdownextension
For more information, see 'Writing on GitHub' in the GitHub Help.
Examples
Syntax guide
Here's an overview of Markdown syntax that you can use anywhere on GitHub.com or in your own text files.
Headers
Emphasis
Lists
Unordered
Ordered
Images
Links
R Markdown Quick Guide
Blockquotes
Markdown Quick Guide Examples
Inline code
GitHub Flavored Markdown
GitHub.com uses its own version of the Markdown syntax that provides an additional set of useful features, many of which make it easier to work with content on GitHub.com.
Note that some features of GitHub Flavored Markdown are only available in the descriptions and comments of Issues and Pull Requests. These include @mentions as well as references to SHA-1 hashes, Issues, and Pull Requests. Task Lists are also available in Gist comments and in Gist Markdown files.
Syntax highlighting
Here's an example of how you can use syntax highlighting with GitHub Flavored Markdown:
You can also simply indent your code by four spaces:
Here's an example of Python code without syntax highlighting:
Task Lists
If you include a task list in the first comment of an Issue, you will get a handy progress indicator in your issue list. It also works in Pull Requests!
Tables
Markdown Help
You can create tables by assembling a list of words and dividing them with hyphens - (for the first row), and then separating each column with a pipe |:
Would become:
| First Header | Second Header |
|---|---|
| Content from cell 1 | Content from cell 2 |
| Content in the first column | Content in the second column |
SHA references
Any reference to a commit's SHA-1 hash will be automatically converted into a link to that commit on GitHub.
Issue references within a repository
Any number that refers to an Issue or Pull Request will be automatically converted into a link.
Username @mentions
Typing an @ symbol, followed by a username, will notify that person to come and view the comment. This is called an '@mention', because you're mentioning the individual. You can also @mention teams within an organization.
Automatic linking for URLs
Any URL (like http://www.github.com/) will be automatically converted into a clickable link.
Strikethrough
Any word wrapped with two tildes (like ~~this~~) will appear crossed out.
Emoji
GitHub supports emoji!
You can use Markdown most places around GitHub:
- Comments in Issues and Pull Requests
- Files with the
.mdor.markdownextension
For more information, see 'Writing on GitHub' in the GitHub Help.
Examples
Syntax guide
Here's an overview of Markdown syntax that you can use anywhere on GitHub.com or in your own text files.
Headers
Emphasis
Lists
Unordered
Ordered
Images
Links
R Markdown Quick Guide
Blockquotes
Markdown Quick Guide Examples
Inline code
GitHub Flavored Markdown
GitHub.com uses its own version of the Markdown syntax that provides an additional set of useful features, many of which make it easier to work with content on GitHub.com.
Note that some features of GitHub Flavored Markdown are only available in the descriptions and comments of Issues and Pull Requests. These include @mentions as well as references to SHA-1 hashes, Issues, and Pull Requests. Task Lists are also available in Gist comments and in Gist Markdown files.
Syntax highlighting
Here's an example of how you can use syntax highlighting with GitHub Flavored Markdown:
You can also simply indent your code by four spaces:
Here's an example of Python code without syntax highlighting:
Task Lists
If you include a task list in the first comment of an Issue, you will get a handy progress indicator in your issue list. It also works in Pull Requests!
Tables
Markdown Help
You can create tables by assembling a list of words and dividing them with hyphens - (for the first row), and then separating each column with a pipe |:
Would become:
| First Header | Second Header |
|---|---|
| Content from cell 1 | Content from cell 2 |
| Content in the first column | Content in the second column |
SHA references
Any reference to a commit's SHA-1 hash will be automatically converted into a link to that commit on GitHub.
Issue references within a repository
Any number that refers to an Issue or Pull Request will be automatically converted into a link.
Username @mentions
Typing an @ symbol, followed by a username, will notify that person to come and view the comment. This is called an '@mention', because you're mentioning the individual. You can also @mention teams within an organization.
Automatic linking for URLs
Any URL (like http://www.github.com/) will be automatically converted into a clickable link.
Strikethrough
Any word wrapped with two tildes (like ~~this~~) will appear crossed out.
Emoji
GitHub supports emoji!
To see a list of every image we support, check out the Emoji Cheat Sheet.
Last updated Jan 15, 2014
