Reddit Markdown Guide

Interactive documents are a new way to build Shiny apps. An interactive document is an R Markdown file that contains Shiny widgets and outputs. You write the report in markdown, and then launch it as an app with the click of a button.

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So, we created a guide to Reddit-flavored Markdown, which explains generally how to format content on new Reddit, and specifically identifies areas where new Reddit-flavored Markdown is different from old Reddit-flavored markdown. You can find the guide on our wiki.

This article will show you how to write an R Markdown report.

The companion article, Introduction to interactive documents, will show you how to turn an R Markdown report into an interactive document with Shiny components.

R Markdown

R Markdown is a file format for making dynamic documents with R. An R Markdown document is written in markdown (an easy-to-write plain text format) and contains chunks of embedded R code, like the document below.

R Markdown files are designed to be used with the rmarkdown package. rmarkdown comes installed with the RStudio IDE, but you can acquire your own copy of rmarkdown from CRAN with the command

R Markdown files are the source code for rich, reproducible documents. You can transform an R Markdown file in two ways.

1. knit - You can knit the file. The rmarkdown package will call the knitr package. knitr will run each chunk of R code in the document and append the results of the code to the document next to the code chunk. This workflow saves time and facilitates reproducible reports.

   Consider how authors typically include graphs (or tables, or numbers) in a report. The author makes the graph, saves it as a file, and then copy and pastes it into the final report. This process relies on manual labor. If the data changes, the author must repeat the entire process to update the graph.

   In the R Markdown paradigm, each report contains the code it needs to make its own graphs, tables, numbers, etc. The author can automatically update the report by re-knitting.

2. convert - You can convert the file. The rmarkdown package will use the pandoc program to transform the file into a new format. For example, you can convert your .Rmd file into an HTML, PDF, or Microsoft Word file. You can even turn the file into an HTML5 or PDF slideshow. rmarkdown will preserve the text, code results, and formatting contained in your original .Rmd file.

   Conversion lets you do your original work in markdown, which is very easy to use. You can include R code to knit, and you can share your document in a variety of formats.

In practice, authors almost always knit and convert their documents at the same time. In this article, I will use the term render to refer to the two step process of knitting and converting an R Markdown file.

You can manually render an R Markdown file with rmarkdown::render(). This is what the above document looks like when rendered as a HTML file.

In practice, you do not need to call rmarkdown::render(). You can use a button in the RStudio IDE to render your reprt. R Markdown is heavily integrated into the RStudio IDE.

Getting started

To create an R Markdown report, open a plain text file and save it with the extension .Rmd. You can open a plain text file in your scripts editor by clicking File > New File > Text File in the RStudio toolbar.

Be sure to save the file with the extension .Rmd. The RStudio IDE enables several helpful buttons when you save the file with the .Rmd extension. You can save your file by clicking File > Save in the RStudio toolbar.

R Markdown reports rely on three frameworks

1. markdown for formatted text
2. knitr for embedded R code
3. YAML for render parameters

The sections below describe each framework.

Markdown for formatted text

.Rmd files are meant to contain text written in markdown. Markdown is a set of conventions for formatting plain text. You can use markdown to indicate

• bold and italic text
• lists
• headers (e.g., section titles)
• hyperlinks
• and much more

The conventions of markdown are very unobtrusive, which make Markdown files easy to read. The file below uses several of the most useful markdown conventions.

The file demonstrates how to use markdown to indicate:

1. headers - Place one or more hashtags at the start of a line that will be a header (or sub-header). For example, # Say Hello to markdown. A single hashtag creates a first level header. Two hashtags, ##, creates a second level header, and so on.

2. italicized and bold text - Surround italicized text with asterisks, like this *without realizing it*. Surround bold text with two asterisks, like this **easy to use**.

3. lists - Group lines into bullet points that begin with asterisks. Leave a blank line before the first bullet, like this

4. hyperlinks - Surround links with brackets, and then provide the link target in parentheses, like this [Github](www.github.com).

You can learn about more of markdown’s conventions in the Markdown Quick Reference guide, which comes with the RStudio IDE.

To access the guide, open a .md or .Rmd file in RStudio. Then click the question mark that appears at the top of the scripts pane. Next, select “Markdown Quick Reference”. RStudio will open the Markdown Quick Reference guide in the Help pane.

Rendering

To transform your markdown file into an HTML, PDF, or Word document, click the “Knit” icon that appears above your file in the scripts editor. A drop down menu will let you select the type of output that you want.

When you click the button, rmarkdown will duplicate your text in the new file format. rmarkdown will use the formatting instructions that you provided with markdown syntax.

Once the file is rendered, RStudio will show you a preview of the new output and save the output file in your working directory.

Here is how the markdown script above would look in each output format.

Note: RStudio does not build PDF and Word documents from scratch. You will need to have a distribution of Latex installed on your computer to make PDFs and Microsoft Word (or a similar program) installed to make Word files.

knitr for embedded R code

The knitr package extends the basic markdown syntax to include chunks of executable R code.

When you render the report, knitr will run the code and add the results to the output file. You can have the output display just the code, just the results, or both.

To embed a chunk of R code into your report, surround the code with two lines that each contain three backticks. After the first set of backticks, include {r}, which alerts knitr that you have included a chunk of R code. The result will look like this

When you render your document, knitr will run the code and append the results to the code chunk. knitr will provide formatting and syntax highlighting to both the code and its results (where appropriate).

As a result, the markdown snippet above will look like this when rendered (to HTML).

To omit the results from your final report (and not run the code) add the argument eval = FALSE inside the brackets and after r. This will place a copy of your code into the report.

To omit the code from the final report (while including the results) add the argument echo = FALSE. This will place a copy of the results into your report.

echo = FALSE is very handy for adding plots to a report, since you usually do not want to see the code that generates the plot.

echo and eval are not the only arguments that you can use to customize code chunks. You can learn more about formatting the output of code chunks at the rmarkdown and knitr websites.

Inline code

To embed R code in a line of text, surround the code with a pair of backticks and the letter r, like this.

knitr will replace the inline code with its result in your final document (inline code is always replaced by its result). The result will appear as if it were part of the original text. For example, the snippet above will appear like this:

YAML for render parameters

You can use a YAML header to control how rmarkdown renders your .Rmd file. A YAML header is a section of key: value pairs surrounded by --- marks, like below

The output: value determines what type of output to convert the file into when you call rmarkdown::render(). Note: you do not need to specify output: if you render your file with the RStudio IDE knit button.

output: recognizes the following values:

• html_document, which will create HTML output (default)
• pdf_document, which will create PDF output
• word_document, which will create Word output

If you use the RStudio IDE knit button to render your file, the selection you make in the gui will override the output: setting.

Slideshows

You can also use the output: value to render your document as a slideshow.

• output: ioslides_presentation will create an ioslides (HTML5) slideshow
• output: beamer_presentation will create a beamer (PDF) slideshow

Note: The knit button in the RStudio IDE will update to show slideshow options when you include one of the above output values and save your .Rmd file.

rmarkdown will convert your document into a slideshow by starting a new slide at each header or horizontal rule (e.g., ***).

Visit rmakdown.rstudio.com to learn about more YAML options that control the render process.

Rmarkdown Table Examples

Recap

R Markdown documents provide quick, reproducible reporting from R. You write your document in markdown and embed executable R code chunks with the knitr syntax.

You can update your document at any time by re-knitting the code chunks.

You can then convert your document into several common formats.

R Markdown documents implement Donald’s Knuth’s idea of literate programming and take the manual labor out of writing and maintaining reports. Moreover, they are quick to learn. You already know ecnough about markdown, knitr, and YAML to begin writing your own R Markdown reports.

In the next article, Introduction to interactive documents, you will learn how to add interactive Shiny components to an R Markdown report. This creates a quick workflow for writing light-weight Shiny apps.

To learn more about R Markdown and interactive documents, please visit rmarkdown.rstudio.com.

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 .md or .markdown extension

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

Reddit Wiki Markdown

Emphasis

Lists

Unordered

Ordered

Images

Links

Blockquotes

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

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:

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

Reddit Markdown Table

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