Markdown Quick Guide

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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.

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

How to do markdowns

Take your Markdown skills to the next level. Learn Markdown in 60 pages. Designed for both novices and experts, The Markdown Guide book is a comprehensive reference that has everything you need to get started and master Markdown syntax. Video Players & Editors. Wear OS by Google. Markor: Markdown Editor - todo.txt - Notes Offline. This article provides an alphabetical reference for writing Markdown for docs.microsoft.com (Docs). Markdown is a lightweight markup language with plain text formatting syntax. Docs supports CommonMark compliant Markdown parsed through the Markdig parsing engine. Docs also supports custom Markdown extensions that provide richer content on the. Markdown quick reference. The Octopus Guides combine content to allow users to specify their entire CI/CD pipeline and access a guide for their specific pipeline. It is sometimes helpful to link to the guides with specific options pre-defined rather than the default options.

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.

Markdown Quick Guide

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.

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.

Once you get the hang of Markdown, it’s an incredibly powerful writing tool which will allow you to write rich content for the web far faster than almost any other method. To get to that point, however, there’s a little bit of a learning curve. We thought we’d put together an all inclusive guide to make that curve a little bit shorter, and potentially teach you a few super-user tricks to Markdown that you might not have known.

What is Markdown?

Markdown is a plain text formatting syntax for writers. It allows you to quickly write structured content for the web, and have it seamlessly converted to clean, structured HTML.

Back in 2004, Apple pundit John Gruber came up with the idea after becoming frustrated by writing long, laborious HTML tags to properly format his content. He devised a simple writing system which would make web based documents both easier to write, and easier to read in their raw state.

Here’s a quick example of Markdown in action:

becomes

The quick brown fox, jumped over the lazy dog.

With just a couple of extra characters, Markdown makes rich document formatting quick and beautiful.

Why do Writers Love Markdown so Much?

“Is that it?” - I hear you ask - “I could just click on a few formatting buttons in most editors and achieve the same thing!”

Very true! But we’re only just getting started. The range of formatting tools has come a very long way since Markdown’s inception in 2004, so you’d be forgiven for wondering what advantages it holds over, say, the “Bold” button in Microsoft Word.

While most novice users do indeed find buttons a bit easier to use, advanced writers often swear by Markdown and nothing else. Why? The biggest reason is writing flow.

Using a traditional writing user interface you have to pause your writing every few minutes (or sometimes seconds) and reach for the mouse in order to click, highlight, click a formatting button, and then click back to where you left off in order to continue. This process creates a tiresome, disjointed experience when all you want to do is get the words out of your head and onto the screen.

Markdown allows you to keep your fingers firmly planted on the keyboard as you apply formatting on the fly. In short: You never have to stop typing or think about anything else in order to apply your styles.

It might seem like a small detail, but it can have a really big effect. Once you start writing in Markdown, it’s really hard to back to the click-fest of the past.

Basic Markdown Formatting

Ok! You’re sold. So how does this work? Let’s dive in:

Markdown was designed with the explicit intention to be easily readable by humans. You should find that most of the syntax is pretty simple and intuitive.

Here are the elements you’ll use most often:

Headings

Headings in Markdown are any line which is prefixed with a # symbol. The number of hashes indicates the level of the heading. One hash is converted to an h1, two hashes to an h2 and so on. There are a total of 6 levels which you can make use of - but for most writing, you’ll rarely ever need more than 3.

Text

If you want to emphasise a word a little bit, wrap it in asterisks. For something that needs more emphasis: double asterisks. If you really want to drive the point home, use triple asterisks. If you prefer, you can also use underscores - they’re completely interchangeable.

To add a link: wrap the text which you want to be linked in square brackets, followed by the URL to be linked to in parenthesis. An easy way to remember this one is to think of it like turning a word into a button. [button] and (place to go when the button is clicked) combine to form a link.

Images

Markdown images have exactly the same formatting as a link, except they’re prefixed with a !. This time, the text in brackets is the alt text - or the descriptive text for the image.

In most Markdown editors, you don’t have to write this code out. They will provide a tool to allow you to upload an image and insert this code automatically. After that, it will appear in your document.


Lists are a formatting nightmare in HTML, but Markdown lists are incredibly easy to manage. For a bullet list, just prefix each like with a * - or - or + and they will be converted to dots. You can also create nested lists; just indent a line with 4 spaces and it will be nested under the line above.

  • Milk
  • Bread

    • Wholegrain
  • Butter

For numbered lists, do exactly the same thing—but use numbers!

Quotes

Markdown Guide Pdf

When you want to add a quote in Markdown, it’s exactly the same as the formatting which you may already be familiar with from your email app of choice when you reply to someone.

To be or not to be, that is the question.

Prefixing the line with a > converts it into a block-quote.

How can I remember all the Markdown syntax?!

It seems a little daunting at first, but you might be surprised how naturally it comes to you after a couple of posts written in Markdown. Most good Markdown editors come with a built-in cheat sheet to make it a little easier to learn.

Github Markdown Guide

Intermediate Markdown Formatting

Markdown Quick Guide Examples

So you’ve got the Markdown basics nailed and you want to move on to bigger and better things? Excellent. There’s much more we can do.

Horizontal Rules

Want to throw-down a quick divider in your article to denote a visual separation between different sections of text? No problem. 3 dashes produce:

A sleek <hr> element.

Code Snippets

Quick

If you’re a technical writer, you may want to use example snippets of code to teach your readers a particular syntax (like I’m doing, with this very blog post). Using a single back-tick around a word in a sentence, you can show a quick code snippet.

Indenting by 4 spaces will turn an entire paragraph into a code-block.

Reference Lists & Titles

If you prefer to use reference lists for your attribution, Markdown can handle this, too. In the above example, all of the links are kept separate in Markdown (so it’s easy to read even in its raw format), and then inserted directly as normal links when converted to HTML.

The quick brown fox, jumped over the lazy dog.

You’ll also notice that we’ve added a title attribute to the links by adding a 'word' in quote marks just after the URL. Anywhere you use a URL, you can follow it with a 'title in quotation marks' to generate a title attribute.

Escaping

Markdown Formatting Guide

What if you literally want to type *literally* - without it appearing in italics? Escaping Markdown characters with a back-slash allows you to use any characters which might be getting accidentally converted into HTML.

Embedding HTML

Possibly the coolest feature of Markdown is that it also just supports plain old HTML. If you find yourself stuck and unable to do what you want in Markdown - you can simply write in regular HTML and it will work just fine.

So you can drop in any HTML, sharing button, JavaScript snippet or iFrame you like and it will work on the page just as normal.

Advanced Markdown

Ok, you want the big guns. Every example so far has been vanilla, normal Markdown. Those code snippets will work absolutely anywhere which supports Markdown syntax.

Now we’re going to look at some syntax which is not standard to native Markdown. They’re extensions of the language.

Automatic Links

Markdown Footnotes

The quick brown fox1 jumped over the lazy dog2.

Syntax Highlighting

Converting HTML to Markdown

If you’re just getting into Markdown and you’ve found yourself with a massive back-log of old files which are written in HTML, you might want to convert them to Markdown to make them easier to work with in future.

Here’s a handy tool by Dom Christie which lets you do exactly that.

What to do next

After just a couple of hours with Markdown, we’re certain that your fingers will be flying across the keys as you pen your latest and greatest post.

Practice these steps to become a pro:

  1. Start with writing your first Markdown document and get a feel for the basics. It comes more quickly than you might think!
  2. Use HTML whenever you want advanced formatting, having this power available to you means you can really do (almost) anything.

Footnotes