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• Markdown Windows
• Markdown Management

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.

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 Windows

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:

Markdown Management

• 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.

Working with Markdown files in Visual Studio Code is simple, straightforward, and fun. Besides VS Code's basic editing, there are a number of Markdown specific features that will help you be more productive.

Markdown extensions

In addition to the functionality VS Code provides out of the box, you can install an extension for greater functionality.

Tip: Click on an extension tile above to read the description and reviews to decide which extension is best for you. See more in the Marketplace.

Markdown preview

VS Code supports Markdown files out of the box. You just start writing Markdown text, save the file with the .md extension and then you can toggle the visualization of the editor between the code and the preview of the Markdown file; obviously, you can also open an existing Markdown file and start working with it. To switch between views, press ⇧⌘V (Windows, Linux Ctrl+Shift+V) in the editor. You can view the preview side-by-side (⌘K V (Windows, Linux Ctrl+K V)) with the file you are editing and see changes reflected in real-time as you edit.

Here is an example with a very simple file.

Tip: You can also right-click on the editor Tab and select Open Preview (⇧⌘V (Windows, Linux Ctrl+Shift+V)) or use the Command Palette (⇧⌘P (Windows, Linux Ctrl+Shift+P)) to run the Markdown: Open Preview to the Side command (⌘K V (Windows, Linux Ctrl+K V)).

Dynamic previews and preview locking

By default, Markdown previews automatically update to preview the currently active Markdown file:

You can lock a Markdown preview using the Markdown: Toggle Preview Locking command to keep it locked to its current Markdown document. Locked previews are indicated by [Preview] in the title:

Editor and preview synchronization

VS Code automatically synchronizes the Markdown editor and the preview panes. Scroll the Markdown preview and the editor is scrolled to match the preview's viewport. Scroll the Markdown editor and the preview is scrolled to match its viewport:

You can disable scroll synchronization using the markdown.preview.scrollPreviewWithEditor and markdown.preview.scrollEditorWithPreviewsettings.

The currently selected line in the editor is indicated in the Markdown preview by a light gray bar in the left margin:

Additionally, double clicking an element in the Markdown preview will automatically open the editor for the file and scroll to the line nearest the clicked element.

Outline view

The Outline view is a separate section in the bottom of the File Explorer. When expanded, it will show the symbol tree of the currently active editor. For Markdown files, the symbol tree is the Markdown file's header hierarchy.

The Outline view is a great way to review your document's header structure and outline.

Extending the Markdown preview

Extensions can contribute custom styles and scripts to the Markdown preview to change its appearance and add new functionality. Here's a set of example extensions that customize the preview:

Using your own CSS

You can also use your own CSS in the Markdown preview with the 'markdown.styles': []setting. This lists URLs for style sheets to load in the Markdown preview. These stylesheets can either be https URLs, or relative paths to local files in the current workspace.

For example, to load a stylesheet called Style.css at the root of your current workspace, use File > Preferences > Settings to bring up the workspace settings.json file and make this update:

Keep trailing whitespace in order to create line breaks

To create hard line breaks, Markdown requires two or more spaces at the end of a line. Depending on your user or workspace settings, VS Code may be configured to remove trailing whitespace. In order to keep trailing whitespace in Markdown files only, you can add these lines to your settings.json:

Markdown preview security

For security reasons, VS Code restricts the content displayed in the Markdown preview. This includes disabling script execution and only allowing resources to be loaded over https.

When the Markdown preview blocks content on a page, an alert popup is shown in the top right corner of the preview window:

You can change what content is allowed in the Markdown preview by clicking on this popup or running the Markdown: Change preview security settings command in any Markdown file:

The Markdown preview security settings apply to all files in the workspace.

Here are the details about each of these security levels:

Strict

This is the default setting. Only loads trusted content and disables script execution. Blocks http images.

It is strongly recommended that you keep Strict security enabled unless you have a very good reason to change it AND you trust all markdown files in the workspace.

Allow insecure content

Keeps scripts disabled but allows content to be loaded over http.

Disable

Disables additional security in the preview window. This allows script execution and also allows content to be loaded over http.

Snippets for Markdown

There are several built-in Markdown snippets included in VS Code - press ⌃Space (Windows, Linux Ctrl+Space) (Trigger Suggest) and you get a context specific list of suggestions.

Tip: You can add in your own User Defined Snippets for Markdown. Take a look at User Defined Snippets to find out how.

Compiling Markdown into HTML

VS Code integrates with Markdown compilers through the integrated task runner. We can use this to compile .md files into .html files. Let's walk through compiling a simple Markdown document.

Step 1: Install a Markdown compiler

For this walkthrough, we use the popular Node.js module, markdown-it.

Note: There are many Markdown compilers to choose from beyond markdown-it. Pick the one that best suits your needs and environment.

Step 2: Create a simple MD file

Open VS Code on an empty folder and create a sample.md file.

Note: You can open a folder with VS Code by either selecting the folder with File > Open Folder or navigating to the folder and typing 'code .' at the command line.

Place the following source code in that file:

Step 3: Create tasks.json

The next step is to set up the task configuration file tasks.json. To do this, run Terminal > Configure Tasks and click Create tasks.json file from templates. VS Code then presents a list of possible tasks.json templates to choose from. Select Others since we want to run an external command.

This generates a tasks.json file in your workspace .vscode folder with the following content:

To use markdown-it to compile the Markdown file, change the contents as follows:

Tip: While the sample is there to help with common configuration settings, IntelliSense is available for the tasks.json file as well to help you along. Use ⌃Space (Windows, Linux Ctrl+Space) to see the available settings.

Step 4: Run the Build Task

Since in more complex environments there can be more than one build task we prompt you to pick the task to execute after pressing ⇧⌘B (Windows, Linux Ctrl+Shift+B) (Run Build Task). In addition, we allow you to scan the output for compile problems. Since we only want to convert the Markdown file to HTML select Never scan the build output from the presented list.

At this point, you should see an additional file show up in the file list sample.html.

If you want to make the Compile Markdown task the default build task to run execute Configure Default Build Task from the global Terminal menu and select Compile Markdown from the presented list. The final tasks.json file will then look like this:

Automating Markdown compilation

Let's take things a little further and automate Markdown compilation with VS Code. We can do so with the same task runner integration as before, but with a few modifications.

Step 1: Install Gulp and some plug-ins

We use Gulp to create a task that automates Markdown compilation. We also use the gulp-markdown plug-in to make things a little easier.

We need to install gulp both globally (-g switch) and locally:

Note: gulp-markdown-it is a Gulp plug-in for the markdown-it module we were using before. There are many other Gulp Markdown plug-ins you can use, as well as plug-ins for Grunt.

You can test that your gulp installation was successful by typing gulp -v. You should see a version displayed for both the global (CLI) and local installations.

Step 2: Create a simple Gulp task

Open VS Code on the same folder from before (contains sample.md and tasks.json under the .vscode folder), and create gulpfile.js at the root.

Place the following source code in that file:

What is happening here?

1. We are watching for changes to any Markdown file in our workspace, i.e. the current folder open in VS Code.
2. We take the set of Markdown files that have changed, and run them through our Markdown compiler, i.e. gulp-markdown-it.
3. We now have a set of HTML files, each named respectively after their original Markdown file. We then put these files in the same directory.

Step 3: Run the gulp default Task

To complete the tasks integration with VS Code, we will need to modify the task configuration from before to run the default Gulp task we just created. You can either delete the tasks.json file or empty it only keeping the 'version': '2.0.0' property. Now execute Run Task from the global Terminal menu. Observe that you are presented with a picker listing the tasks defined in the gulp file. Select gulp: default to start the task. We allow you to scan the output for compile problems. Since we only want to convert the Markdown file to HTML select Never scan the build output from the presented list. At this point, if you create and/or modify other Markdown files, you see the respective HTML files generated and/or changes reflected on save. You can also enable Auto Save to make things even more streamlined.

If you want to make the gulp: default task the default build task executed when pressing ⇧⌘B (Windows, Linux Ctrl+Shift+B) run Configure Default Build Task from the global Terminal menu and select gulp: default from the presented list. The final tasks.json file will then look like this:

Step 4: Terminate the gulp default Task

The gulp: default task runs in the background and watches for file changes to Markdown files. If you want to stop the task, you can use the Terminate Task from the global Terminal menu.

Next steps

Read on to find out about:

• CSS, SCSS, and Less - Want to edit your CSS? VS Code has great support for CSS, SCSS, and Less editing.

Common questions

Is there spell checking?

Not installed with VS Code but there are spell checking extensions. Check the VS Code Marketplace to look for useful extensions to help with your workflow.

Does VS Code support GitHub Flavored Markdown?

No, VS Code targets the CommonMark Markdown specification using the markdown-it library. GitHub is moving toward the CommonMark specification which you can read about in this update.

In the walkthrough above, I didn't find the Configure Task command in the Command Palette?

You may have opened a file in VS Code rather than a folder. You can open a folder by either selecting the folder with File > Open Folder or navigating to the folder and typing 'code .' at the command line.