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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.

⭐ AnyConv is a five-star HTML to MD converter tool ⭐ ️Convert html files to md online in seconds ✅ No software installation required ✅ Absolutely free ✅ Completely safe. Changing html to md is now. Markdown is a lightweight markup language for creating formatted text using a plain-text editor. John Gruber and Aaron Swartz created Markdown in 2004 as a markup language that is appealing to human readers in its source code form. Markdown is widely used in blogging, instant messaging, online.

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

Html To Markdown Online Conversion

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.

The Gitiles source browser automatically renders *.md Markdown files into HTML for simplified documentation.

Access controls

Access controls for documentation is identical to source code.

Documentation stored with source files shares the same permissions. Documentation stored in a separate Git repository can use different access controls. If Gerrit Code Review is being used, branch level read permissions can be used to grant or restrict access to any documentation branches.

READMEs

Files named README.md are automatically displayed below the file's directory listing. For the top level directory this mirrors the standard GitHub presentation.

We recommend that Git repositories have an up-to-date top-level README.md file.

Markdown syntax

Gitiles supports the core Markdown syntax described in Markdown Basics. Additional extensions are supported to more closely match GitHub Flavored Markdown and simplify documentation writing.

Paragraphs

Paragraphs are one or more lines of consecutive text, followed by one or more blank lines. Line breaks within a paragraph are ignored by the parser, allowing authors to line-wrap text at any comfortable column width.

Headings

Headings can be indicated by starting the line with one or more # marks. The number of # used determines the depth of the heading in the document outline. Headings 1 through 6 (######) are supported.

Headings can also use the less popular two line and ------ forms to create H1 and H2 level headers:

This form is discouraged as maintaining the length of the or --- lines to match the preceding line can be tedious work that is unnecessary with the # headers.

Lists

A bullet list:

will render into HTML as:

• Fruit
  • Orange
  • Pear
• Cake

The second level items (above Orange, Pear) must be indented with more spaces than the item they are nested under. Above 2 spaces were used. Additionally, the entire list must be preceded and followed by a blank line.

A numbered list:

will render into HTML as:

1. Fruit
   1. Orange
   2. Pear
2. Cake

List items will be renumbered sequentially by the browser, which is why 5 above displays as 2. Even with this feature it is a good idea to maintain list item numbers in the source Markdown to simplify reading the source file.

Like bullet lists, numbered lists can be nested by using more leading space than the prior list item.

Paragraphs can be properly nested within lists by indenting with at least 2 leading spaces:

Tables

Requires markdown.tables to be true (default).

Simple tables are supported with column alignment. The first line is the header row and subsequent lines are data rows:

will render as:

Placing : in the separator line indicates how the column should be aligned. A colon on the left side is a left-aligned column; a colon on the right-most side is right-aligned; a colon on both sides is center-aligned. If no alignment is specified, the column is aligned with the default for HTML tags (left-aligned by default unless overridden by css).

Empty table cells are indicated by whitespace between the column dividers (| |) while multiple column cells omit the whitespace.

Emphasis

Emphasize paragraph text with italic and bold styles. Either _ or * can be used for italic (1 character) and bold text (2 characters). This allows styles to be mixed within a statement:

It is strongly encouraged to review documentation for typos.

Emphasis within_words_is_ignored which helps write technical documentation. Literal *bold* can be forced by prefixing the opening * with such as *bold*.

Strikethrough

Requires markdown.strikethrough to be true (default).

Text can be struck out within a paragraph:

Note two tildes are required (~~) on either side of the struck out section of text.

Blockquotes

Blockquoted text can be used to stand off text obtained from another source:

renders as:

Sir Winston Churchill once said:

A lie gets halfway around the world before the truth has a chance to get its pants on.

Code (inline)

Use backticks to markup inline code within a paragraph:

Code (blocks)

Create a fenced code block using three backticks before and after a block of code, preceeded and followed by blank lines:

Text within a fenced code block is taken verbatim and is not processed for Markdown markup.

Syntax highlighting can optionally be enabled for common languages by adding the language name in lowercase on the opening line. Supported languages include:

Web

• css
• dart
• html
• javascript, js
• json

Markup

• tex, latex
• wiki
• xml
• xquery
• xsl
• yaml

Other

• clj (Clojure)
• erlang
• hs (Haskell)
• lisp
• matlab
• ml (OCaml, SML, F#)
• r
• rust
• sql
• vhdl

Horizontal rules

If markdown.ghthematicbreak is true, a horizontal rule can be inserted using GitHub style -- surrounded by blank lines. Alternatively repeating - or * and space on a line will also create a horizontal rule:

Links

Wrap text in [brackets] and the link destination in parens (http://...) such as:

Links can also use references to obtain URLs from elsewhere in the same document. This style can be useful if the same URL needs to be mentioned multiple times, is too long to cleanly place within text, or the link is within a table cell:

References can be simplified if the text alone is sufficient:

Automatic hyperlinking can be used where the link text should obviously also be the URL:

Well formed URLs beginning with https://, http://, and mailto: are used as written for the link's destination. Malformed URLs may be replaced with about:invalid#zSoyz to prevent browser evaluation of dangerous content.

HTML escaping of URL characters such as & is handled internally by the parser/formatter. Documentation writers should insert the URL literally and allow the parser and formatter to make it HTML safe.

Relative links such as ../src/api.md are resolved relative to the current markdown's file path within the Git repository. Absolute links such as /src/api.md are resolved relative to the top of the enclosing Git repository, but within the same branch or Git commit. Links may point to any file in the repository. A link to a *.md file will present the rendered markdown, while a link to a source file will display the syntax highlighted source.

Named anchors

Explicit anchors can be inserted anywhere in the document using , or {#tag} if markdown.namedanchor is true.

Implicit anchors are automatically created for each heading. For example ## Section 1 will have the anchor Section-1.

Anchor generation

• letters and digits, after removing accents (á → a)
• spaces are replaced with hyphens (-)
• other characters are replaced with underscores (_)
• runs of hyphens and underscores are collapsed

If a document contains the same named subsection under different parents the parent anchor will prefix the subsections to disambiguate. For example the following document will have anchors Running-Format and Coding-Format and Libraries as that subsection is unique:

When placed in a section header the explicit anchor will override the automatic anchor. The following are identical and associate the anchor live-examples with the section header instead of the automaticly generated name Examples.

Images

Similar to links but begin with ! to denote an image reference:

For images the text in brackets will be included as the alt text for screen readers.

Well formed image URLs beginning with https:// and http:// will be used as written for the attribute. Malformed URLs will be replaced with a broken data: reference to prevent browsers from trying to load a bad destination.

Relative and absolute links to image files within the Git repository (such as ../images/banner.png) are resolved during rendering by inserting the base64 encoding of the image using a data: URI. Only PNG (*.png), JPEG (*.jpg or *.jpeg), GIF (*.gif) and WebP (*.webp) image formats are supported when referenced from the Git repository.

Unsupported extensions or files larger than image size limit (default 256K) will display a broken image.

Inline image caching

Gitiles allows browsers to locally cache rendered markdown pages. Cache invalidation is triggered by the markdown file being modified and having a different SHA-1 in Git. Inlined images may need a documentation file update to be refreshed when viewed through unstable URLs like /docs/+/master/index.md.

HTML

Most HTML tags are not supported. HTML will be dropped on the floor by the parser with no warnings, and no output from that section of the document.

If markdown.safehtml is true there are small exceptions for
,

Site layout

Gitiles includes additional support to create functional documentation sites served directly from Git repositories.

Navigation bar

A top level navigation bar is automatically included on all pages if there is a navbar.md file present in the top of the repository. This file should be a simple bulleted list of links to include in the navigation bar.

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.

The Gitiles source browser automatically renders *.md Markdown files into HTML for simplified documentation.

Access controls

Access controls for documentation is identical to source code.

Documentation stored with source files shares the same permissions. Documentation stored in a separate Git repository can use different access controls. If Gerrit Code Review is being used, branch level read permissions can be used to grant or restrict access to any documentation branches.

READMEs

Files named README.md are automatically displayed below the file's directory listing. For the top level directory this mirrors the standard GitHub presentation.

We recommend that Git repositories have an up-to-date top-level README.md file.

Markdown syntax

Gitiles supports the core Markdown syntax described in Markdown Basics. Additional extensions are supported to more closely match GitHub Flavored Markdown and simplify documentation writing.

Paragraphs

Paragraphs are one or more lines of consecutive text, followed by one or more blank lines. Line breaks within a paragraph are ignored by the parser, allowing authors to line-wrap text at any comfortable column width.

Headings

Headings can be indicated by starting the line with one or more # marks. The number of # used determines the depth of the heading in the document outline. Headings 1 through 6 (######) are supported.

Headings can also use the less popular two line and ------ forms to create H1 and H2 level headers:

This form is discouraged as maintaining the length of the or --- lines to match the preceding line can be tedious work that is unnecessary with the # headers.

Lists

A bullet list:

will render into HTML as:

• Fruit
  • Orange
  • Pear
• Cake

The second level items (above Orange, Pear) must be indented with more spaces than the item they are nested under. Above 2 spaces were used. Additionally, the entire list must be preceded and followed by a blank line.

A numbered list:

will render into HTML as:

1. Fruit
   1. Orange
   2. Pear
2. Cake

List items will be renumbered sequentially by the browser, which is why 5 above displays as 2. Even with this feature it is a good idea to maintain list item numbers in the source Markdown to simplify reading the source file.

Like bullet lists, numbered lists can be nested by using more leading space than the prior list item.

Paragraphs can be properly nested within lists by indenting with at least 2 leading spaces:

Tables

Requires markdown.tables to be true (default).

Simple tables are supported with column alignment. The first line is the header row and subsequent lines are data rows:

will render as:

Placing : in the separator line indicates how the column should be aligned. A colon on the left side is a left-aligned column; a colon on the right-most side is right-aligned; a colon on both sides is center-aligned. If no alignment is specified, the column is aligned with the default for HTML tags (left-aligned by default unless overridden by css).

Empty table cells are indicated by whitespace between the column dividers (| |) while multiple column cells omit the whitespace.

Emphasis

Emphasize paragraph text with italic and bold styles. Either _ or * can be used for italic (1 character) and bold text (2 characters). This allows styles to be mixed within a statement:

It is strongly encouraged to review documentation for typos.

Emphasis within_words_is_ignored which helps write technical documentation. Literal *bold* can be forced by prefixing the opening * with such as *bold*.

Strikethrough

Requires markdown.strikethrough to be true (default).

Text can be struck out within a paragraph:

Note two tildes are required (~~) on either side of the struck out section of text.

Blockquotes

Blockquoted text can be used to stand off text obtained from another source:

renders as:

Sir Winston Churchill once said:

A lie gets halfway around the world before the truth has a chance to get its pants on.

Code (inline)

Use backticks to markup inline code within a paragraph:

Code (blocks)

Create a fenced code block using three backticks before and after a block of code, preceeded and followed by blank lines:

Text within a fenced code block is taken verbatim and is not processed for Markdown markup.

Syntax highlighting can optionally be enabled for common languages by adding the language name in lowercase on the opening line. Supported languages include:

Web

• css
• dart
• html
• javascript, js
• json

Markup

• tex, latex
• wiki
• xml
• xquery
• xsl
• yaml

Other

• clj (Clojure)
• erlang
• hs (Haskell)
• lisp
• matlab
• ml (OCaml, SML, F#)
• r
• rust
• sql
• vhdl

Horizontal rules

If markdown.ghthematicbreak is true, a horizontal rule can be inserted using GitHub style -- surrounded by blank lines. Alternatively repeating - or * and space on a line will also create a horizontal rule:

Links

Wrap text in [brackets] and the link destination in parens (http://...) such as:

Links can also use references to obtain URLs from elsewhere in the same document. This style can be useful if the same URL needs to be mentioned multiple times, is too long to cleanly place within text, or the link is within a table cell:

References can be simplified if the text alone is sufficient:

Automatic hyperlinking can be used where the link text should obviously also be the URL:

Well formed URLs beginning with https://, http://, and mailto: are used as written for the link's destination. Malformed URLs may be replaced with about:invalid#zSoyz to prevent browser evaluation of dangerous content.

HTML escaping of URL characters such as & is handled internally by the parser/formatter. Documentation writers should insert the URL literally and allow the parser and formatter to make it HTML safe.

Relative links such as ../src/api.md are resolved relative to the current markdown's file path within the Git repository. Absolute links such as /src/api.md are resolved relative to the top of the enclosing Git repository, but within the same branch or Git commit. Links may point to any file in the repository. A link to a *.md file will present the rendered markdown, while a link to a source file will display the syntax highlighted source.

Named anchors

Explicit anchors can be inserted anywhere in the document using , or {#tag} if markdown.namedanchor is true.

Implicit anchors are automatically created for each heading. For example ## Section 1 will have the anchor Section-1.

Anchor generation

• letters and digits, after removing accents (á → a)
• spaces are replaced with hyphens (-)
• other characters are replaced with underscores (_)
• runs of hyphens and underscores are collapsed

If a document contains the same named subsection under different parents the parent anchor will prefix the subsections to disambiguate. For example the following document will have anchors Running-Format and Coding-Format and Libraries as that subsection is unique:

When placed in a section header the explicit anchor will override the automatic anchor. The following are identical and associate the anchor live-examples with the section header instead of the automaticly generated name Examples.

Images

Similar to links but begin with ! to denote an image reference:

For images the text in brackets will be included as the alt text for screen readers.

Well formed image URLs beginning with https:// and http:// will be used as written for the attribute. Malformed URLs will be replaced with a broken data: reference to prevent browsers from trying to load a bad destination.

Relative and absolute links to image files within the Git repository (such as ../images/banner.png) are resolved during rendering by inserting the base64 encoding of the image using a data: URI. Only PNG (*.png), JPEG (*.jpg or *.jpeg), GIF (*.gif) and WebP (*.webp) image formats are supported when referenced from the Git repository.

Unsupported extensions or files larger than image size limit (default 256K) will display a broken image.

Inline image caching

Gitiles allows browsers to locally cache rendered markdown pages. Cache invalidation is triggered by the markdown file being modified and having a different SHA-1 in Git. Inlined images may need a documentation file update to be refreshed when viewed through unstable URLs like /docs/+/master/index.md.

HTML

Most HTML tags are not supported. HTML will be dropped on the floor by the parser with no warnings, and no output from that section of the document.

If markdown.safehtml is true there are small exceptions for
,