Publish R Markdown On Github

admin



3.2 GitHub Pages

Use multiple languages including R, Python, and SQL. R Markdown supports a reproducible workflow for dozens of static and dynamic output formats including HTML, PDF, MS Word, Beamer, HTML5 slides, Tufte-style handouts, books, dashboards, shiny applications, scientific articles, websites, and more.

  1. According to a response from the RStudio team, the 'standard' solution would be to follow the instructions for 'Using R Markdown with RStudio', and notice the button on the third screenshot with the '.
  2. While it's not possible to host fully-fledged Shiny apps on Github pages (Indeed, as @Gregor suggested, shinyapps.io is useful for this), the devs for Shiny have been working to make some of the functionality run completely on the client-side via htmlwidgets.

GitHub Pages (https://pages.github.com) is a very popular way to host static websites (especially those built with Jekyll), but its advantages are not obvious or appealing compared to Netlify. We recommend that you consider Netlify + Hugo due to these reasons:

Publish R Markdown On Github

  • Redirecting URLs is awkward with GitHub Pages but much more straightforward with Netlify.38 This is important especially when you have an old website that you want to migrate to Hugo; some links may be broken, in which case you can easily redirect them with Netlify.

  • One of the best features of Netlify that is not available with GitHub Pages is that Netlify can generate a unique website for preview when a GitHub pull request is submitted to your GitHub repository. This is extremely useful when someone else (or even yourself) proposes changes to your website, since you have a chance to see what the website would look like before you merge the pull request.

Basically, Netlify can do everything that GitHub Pages can, but there is still one little missing feature, which is closely tied to GitHub itself, which is GitHub Project Pages. This feature allows you to have project websites in separate repositories, e.g., you may have two independent websites https://username.github.io/proj-a/ and https://username.github.io/proj-b/, corresponding to GitHub repositories username/proj-a and username/proj-b, respectively. However, since you can connect any GitHub repositories with Netlify, and each repository can be associated with a domain or subdomain name, you may replace GitHub Project Pages with different subdomains like proj-a.netlify.com and proj-b.netlify.com. The actual limitation is that you cannot use subpaths in the URL but you can use any (sub)domain names.

Although GitHub does not officially support Hugo (only Jekyll is supported), you can actually publish any static HTML files on GitHub Pages, even if they are not built with Jekyll. The first requirement for using GitHub Pages is that you have to create a GitHub repository named username.github.io under your account (replace username with your actual GitHub username), and what’s left is to push your website files to this repository. The comprehensive documentation of GitHub Pages is at https://pages.github.com, and please ignore anything related to Jekyll there unless you actually use Jekyll instead of Hugo. To make sure GitHub does not rebuild your website using Jekyll and just publish whatever files you push to the repository, you need to create a (hidden) file named .nojekyll in the repository.39 GitHub offers a free subdomain username.github.io, and you can use your own domain name by configuring its A or CNAME records to point it to GitHub Pages (consult the GitHub Pages documentation for instructions).

Your public/ directory should be the GIT repository. You have two possible choices for setting up this repository locally. The first choice is to follow the default structure of a Hugo website like the diagram below, and initialize the GIT repository under the public/ directory:

If you know how to use the command line, change the working directory to public/, and initialize the GIT repository there:

The other choice is to clone the GitHub repository you created to the same directory as your website source:

And the structure looks like this:

The source directory and the username.github.io directory are under the same parent directory. In this case, you need to set the option publishDir = '../username.github.io' in source/config.toml.

Publish r markdown on github free

This article covers the various ways you can publish Distill articles, including:

  • Sharing a standalone HTML file using E-mail, Dropbox, etc.

  • Publishing to RPubs or RStudio Connect.

  • Using GitHub Pages to host your article on GitHub

Note that it’s also possible to publish collections of Distill articles as a website (see the article on publishing websites for additional details).

Standalone HTML

When you render a Distill article using R Markdown, all of the content required to render the article (images generated by R plots, required CSS and JavaScript, etc.) are bundled into a single HTML file.

Often the simplest way to share a Distiill article is to share this HTML file using the same means you use to share other document types like spreadsheets, presentations, and PDFs. You can send the article as an E-mail attachment or uploading it to Dropbox or any other file sharing service.

This type of sharing is suitable for private communications to small groups. If you want to make your article available more broadly the following sections cover various ways to do that.

RPubs & RStudio Connect

RPubs is a free service from RStudio for sharing documents on the web. RStudio Connect is a server product from RStudio for secure sharing of applications, reports, and plots.

You can publish to RPubs or RStudio Connect directly from within the R Markdown document preview window by clicking the Publish button:

Note that all documents published to RPubs are publicly visible, so you should only publish content you want to share publicly.

Unlike RPubs, RStudio Connect is a server that you run inside an organization, so is suitable for publishing content that you only want visible within your organization’s network.

GitHub Pages

Publish R Markdown On Github Download

GitHub Pages is a service that lets you publish a website from any GitHub repository. While the service supports publishing full websites, it’s also a perfectly suitable place to publish a single Distill article.

Here are the steps required to publish a Distill article to GitHub Pages:

  1. Create a new Git repository that will be used to host your article.

  2. Configure your repository to publish the contents of the master branch (you can do from the Settings page for the repository):

  3. Create a file named .nojekyll in your repository (this is required to disable some processing of HTML files that GitHub does by default). You can do this with the following code:

  4. Create a Distill article named index.Rmd within the repository (using this name will allow your article to be served as the default web page for the repository).

  5. Add appropriate metadata to the article. The article should at a minimum include title and description fields, and should also specify self_contained: false (this will make the article load faster and will enable you to add a preview image for sharing the article on Slack, Twitter, etc.):

  6. Write and render your article using R Markdown.

  7. Push the article (including the HTML file generated when you rendered it) to GitHub. Your article is now published!

GitHub Pages are served on the github.io domain (with your GitHub account as a sub-domain). For example, if your GitHub username is jsmith and your repository is named distill-article then the article will be available at https://jsmith.github.io/distill-article.

Other services

R Markdown Cheat Sheet

Note that any web server or web host capable of hosting a static website can equally well host a single Distill article. See the article on publishing Distill websites for details on publishing articles on a variety of other services including Netlify, Firebase, Site44, and Amazon S3.