This lesson is in the early stages of development (Alpha version)

Publishing your project


Teaching: 10 min
Exercises: 0 min
  • What are the options for you to publish your project?

  • What free and open publishing resources are available?

  • What aspects should guide your choice?

  • Identify different ways you can publish your project.

  • Overview of some free and open resources available.

  • Learn which factors should guide your decision-making process.

What is Next?

Once you have completed your Rmd manuscript following all the best practices for reproducibility, including organizing your project files what is next? The answer depends on your plans to move forward. Let’s explore some scenarios:

If you plan to share your insights with your community right away

Publishing with Rpubs

Notice the “Publish” button in the upper right corner of your Knit output. Click this to publish to Rpubs. This is where you’ll need an Rpubs account as mentioned in setup for this workshop.

Click the publish button Publish button in RStudio

and you’ll be presented with the following panels:

Publish to RPubs or RStudio Connect (The other option in the dialog box, RStudio Connect, is a standalone publishing platform for teams to share content. It requires purchase to host and use.)

Confirm Publish to RPubs

The first time you publish, RStudio will likely ask if you want to install some needed packages; say yes. RStudio will then open up a web browser to allow you sign in to

At the end of the publish process your paper will be live on the internet with a URL similar to:

RStudio also saves an HTML version of your knit document to your local file system. Look for it in the results directory in the same directory as the R-markdown file in your R-Studio project directory.
This html document is self-contained and highly portable. Images are encoded directly into the HTML so you can easily move it to any web hosting you have available.

Publishing as website on GitHub

Another, better, but slightly more involved option for publishing an R Markdown document on the web is to use GitHub and GitHub Pages. It is out of the scope of this lesson to use GitHub, but briefly, GitHub is a widely-used version control and collaboration system. RStudio has built-in support for GitHub: in the upper right panel of your RStudio window, look for the Git tab, which allows you to sync your R Markdown project with a remote repository stored on To enable publishing to GitHub Pages, go to the Settings page of your repository on GitHub and select a branch (“branch” is a repository term) to publish. Name your main R Markdown file index.Rmd, and render it to HTML as index.html. With GitHub Pages enabled on your repository, the HTML file in your repository at will appear on the web as

Other document types

When you create a new R-markdown file in R Studio you are presented with a choice of Output Formats:

RStudio output formats

For the purposes of this workshop we’re using HTML as the output format but other types are available. You can render your R Markdown as a document, a presentation or a Shiny app. With the default installation of R-Studio HTML output is most likely to work. Other formats may require additional R packages and/or code libraries be installed on your computer. R Studio also has a templating system to help with creating R Markdown files with common elements, YAML metadata and rendering instructions. This can be very helpful for example if you want to create a weekly or monthly report documenting an ongoing experiment, study or other changing data.

If you are willing to publish your manuscript through a peer-reviewed journal

Key Points

  • You may choose to share and publish your data project before publishing its associated manuscript.

  • Sharing the code, data and documentation is necessary to allow for inspection and research reproducibility.