Customize your research website

workflowr version 1.1.1

John Blischak

2018-07-06

There are many ways to customize your research website. Below are some common options.

Adding project details

workflowr automatically creates many files when the project is first started. As a first step for customizing your site, add the following information:

Changing the theme

The theme is defined in the file analysis/_site.yml. The default is cosmo, but the rmarkdown package accepts multiple Bootstrap themes. These are listed in the rmarkdown documentation. Go to bootswatch.com to compare the bootstrap themes. When typing the theme, make sure it is all lowercase (e.g. spacelab, united, etc.).

When experimenting with different themes, you’ll want to build a fast-running file, e.g. likely analysis/index.Rmd, instead of rebuilding the entire site every time. Click the RStudio Knit button or run wflow_build() in the R console to preview each theme:

wflow_build("analysis/index.Rmd")

Once you have chosen a theme, update the website by running the following:

wflow_publish("analysis/_site.yml", "Change the theme", republish = TRUE)

This commits analysis/_site.yml, re-builds every previously published HTML file using the new theme, and commits all the republished HTML pages.

Customize the navigation bar

The navigation bar appears on the top of each page. By default it includes links to index.html (Home), about.html (About), license.html (License), and the workflowr repository (the GitHub icon). This is all specified in analysis/_site.yml. To start, replace the URL to the workflowr GitHub repository with the URL to your GitHub repository.

If you have other important pages, you can add them as well. For example, to add the text “The main result” which links to main-result.html, you would add the following:

    - text: "The main result"
      href: main-result.html

You can also create a drop-down menu from the navigation bar. See the rmarkdown documentation for instructions.

Similar to changing the theme above, you will need to re-render each page of the website (the navbar is embedded within each individual HTML file). Thus you could run the same command as above:

wflow_publish("analysis/_site.yml", "Add main result page to navbar",
              republish = TRUE)

Setup SSH keys

Using the https protocol to communicate with GitHub is tedious because it requires entering your GitHub username and password. Using SSH keys for authentication removes the password requirement. Follow these GitHub instructions for creating SSH keys and linking them to your GitHub account. You’ll need to create separate SSH keys and link them each to GitHub for each machine where you clone your Git repository.

After you create your SSH keys and add them to your GitHub account, you’ll need to instruct your local Git repository to use the SSH protocol. For a hypothetical GitHub username of “myname” and GitHub repository of “myproject”, you would change the remote “origin” (the default name by convention) using the function wflow_git_remote():

wflow_git_remote(remote = "origin", user = "myname", repo = "myproject",
              protocol = "ssh", action = "set_url")

Alternatively you could update the remote URL using Git directly in the shell. See this GitHub documentation on changing a remote URL for instructions.

Change the session information function

The default function used to report the session information is sessionInfo(). To change this, you can edit this setting in _workflowr.yml. For example, to instead use devtools::session_info(), add the following line to _workflowr.yml:

sessioninfo: "devtools::session_info()"

If you’d prefer to manually insert a more complex report of the session information, disable the automatic reporting by adding the following to _workflowr.yml:

sessioninfo: ""

Note however that workflowr will still check for the presence of a session information function. Specifically it expects to find either sessionInfo or session_info somewhere in the R Markdown document.