How to render a single qmd-file to html or pdf

Clicking Render in RStudio defaults to render all qmd files in the directory (“project”) and to render both html and pdf. To save time in rendering, you can install quarto R package


and then render just one file and choose the target to be html with

quarto_render("template2.qmd", output_format = "html")

and when you are ready to submit the pdf, use

quarto_render("template2.qmd", output_format = "pdf")

quarto R package is available as pre-installed in JupyterHub (you may need to restart your server o get the new image).

If the rendering to pdf doesn’t work, you can print the html to pdf file, but do make sure to turn off “More setings -> Print headers and footers” to avoid accidentally printing your identity.

How to use R and RStudio remotely

Option 1: Using R and RStudio via JupyterHub

Instead of installing RStudio on your computer, you can use it in your web browser:

  • Information about Aalto JupyterHub
  • Go to
  • Choose CS-E5710 - Bayesian Data Analysis (2023)
  • In the Launcher click RStudio
  • In the RStudio Files pane (bottom right) you can create folders for your work and upload files from your computer to the server
    • The notebooks folder is the only persistent folder (stays there if you sign out) so save everything to that folder!
    • You may get an error when uploading a large zip file, but uploading smaller zip files work. If you can’t upload demo zip file contact the course staff via Zulip.
    • You may access your data as a network drive by SMB mounting it on your own computer - see Accessing JupyterHub data. This allows you to have total control over your data.
  • After uploading files, use Files pane to open them (e.g. an RMarkdown or Quarto notebook)
  • Knitting of R, Rmd, and qmd files works as well (tested 24th August)
  • CmdStanR used later in the course has been tested to work 24th August.
    • To use CmdStanR:
      • If you do not see the following output, please contact us on Zulip: This is cmdstanr version 0.6.0
        - CmdStanR documentation and vignettes:
        - CmdStan path: /coursedata/cmdstan
        - CmdStan version: 2.33.0
  • There is a limited memory available (3Gib) and bigger models and datasets can run out of memory with cryptic error message, but the demos and assignment models should run (if not, then contact the course staff via Zulip).
  • See also Aalto JupyterHub FAQ and bugs

Option 2: Use Aalto Linux via remote-desktop solution provided by Aalto-IT.

  • Information about Aalto remote desktop
  • Go to
  • Download VMWare Horizon application or use the web portal
    • If using the VMWare Horizon application, click on New Server and enter
  • Enter your aalto username (aalto email works too) and password in the respective fields.
  • Select Ubuntu 20.04
  • Click Activities, start typing RStudio in the search bar, and click RStudio.

How to access the BDA R (and Python) demos on CS JupyterHub

  • Go to on your favorite web-browser.