In the spirit of learning in public, I wanted an excuse to dive into Quarto to learn more about publishing formats beyond simple PDF and HTML documents.

If you’re not familiar, Quarto (quarto.org) is the successor to RMarkdown, the next-generation scientific publishing system that works natively with Python, R, and OJS. If you already have RMarkdown you probably don’t have to do anything to it to get it to render with Quarto. The wonderful thing about Quarto (and to a lesser extent, RMarkdown) is that you can write one single input document and render many types of output documents — HTML, PDF, Word docs, presentations (Powerpoint, Beamer, RevealJS), dashboards, websites, books, blogs, and more). And, Quarto Live, you can embed WebAssembly-powered interactive code blocks for R and Python right into a Quarto document (example here).

I demonstrate here how I turned an old course website of mine made from a bunch of RMarkdown documents into a polished e-book using Quarto. I also briefly point out Quarto Manuscripts and Quarto Dashboards at the end.

You can read the book or download a PDF at https://bdsr.stephenturner.us/.

My old course website

Back when I was faculty at UVA I started a series of workshops in response to the growing demand for practical education in data science and bioinformatics that the traditional coursework at the time lacked. I eventually turned this into a graduate course, and later into a course directed to faculty seeking a career in translational science. The course was a Software Carpentry style live coding hands-on course, mostly using R, that covered topics including data manipulation with dplyr, visualization with ggplot2, predictive modeling with caret, text mining with tidytext, RNA-seq analysis with DESeq2, basic statistics, survival analysis, and other topics.

I made the course website using RMarkdown Websites — a feature that I don’t think ever got much traction, but I found incredibly useful. You put a _site.yml file in the root of your project, and you got a little “Build Website” button in the RStudio build pane. Hit that button and it would render all the RMarkdown documents in the project, and give you a website with pages listed as they are in the _site.yml file. I took a lot of inspiration from Jenny Bryan’s old STAT545 course, and borrowed teaching ideas from other courses and blog posts around the internet.

This actually worked fairly well! My old workshop and course material website is still alive at stephenturner.github.io/workshops (screenshot below), and the code is all open on GitHub (github.com/stephenturner/workshops)

Quarto books

—Quarto has entered the chat—

Quarto showed up on my radar in 2022 at the last rstudio::conf (before it became posit::conf), where Posit announced the name change, public benefit corp status, Shiny for Python, and, Quarto. I’ve slowly switched most of my technical authoring from RMarkdown to Quarto. I had always been a big fan of the rticles package, and now Quarto is starting to catch up with journal article templates (I wrote the biorecap paper using a generic arXiv Quarto template).

I have bookmarks to so many great reference books including R for Data Science, Hands on Programming with R, and Python for Data Analysis, all of which are written as Quarto books.

The docs (quarto.org/docs/books) looked fairly simple. Just stick a bunch of qmd files in a directory and reference them in a _quarto.yml file. I wanted an excuse to explore the book authoring experience with Quarto, so I grabbed all the source code from my old course website to give it a try.

I intended to write this as a short tutorial, but there’s no tutorial here, because I really didn’t have to do anything! All the RMarkdown source from my old website just worked. There were a few slight customizations I made to the _quarto.yml from my old _site.yml. I updated a little bit of the verbiage to refer to book Chapters instead of lessons, and I updated a few places to use cross-references instead of hard-coded hyperlinks. I followed the GitHub pages publishing docs to configure my gh-pages branch to serve up the content I push to the main branch after running quarto publish gh-pages. And I stuck a custom subdomain on the repo so I could serve at bdsr.stephenturner.us instead of the default stephenturner.github.io/bdsr. The process took me about an hour or so. The book website is live at bdsr.stephenturner.us, and the publish command automatically makes both PDF and EPUB versions available.

Biological Data Science with R

The book is based on course material I developed around 2015 and taught through 2018, so it’s starting show its age. There are some dplyr functions that are deprecated or superseded, it uses gather() and spread() from tidyr instead of pivot_*(), and it’s using caret and related packages instead of tidymodels. And, in the predictive modeling and forecasting chapter, there’s a section on forecasting influenza-like illness that shows perfectly regular seasonal ILI patterns through 2019-2021, a counterfactual that co-instructor and co-author VP (Pete) Nagraj and I published a paper on years later.

Learning more

I recently wrote a short essay about learning in public:

Learning in Public

Stephen Turner

·

September 24, 2024

Read full story

In that spirit I wanted to share a few resources related to books and other Quarto topics I’ve been reading.

The Quarto Books documentation is a well-organized place to start to get more info on publishing a book with Quarto, and you can find other great examples in the gallery. I also wanted call out two relatively new Quarto output document types that are worth looking at.

Quarto Manuscripts

Mine Cetinkaya-Rundel, Professor of the Practice of Statistical Science at Duke University, gave a great talk about Quarto Manuscripts at the R/Medicine conference earlier this year. The talk was awesome. With Quarto Manuscripts you can write a narrative and include additional R/Python/Etc notebooks alongside the manuscript, and render the output in multiple formats. See the example here, and Mine’s talk below.

Quarto Dashboards

I’ve used and recommended flexdashboard for making static or Shiny-enabled dashboards using RMarkdown. When Quarto first launched, dashboards were missing for at least a year. Quarto 1.4 was released earlier this year, introducing Quarto Dashboards along with other new features. See the short video below from Posit.