Yihui Xie

With Quarto Coming, is R Markdown Going Away? No.

Yihui Xie / 2022-04-29


So you have heard of Quarto, a new tool based on Pandoc for technical publishing. When you first see a .qmd document (Quarto), it looks quite similar to an .Rmd document (R Markdown), which can easily confuse R Markdown users. Questions can arise naturally: Why inventing a new system? Why cannot you just add the new features to the existing R Markdown ecosystem? Is R Markdown going to be retired? I will share some thoughts in this post. For those who prefer reading a shorter official FAQ, please visit the Quarto website and you can skip my post.

Is R Markdown going away?

Let me answer the most important and urgent question first: R Markdown is not going away. Rest assured that we will still actively maintain it. This is still an important part of my job. That said, we will probably not try to backport Quarto features into R Markdown (unless it is fairly straightforward and takes little effort). That means it is unlikely that you will be too excited about a certain future release of a package in the R Markdown ecosystem that we maintain (I cannot say this for other package maintainers but only ourselves).

Should you switch?

Should you switch to Quarto? Not necessarily. If you find R Markdown meet your need, you can definitely stay there. It is not imperative to switch. Quarto’s goal is to cover most features of R Markdown eventually, but it may be impossible to become a strict superset of R Markdown. For example, it is by design that each Quarto book chapter file is rendered in a new session (i.e., bookdown’s Knit-and-Merge approach), and there is no support for bookdown’s Merge-and-Knit approach. This means if your later book chapter needs to reuse objects from a previous chapter, you will have to come up with your own solution.

Speaking of my own work based on R Markdown, I do not have a plan to switch yet. Personally, I’m most interested in the Quarto book format. I will try it if I write a new book in the future. R Markdown and Quarto have a lot in common in most output formats. I want to mention the two things that have distinct foundations below: one is slides (xaringan is an outlier based on remark.js instead of Pandoc), and the other is websites (blogdown is primarily based on Hugo, and Pandoc can be optional). By comparison, Quarto is built exclusively on top of Pandoc.

For slides, I will stay with xaringan because it is powerful enough to me and I’m a minimalist. Quarto’s revealjs presentation is amazingly powerful, but most of time all I need on my slides is really just a slide title plus a bullet list. Actually I’m interested in creating a minimal presentation package that is more lightweight and much less powerful than xaringan. Yes, I still want to create a presentation package that will not accidentally become popular (if I fail this time, I might just resort to presenting with a .txt file someday).

For blogs and websites, I’m impressed by the beauty of Quarto websites, but I will definitely stay with blogdown myself (of course I’m biased). Following the tips from blogdown::check_site(), you can almost be sure that your site will remain stable for years. For example, I’m still using a rather old version of Hugo (0.25.1), and it has been working well for five years. The theme does not use any fancy or advanced technologies. Hugo’s unbeatable speed is also important to me because I have thousands of posts on this site. Continuous deployment and PR preview with Github/Netlify/Vercel are awesome, mature, and indispensable to me. Other than resisting the recurring urge to tweak CSS or even change the theme, there is little I need to do in terms of maintaining the site. I found Rakhim’s webcomic below in 2020 and it resonated well with me. That is, we tend to spend too much time on setting up a blog or learning or teaching how to set up one, instead of choosing one tool, sitting down, and writing for 10 years. My journey before Hugo was quite long, too (I had used several PHP-based frameworks and Jekyll), and I think I have settled down since 2017.

Blogging vs. blog setups

If you are a distill user, however, I think it makes more sense to switch to Quarto (like Danielle Navarro did), since a distill website is much more similar to a Quarto website. By comparison, a Hugo site is usually much more flexible and complicated, and the theme can be totally different, so you cannot just throw your source files into Quarto and expect a similar site to be generated.

As a technical note, one nice thing about Quarto is that it is a single self-contained binary like Hugo, so hopefully someday it will be supported by Netlify or Vercel and we will get the same nice workflow like Hugo and other static site generators. Similarly, since it is a single binary, it is possible to pin your project to an older version of Quarto. This is often hard for other software packages because they have other dependencies, which means you will have to manage all the dependencies.

Why inventing a new tool instead of improving R Markdown?

When seeing a new tool, you may think of this XKCD cartoon:

Standards (xkcd)

Yes, we have already got R Markdown and Jupyter. Both are great. Even though both support multiple computing languages, I feel as if R Markdown’s birth certificate had a letter “R” stamped on it, and Jupyter had a “Python” stamp. It may feel odd to tell Python users that they absolutely can run Python code in an R Markdown document (and it is awesome that Python and R can interoperate), but… but they have to install R in the first place in order to use… Python.

Quarto has made R optional to Jupyter users, and Python optional to R users. You can choose between the two (but have to choose one). For R users, Quarto uses the same backend as R Markdown, i.e., the knitr package.

R Markdown workflow

Quarto workflow

The main technical difference between Quarto and R Markdown is that Quarto makes heavy use of Pandoc’s Lua filters. One example is the implementation of figure cross-references. I have to admit that I never liked my own implementation in bookdown, which was hackish. That’s why I have never ported this important and useful feature back into rmarkdown. Using Lua filters to process the Markdown document is more robust, and can make one feature available in multiple output formats.

Another benefit of Quarto is that it tries to bring all nice things into one software package. Well, I’m not sure if everyone would agree that this is a benefit. Some people may prefer smaller pieces of software instead of a monolithic package. In the current R Markdown ecosystem, you have to use a dedicated package (sometimes among several competing packages) for a particular task. If you have already been familiar with these individual packages, it is totally fine that you continue to use them.

We have learned a lot from developing R Markdown, and I think it’s great to let a wider audience (e.g., the Jupyter community) benefit from our learning.1 For this reason, it can be easier that Quarto is developed as a single package instead of a dozen command-line utilities, because newcomers from other communities would face less paradox of choice.2

Summary

Quarto is an attempt to generalize the R Markdown ecosystem, so that all useful features for authoring and publishing technical content can be made available to a larger world outside R. Quarto’s heavy investment in Pandoc Lua filters means that it is not tied to a specific backend that generates the .md (Markdown) output file. In case a new tool (oh God, no thanks) like knitr and jupyter be invented, Quarto can integrate with it, too.3

At this point, I think the benefits for other communities to try Quarto are more significant than R users. R Markdown will continue to exist and be maintained (bug fixes and relatively small enhancements). I do not think R Markdown users need to hurry to the switch. Another thing that may give you some peace of mind is that Quarto can render .Rmd documents without any modification, too, so you can continue to write .Rmd instead of .qmd. If you like Quarto’s rendering, great. If not, the door is still wide open for you to come back.

Disclaimer: I have to admit that I’m far from a Quarto expert yet, although I have been watching Quarto grow. My contribution to Quarto is still quite limited (mainly from the knitr side). My thoughts here may not be accurate. When in doubt, please consult the official documentation at https://quarto.org.


  1. One example is TinyTeX and the R package tinytex. Quarto has basically rewritten tinytex::latexmk() using TypeScript so that everyone can enjoy the benefits of this original R function.

  2. But is Quarto itself, as a new tool, contributing to the paradox? That sounds like a good question. I cannot really say no.

  3. Quarto is mainly written in TypeScript, not R or Python.