RMarkdown Tips and Tricks

This document provides a collection of my tweets containing tips and tricks related to RMarkdown. This document is mostly to organize my own thoughts since it became increasingly difficult to find the tweet I had in mind and also to remember which tip I had shared and which I wanted to share. And, although it’s for personal use, I am hoping that others might also find these tips and tricks useful. I will keep updating this document as I add new tweets.

If you are reading this on GitHub README, see this webpage instead to see the tweets rendered properly: https://indrajeetpatil.github.io/RmarkdownTips/

All the source code for this document can be found on GitHub: https://github.com/IndrajeetPatil/RmarkdownTips

Ackowledgments

Most of these tips are from Yihui Xie’s books and I would highly recommend that you check them out. Except for the knitr, all other books are available online for free.

I would also like to thank Christophe Dervieux, who has patiently answered my Rmarkdown-related questions, queries, and comments on Twitter, GitHub, and StackOverflow. His kindness and patience is boundless, not to mention his knowledge of the markdown-universe.

Tweets with tips and tricks

These are in no particular order, and, like my brain, these are scattered all over the place. 😅

Embed one chunk in another chunk

Reusing code chunks in \#rmarkdown (using `<<>>`) is a really cool feature, esp. in teaching contexts! ♻️

You can introduce students to code components piece-by-piece without having to repeat yourself in the underlying document! 👩‍🏫

For more, see-https://t.co/Hup2mjd6dl\#rstats pic.twitter.com/KCdEhs2ACv

— Indrajeet Patil (@patilindrajeets) July 9, 2021

Render R Markdown with rmarkdown::render()

Sometimes you may wish to render an \#rmarkdown document from a code chunk of *another* document.
E.g., if you're writing a paper and want to render the supplementary info document from the main document.

Doing so is as simple as this 👇! 🙌

Ref. https://t.co/FDfAZ2q7WA\#rstats pic.twitter.com/9In6J8dlNl

— Indrajeet Patil (@patilindrajeets) July 13, 2021

Child documents

Sometimes you want to:
♻️ reuse text (e.g. methods, session info) across documents
✂️ break a long document into smaller ones

In \#rmarkdown, you can create a "child" document and insert its contents into a "parent" document! 👩‍👦https://t.co/QOtOxwwmbN

🎥 1-min demo👇\#rstats pic.twitter.com/tMzF6HUuTb

— Indrajeet Patil (@patilindrajeets) July 8, 2021

Line numbers for code blocks

If you want to, \#rmarkdown provides a chunk option to easily add line numbers to source code and output text! 🧮

Ref: https://t.co/bM2oL6kpqt

N.B.
- You'll need to use syntax highlighting theme `tango`.
- Although only HTML output is shown, it works for PDF as well.\#rstats pic.twitter.com/8wKwA9uTwt

— Indrajeet Patil (@patilindrajeets) July 6, 2021

Knitting with Infinite Moon Reader

Maybe I was the only one who didn't know this for a long time, but you don't have to knit \#rmarkdown document for a preview *every time* you make a change.

Just run `xaringan::infinite_moon_reader()` function, and the preview will change after saving the document! 🙌🕺\#rstats pic.twitter.com/Tz3Y6hNGh3

— Indrajeet Patil (@patilindrajeets) February 27, 2021

Multi-column layout with Pandoc’s fenced div

Sometimes (especially in a teaching context or in a publication) you want to display text, code blocks, plots, etc. side-by-side for comparison.

In \#rmarkdown, you can create a multi-column layout using Pandoc's fenced Div! 🍎🍏

For more, see:https://t.co/Ul7QWt3aOd\#rstats pic.twitter.com/QPdGtnpK32

— Indrajeet Patil (इंद्रजीत पाटील) (@patilindrajeets) July 23, 2022

Side-by-side plots in code chunk

If you've got a code chunk in \#rmarkdown that produces multiple plots, they will by default be shown sequentially.

But sometimes one may want them to be instead displayed side-by-side 👯

Below is a 1-min demo of how to do so 🙌
For more, see: https://t.co/KXLAuEXP78\#rstats pic.twitter.com/cNBn4WnJWZ

— Indrajeet Patil (@patilindrajeets) May 11, 2021

Side-by-side tables in code chunk

If an \#rmarkdown code chunk has multiple dataframes, they will be displayed one on top of another.

But what if we want them to be instead displayed side-by-side (maybe to compare them?) 👯

Here is a \< 1-min demo of how to do so
For more, see: https://t.co/gUJZLfYxNR\#rstats pic.twitter.com/xDHQB9lFjD

— Indrajeet Patil (@patilindrajeets) June 23, 2021

Skipping evaluation of specific lines of code

You know how you can turn off code evaluation for a chunk by setting `eval=FALSE` in \#rmarkdown.

I was today years old when I realized that, if you have multiple lines of code, you can also selectively skip evaluation of only *specific* lines of code! 🤯\#rstats pic.twitter.com/KbVSzoVRAX

— Indrajeet Patil (@patilindrajeets) June 14, 2021

Parametrized reports

If you have to create a report template that can be reused across multiple similar scenarios, \#rmarkdown provides just the tool: Parameterized reports! 👏https://t.co/zuQ6H3y037

This is how you can generate hundreds of documents/reports with a single line of code! 🤯\#rstats pic.twitter.com/PWyS10ATlV

— Indrajeet Patil (@patilindrajeets) June 21, 2021

Inline formatting

ICYMI, you can use {n+1} backticks (\`) in \#rmarkdown document to show literal code with {n} backticks. 💡

This is really useful when you want to print the code *verbatim* in instructive tutorials, talks, etc. 🧑‍🏫https://t.co/cNVZ8Zmq4A\#rstats pic.twitter.com/t5cpXvCZwk

— Indrajeet Patil (@patilindrajeets) May 16, 2021

Using verbatim engine for teaching

The new {verbatim} engine in {knitr} 📦 is going to be an absolute game-changer for teaching \#rmarkdown to newbies! 🤩https://t.co/Sn46mZDfFo\#rstats pic.twitter.com/ZCLsM6iLX6

— Indrajeet Patil (इंद्रजीत पाटील) (@patilindrajeets) January 10, 2022

Custom CSS

If you know a bit of CSS, the sky is the limit for how much you can customize \#rmarkdown outputs. 🌈

For example, this quick demo shows how I can write custom css to use my favorite font (Google's RobotoCondensed) for the text body. 🔤

For more:https://t.co/dS4jLSr1Rs\#rstats pic.twitter.com/8XzSrGNeXO

— Indrajeet Patil (@patilindrajeets) March 4, 2021

Additional templates in other packages

Another reason why I ❤️ writing in \#rmarkdown:
If you install a few additional packages, you can choose from a huge collection of ready-made templates! 👏

Doesn't matter if you are writing a journal article, CV, handout, etc.

One authoring framework to cover it all 💪\#rstats pic.twitter.com/hOIHigWEP8

— Indrajeet Patil (@patilindrajeets) March 13, 2021

Tufte-style margin content

Sometimes while in \#rmarkdown, I have content (code, equation, etc.) that isn't crucial for the main narrative but also interesting enough not to be included as a caption.

This is where Tufte-style's margin content comes to the rescue! 🌟

See:https://t.co/fUvD7NkYai\#rstats pic.twitter.com/c6Lbz4MqDp

— Indrajeet Patil (@patilindrajeets) March 23, 2021

Multiple output formats

Although \#rmarkdown creates all sorts of outputs, not everything will work across outputs. E.g. I love including gifs in docs. This works in HTML but fails when knitted to PDF.

✅ How can one make doc robust to multiple outputs?
See demo 📽️

Ref:https://t.co/A0fqXzpGnw\#rstats pic.twitter.com/RbUUifhPdg

— Indrajeet Patil (@patilindrajeets) May 20, 2021

Changing graphical devices

Sometimes you may prefer a certain graphical device to render plots (e.g. PNG), but the journal or stakeholders might request different formats. 📸

📽️ shows how easy it is to produce plots for multiple devices at once using \#rmarkdown docs! 🙌https://t.co/KXLAuEXP78\#rstats pic.twitter.com/w0IBAyGZmJ

— Indrajeet Patil (@patilindrajeets) May 27, 2021

Additional arguments to graphical devices

Not only can you change the graphical device used in \#rmarkdown via chunk options, but you can also provide additional arguments to the device itself! 🖼️https://t.co/KXLAuEXP78

Of course, arguments depend on:
output (HTML, PDF, etc.) and device (PNG, JPEG, etc.)\#rstats pic.twitter.com/hBe8DG09XU

— Indrajeet Patil (@patilindrajeets) June 17, 2021

Include appendix after bibliography

If you write a manuscript in \#rmarkdown, the references are included by default at the end of the article.
But what if you also wish to include appendices? 🤔

This demo 📽️ shows how you can force a position for a bibliography. 💡

For more, see:https://t.co/4kqTvNeOSh\#rstats pic.twitter.com/IbDTHYcSBr

— Indrajeet Patil (@patilindrajeets) July 26, 2021

Confusion between eval, echo, include

At least once a month, I get confused about which of these {knitr} options I actually want to use 🙊
eval, echo, include.

So I finally made a quick table for myself. Maybe you’ll also find it useful. 📄

For more, see:https://t.co/QZwA6kWBB3

✅: yes, ❌: no\#rstats \#rmarkdown pic.twitter.com/Q795O3vVKq

— Indrajeet Patil (@patilindrajeets) June 15, 2021

Set the document title dynamically

One of the coolest things about \#rmarkdown is that you can use \#rstats code literally anywhere - even while specifying the metadata in YAML! 🤯

This means you can dynamically change the title (and other metadata) for the document 🪄

For more, see:https://t.co/8GAjY3lrN6 pic.twitter.com/VI6Nct5vDY

— Indrajeet Patil (@patilindrajeets) April 24, 2021

In-body syntax for chunk options

ICYMI, {knitr} 📦 now provides an alternate (and IMO more readable) way to specify code chunk options! 📑https://t.co/Sn46mZUR3Y

Chunk options written in the chunk header can be pretty hard to read, esp. when there are too many, or some are too long.\#rstats \#DataScience pic.twitter.com/kR0SUTd7XC

— Indrajeet Patil (इंद्रजीत पाटील) (@patilindrajeets) June 10, 2022

Option aliases

If you feel that you spend too much time typing (even with autocomplete) some oft-used {knitr} chunk options in \#rmarkdown, you can use the {set_alias} function to create shorthands! 🙌https://t.co/94siAzrjAO

Here is a demo 📽️\#rstats pic.twitter.com/6LPso8aeCN

— Indrajeet Patil (@patilindrajeets) July 20, 2021

Reducing size with prettydoc

For some reason, if you need to reduce the file size of \#rmarkdown's HTML output, but also don't want to compromise on the simplicity and pleasantness afforded by the default HTML template, you can instead use `prettydoc`'s HTML templates 🙌💅https://t.co/ONHY0Xdxt4\#rstats pic.twitter.com/i2laRd0bMw

— Indrajeet Patil (@patilindrajeets) April 6, 2021

Cross-referencing with bookdown

One reason I prefer `bookdown` 📦's wrapper functions: cross-referencing is easier!

In this little demo, I show how you can cross-reference figures if you switch from `rmarkdown::html_document` to `bookdown::html_document2` 👏https://t.co/c6Mqyc33m2\#rstats \#rmarkdown pic.twitter.com/YuY40AWHxH

— Indrajeet Patil (@patilindrajeets) March 16, 2021

Preserving spaces

Also see Yihui’s much simpler solution in the thread

I was today years old when I figured out how to preserve spaces in \#rmarkdown 🙈\#rstats pic.twitter.com/vJkBHW1yUe

— Indrajeet Patil (@patilindrajeets) April 30, 2021

Using YAML pipe operator ( | )

If you need to use special characters while writing \#rmarkdown YAML details, you can use the pipe operator ( \| ) in YAML to avoid having to escape any characters! 🙌https://t.co/kRFkcRs2if\#rstats pic.twitter.com/bTWFFgIdzg

— Indrajeet Patil (@patilindrajeets) August 11, 2021

Formatting/styling code

Please spare your colleagues or collaborators by properly formatting your \#rmarkdown code to make it more pleasant to read. 💅

No excuses when doing so is as easy as this! 🙌

For more, see: https://t.co/YFREna5s2D\#rstats pic.twitter.com/N5u6uNxi9y

— Indrajeet Patil (@patilindrajeets) May 4, 2021

Bootstrap themes

Sunday morning playing around with (bootstrap) themes for \#rmarkdown's HTML output ☕️

Here is a complete list of available options 🎨https://t.co/HOT3533ace\#rstats pic.twitter.com/2sYsyFWSUL

— Indrajeet Patil (@patilindrajeets) May 9, 2021

Description lists in HTML vignettes

AFAIK, it is not straightforward in \#rmarkdown to create description lists (https://t.co/Ojb7IZjDBs) in plain HTML documents, but that shouldn't stop you from easily using them in HTML vignettes for packages! 🗒️\#rstats pic.twitter.com/VO42Uq6NfC

— Indrajeet Patil (इंद्रजीत पाटील) (@patilindrajeets) November 8, 2021

Code highlighting styles

In case you missed it, you can choose from different code highlighting styles in \#rmarkdown and don't need to always stick to the default one. 🎨

My favorites are "kate" and "espresso". What are yours? 💅\#rstats pic.twitter.com/bmaq7672Zn

— Indrajeet Patil (@patilindrajeets) May 7, 2021

Shiny Documents

Static reports are the past; the future lies with dynamic, \#shiny reports in \#rmarkdown!

The reader (boss?, customer?, …) can change the parameters as they see fit and the analysis in the document will adjust immediately. 🪄

For more, see:https://t.co/4bhChsVoqu\#rstats pic.twitter.com/wLZZ184vP4

— Indrajeet Patil (@patilindrajeets) May 3, 2021

Keyboard short-cut to split chunk

Here is a cool \#rmarkdown short-cut that helps shave off some typing.

In case you have multiple outputs from the same code chunk, and then you decide to split that code into separate chunks, you can do so with a short-cut:

Windows: Ctrl + Alt + I
Mac: Cmd + Option + I\#rstats pic.twitter.com/MkHHQ2Xygm

— Indrajeet Patil (@patilindrajeets) March 6, 2021

Interactive dashboards

I don't get to use the interactive dashboards often in my work and that's a real pity because they are so wicked COOL! 🤩https://t.co/VuFF96bMDu

And all it takes is changing the output parameter in \#rmarkdown! As simple as that 😯\#rstats pic.twitter.com/coU69aKDEl

— Indrajeet Patil (@patilindrajeets) March 25, 2021

Data frame printing

In case you missed it, you can specify `df_print` argument in \#rmarkdown YAML to specify your preferred method for printing dataframes! 📄https://t.co/N9MPUzrj3Q

And, if you like none of these, there is always @haozhu233's `kableExtra`! 🤩https://t.co/8OReWQpDP2\#rstats pic.twitter.com/Ru8OtYjirm

— Indrajeet Patil (@patilindrajeets) March 7, 2021