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
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.
These are in no particular order, and, like my brain, these are scattered all over the place. 😅
Reusing code chunks in \#rmarkdown (using `<<>>`) is a really cool feature, esp. in teaching contexts! ♻️
— Indrajeet Patil (@patilindrajeets) July 9, 2021
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
rmarkdown::render()Sometimes you may wish to render an \#rmarkdown document from a code chunk of *another* document.
— Indrajeet Patil (@patilindrajeets) July 13, 2021
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
Sometimes you want to:
— Indrajeet Patil (@patilindrajeets) July 8, 2021
♻️ 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
If you want to, \#rmarkdown provides a chunk option to easily add line numbers to source code and output text! 🧮
— Indrajeet Patil (@patilindrajeets) July 6, 2021
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
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.
— Indrajeet Patil (@patilindrajeets) February 27, 2021
Just run `xaringan::infinite_moon_reader()` function, and the preview will change after saving the document! 🙌🕺\#rstats pic.twitter.com/Tz3Y6hNGh3
Sometimes (especially in a teaching context or in a publication) you want to display text, code blocks, plots, etc. side-by-side for comparison.
— Indrajeet Patil (इंद्रजीत पाटील) (@patilindrajeets) July 23, 2022
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
If you've got a code chunk in \#rmarkdown that produces multiple plots, they will by default be shown sequentially.
— Indrajeet Patil (@patilindrajeets) May 11, 2021
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
If an \#rmarkdown code chunk has multiple dataframes, they will be displayed one on top of another.
— Indrajeet Patil (@patilindrajeets) June 23, 2021
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
You know how you can turn off code evaluation for a chunk by setting `eval=FALSE` in \#rmarkdown.
— Indrajeet Patil (@patilindrajeets) June 14, 2021
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
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
— Indrajeet Patil (@patilindrajeets) June 21, 2021
This is how you can generate hundreds of documents/reports with a single line of code! 🤯\#rstats pic.twitter.com/PWyS10ATlV
ICYMI, you can use {n+1} backticks (\`) in \#rmarkdown document to show literal code with {n} backticks. 💡
— Indrajeet Patil (@patilindrajeets) May 16, 2021
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
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
If you know a bit of CSS, the sky is the limit for how much you can customize \#rmarkdown outputs. 🌈
— Indrajeet Patil (@patilindrajeets) March 4, 2021
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
Another reason why I ❤️ writing in \#rmarkdown:
— Indrajeet Patil (@patilindrajeets) March 13, 2021
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
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.
— Indrajeet Patil (@patilindrajeets) March 23, 2021
This is where Tufte-style's margin content comes to the rescue! 🌟
See:https://t.co/fUvD7NkYai\#rstats pic.twitter.com/c6Lbz4MqDp
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.
— Indrajeet Patil (@patilindrajeets) May 20, 2021
✅ How can one make doc robust to multiple outputs?
See demo 📽️
Ref:https://t.co/A0fqXzpGnw\#rstats pic.twitter.com/RbUUifhPdg
Sometimes you may prefer a certain graphical device to render plots (e.g. PNG), but the journal or stakeholders might request different formats. 📸
— Indrajeet Patil (@patilindrajeets) May 27, 2021
📽️ 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
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
— Indrajeet Patil (@patilindrajeets) June 17, 2021
Of course, arguments depend on:
output (HTML, PDF, etc.) and device (PNG, JPEG, etc.)\#rstats pic.twitter.com/hBe8DG09XU
If you write a manuscript in \#rmarkdown, the references are included by default at the end of the article.
— Indrajeet Patil (@patilindrajeets) July 26, 2021
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
eval, echo, includeAt least once a month, I get confused about which of these {knitr} options I actually want to use 🙊
— Indrajeet Patil (@patilindrajeets) June 15, 2021
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
One of the coolest things about \#rmarkdown is that you can use \#rstats code literally anywhere - even while specifying the metadata in YAML! 🤯
— Indrajeet Patil (@patilindrajeets) April 24, 2021
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
ICYMI, {knitr} 📦 now provides an alternate (and IMO more readable) way to specify code chunk options! 📑https://t.co/Sn46mZUR3Y
— Indrajeet Patil (इंद्रजीत पाटील) (@patilindrajeets) June 10, 2022
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
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
— Indrajeet Patil (@patilindrajeets) July 20, 2021
Here is a demo 📽️\#rstats pic.twitter.com/6LPso8aeCN
prettydocFor 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
bookdownOne reason I prefer `bookdown` 📦's wrapper functions: cross-referencing is easier!
— Indrajeet Patil (@patilindrajeets) March 16, 2021
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
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
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
Please spare your colleagues or collaborators by properly formatting your \#rmarkdown code to make it more pleasant to read. 💅
— Indrajeet Patil (@patilindrajeets) May 4, 2021
No excuses when doing so is as easy as this! 🙌
For more, see: https://t.co/YFREna5s2D\#rstats pic.twitter.com/N5u6uNxi9y
Sunday morning playing around with (bootstrap) themes for \#rmarkdown's HTML output ☕️
— Indrajeet Patil (@patilindrajeets) May 9, 2021
Here is a complete list of available options 🎨https://t.co/HOT3533ace\#rstats pic.twitter.com/2sYsyFWSUL
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
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. 🎨
— Indrajeet Patil (@patilindrajeets) May 7, 2021
My favorites are "kate" and "espresso". What are yours? 💅\#rstats pic.twitter.com/bmaq7672Zn
Static reports are the past; the future lies with dynamic, \#shiny reports in \#rmarkdown!
— Indrajeet Patil (@patilindrajeets) May 3, 2021
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
Here is a cool \#rmarkdown short-cut that helps shave off some typing.
— Indrajeet Patil (@patilindrajeets) March 6, 2021
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
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
— Indrajeet Patil (@patilindrajeets) March 25, 2021
And all it takes is changing the output parameter in \#rmarkdown! As simple as that 😯\#rstats pic.twitter.com/coU69aKDEl
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
— Indrajeet Patil (@patilindrajeets) March 7, 2021
And, if you like none of these, there is always @haozhu233's `kableExtra`! 🤩https://t.co/8OReWQpDP2\#rstats pic.twitter.com/Ru8OtYjirm