R Markdown Tips, Tricks, and Shortcuts – Dataquest


R Markdown is an open-source device for producing reproducible experiences in R. It helps you retain all your code, outcomes, and writing in a single place, and format all of it in a approach that is engaging and digestible.

It’s a worthwhile device for presenting your knowledge work to others, too. With R Markdown, you’ve got the choice to export your work to quite a few codecs together with PDF, Microsoft Word, a slideshow, or an html doc to be used on a web site.

R Markdown is a robust device as a result of it may be used for knowledge evaluation and knowledge science, to collaborate with others, and talk outcomes to choice makers.

In this weblog publish we’ll take a look at some ideas, methods, and shortcuts for working with R Markdown in RStudio. (If you’d wish to be taught extra about RStudio, take a look at this Dataquest weblog publish for RStudio ideas and methods!)

We love utilizing R Markdown for coding in R and authoring content material. In reality, we wrote this weblog publish in R Markdown! Let’s take a look at some explanation why!

1. Keyboard Shortcuts

Knowing R Markdown keyboard shortcuts will save plenty of time when creating experiences.

Here are among the important R Markdown shortcuts:

  • Insert a brand new code chuck with Command + Option + I on a Mac, or Ctrl + Alt + I on Linux and Windows.
  • Output your doc within the format laid out in your YAML header with Command + Shift + Ok on a Mac, or Ctrl + Shift + Ok on Linux and Windows. The “k” is brief for “knit”!

Next we’ll cowl shortcuts to run code chunks. But earlier than doing this it’s typically a good suggestion to restart your R session and begin with a clear setting. Do this with Command + Shift + F10 on a Mac or Ctrl + Shift + F10 on Linux and Windows.

  • Run all chunks above the present chunk with Command + Option + P on a Mac; Ctrl + Alt + P on Linux and Windows.
  • Run the present chunk with Command + Option + C or Command + Shift + Enter on a Mac; Ctrl + Alt + C or Ctrl + Shift + Enter on Linux and Windows.
  • Run the following chunk with Command + Option + N on a Mac; Ctrl + Alt + N on Linux and Windows.
  • Run all chunks with Command + Option + R or Command + A + Enter on a Mac; Ctrl + Alt + R or Ctrl + A + Enter on Linux and Windows.

2. Quickly Preview Your Document

R Markdown offers many format choices for compiling your doc. But rendering your work as a PDF or a presentation can take for much longer than compiling to HTML. For this purpose, it’s usually helpful to output your doc to HTML whereas authoring as a result of this allows to iterate rapidly.

When you open a brand new R Markdown file, the default output format is HTML — if you compile your report, you’ll be able to simply view it in an internet browser. This default setting can prevent time! When you close to a completed product, you modify the output to the format of your selecting and make the ultimate touches then.

New Document

3. Know Your Code Chunk Options

One of the nice issues about R Markdown is that you’ve many choices for controlling how every chunk of code is evaluated and introduced. This means that you can construct shows and experiences from the bottom up, together with code, plots, tables, and photographs, whereas solely presenting the important info to the supposed viewers. For instance, you’ll be able to embrace a plot of your outcomes with out exhibiting the code used to generate it.

Mastering these code chunk choices is crucial to changing into a proficient R Markdown consumer:

  • echo = FALSE: Hide the code, however run code and produce all outputs, plots, warnings and messages.
  • eval = FALSE: Show code, however don’t consider it.
  • fig.present = "hide": Hides plots.
  • embrace = FALSE: Runs code, however suppresses all output. This is useful for setup code. You can see an instance of this within the first code chunk if you open a brand new R Markdown doc!
  • message = FALSE: Prevent packages from printing messages after they load. This additionally suppress messages generated by capabilities.
  • outcomes = "hide": Hides printed output.
  • warning = FALSE: Prevents packages and capabilities from displaying warnings.

4. Use Inline Code

Directly embed R code into an R Markdown doc with inline code. This is beneficial if you wish to embrace details about your knowledge within the written abstract.

Use inline code with r and add the code to guage inside the backticks. For instance, we used inline code when penning this weblog publish to routinely quantity every part, in order that we didn’t should manually add them ourselves. So how did we do it? We began by making a variable known as tip_number and within the setup code chunk, and set the worth to zero, like this:

`tip_number <- 0`

Then we added the next inline code to every part to develop the quantity by one at every iteration:

`r paste0(tip_number <- tip_number + 1, ". ")`

Hey, wait a minute! How did we embrace that final line of code on this weblog publish authored in R Markdown with out messing up the part numbering beneath? With code chunk choices! The code instance above is written in a code chunk with the choice eval = FALSE to stop the code from working. Like this:

Eval False

As you’ll be able to see, R Markdown is a robust device as a result of it offers you a number of management over the output of your doc!

5. Use TinyTex

With R Markdown you should utilize the LaTeX doc preparation system to output high-quality experiences. LaTeX is particularly helpful when experiences embrace scientific or mathematical symbols and notation. For instance, we use LaTeX right here at Dataquest for authoring statistics content material that makes use of mathematical notation.

But LaTeX distributions akin to TeX Live, MiKTeX, and MacTeX, require about 5 gigabytes of disk area in your onerous drive! In distinction, TinyTex makes use of solely about 150 megabytes when it’s put in.

Install TinyTex with set up.packages('tinytex') or tinytex::install_tinytex(). Uninstall TinyTex with tinytex::uninstall_tinytex().

With TinyTex put in, there may be nothing else it’s worthwhile to do to output a PDF doc when you’ve specified PDF because the output format!

To compile a LaTeX doc to PDF, name considered one of these tinytex capabilities: pdflatex(), xelatex(), and lualatex(). The perform to make use of will depend on the LaTeX engine that you just wish to use.

TinyTex developer and R Markdown famous person Yihui Xie says that’s about all the typical R consumer must find out about TinyTex. Why? Because the LaTeX capabilities talked about will routinely detect and set up any lacking LaTeX packages which can be required!

6. Generate an R Markdown Document with an R Script

Did which you can generate an R Markdown doc from an R Script? To do that, seize commentary with #'. You may even specify code chunk choices with #+. Here’s an instance:

R Script

This R script is saved with the file title “r_script.R”. To render this doc as an R Markdown doc, we specify the spin() perform from knitr, like this:

knitr::spin("r_script.R", knit = FALSE, format = "Rmd")

This generates an R Markdown doc that appears like this:

R Markdown

And if you knit this doc, this HTML output is returned:

R Markdown

7. Generate an R Script with an R Markdown Document

You could also be questioning if there’s a strategy to convert an R Markdown doc to an R Script? There is! The knitr package deal additionally gives a perform for that, known as purl(). Here’s the command to transform our R Markdown doc again to an R script:

knitr::purl("r_script.Rmd", documentation = 2)

Note that you will need to specify documentation = 2 to return full documentation in #' feedback. If your doc is pure code, specify documentation = 0.

8. Add Line Breaks in R Markdown

How troublesome can it’s so as to add a line break in your output? It’s not. But figuring this out could be a bit tough!

To break a line in R Markdown and have it seem in your output, use two trailing areas and then hit return. Let’s take a look at an instance.

Here, we didn’t specify two trailing areas between the 2 sentences within the first (high) group. But we did specify two trailing areas between the 2 sentences within the second (backside) group.

Line Break

The consequence after we knitted the doc? Check it out!

Line Break

9. Add Blank Lines in R Markdown

Because we simply coated line breaks, let’s additionally focus on easy methods to add empty strains to your doc. This may be helpful if you wish to add white area to scale back muddle in your doc.

To have one or many empty strains seem in your output, specify <br>. Let’s take a look at an instance.

Here, we didn’t specify two <br> instructions between the 2 sentences within the first (high) group. But we did specify two <br> instructions between the 2 sentences within the second (backside) group.

Blank Line

And right here’s the consequence!

Blank Line

10. Query SQL in R Markdown

You can question SQL in R Markdown by making a {sql} code chunk.

You’ll begin by producing an in-memory SQL database to make use of on this instance. You’ll generate a SQL database of the well-known “mtcars” dataset. Here’s the code:

Create DB

In a brand new code chunk, write a SQL question to pick all automobiles from the database with a four-cylinder engine. Be positive to alter the kind of this chunk to {sql}. This command returns a dataframe that you just’ll save as mt_cars_df:

SQL Query

Specify output.var = "mt_cars_df" to save lots of the outcomes of your question to a dataframe. The dataframe appears to be like like this:


You can use this dataframe in R code chunks to carry out evaluation or to generate a ggplot, for instance:

ggplot code


11. Use Chunk Names

Naming code chunks may be helpful for lengthy paperwork with many chunks. With R code chunks, for instance, title the chunk like this: {r my_boring_chunk_name}.

With named code chunks, you’ll be able to navigate between chunks within the code chunk navigator included on the backside of the R Markdown window pane. This may make plots straightforward to determine by title to allow them to be utilized in different sections of your doc.

We’ve added chunk names to the SQL instance from above. Here’s what we see within the navigator:

Chunk Name

12. Take it to the Cloud!

RStudio now gives a cloud-based model of RStudio Desktop known as RStudio Cloud. RStudio Cloud means that you can writer in R Markdown with out putting in software program, you solely want an internet browser.

Work in RStudio Cloud is organized into initiatives just like the desktop model, however RStudio Cloud allows you to specify the model of R you want to use for every challenge.

RStudio Cloud additionally makes it straightforward and safe to share initiatives with colleagues, and ensures that the working setting is totally reproducible each time the challenge is accessed. This is nice for writing reproducible experiences in R Markdown!

As you’ll be able to see, the format of RStudio Cloud is similar to authoring an R Markdown doc in RStudio Desktop:


Bonus: R Markdown Cheatsheet

RStudio has printed quite a few cheatsheets for working with R, together with an in depth cheatsheet on utilizing R Markdown! The R Markdown cheatsheet may be accessed from inside RStudio by deciding on Help > Cheatsheets > R Markdown Cheat Sheet.

Additional Resources

RStudio has printed just a few in-depth easy methods to articles about utilizing R Markdown. Find them right here.

The R Markdown Cookbook is a complete, free on-line guide that countains virtually every little thing it’s worthwhile to find out about R Markdown.


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