Tips and tricks in RStudio and R Markdown

Antoine Soetewey 2020-01-21 11 minute read
Photo by Juan Gomez

Photo by Juan Gomez

If you have the chance to work with an experienced programmer, you may be amazed by how fast she can write code. In this article, I share some tips and shortcuts you can use in RStudio and R Markdown to speed up the writing of your code.

Run code

You most probably already know this shortcut but I still mention it for new R users. From your script you can run a chunk of code with:

command + Enter on Mac
Ctrl + Enter on Windows

Insert a comment in R and R Markdown

To insert a comment:

command + Shift + C on Mac
Ctrl + Shift + C on Windows

This shortcut can be used both for:

  • R code when you want to comment your code. It will add a # at the beginning of the line
  • for text in R Markdown. It will add <!-- and --> around the text

Note that if you want to comment more than one line, select all the lines you want to comment then use the shortcut. If you want to uncomment a comment, apply the same shortcut.

Knit a R Markdown document

You can knit R Markdown documents by using this shortcut:

command + Shift + K on Mac
Ctrl + Shift + K on Windows

Code snippets

Code snippets is usually a few characters long and is used as a shortcut to insert a common piece of code. You simply type a few characters then press Tab and it will complete your code with a larger code. Tab is then used again to navigate through the code where customization is required. For instance, if you type fun then press Tab, it will auto-complete the code with the required code to create a function:

name <- function(variables) {
  
}

Pressing Tab again will jump through the placeholders for you to edit it. So you can first edit the name of the function, then the variables and finally the code inside the function (try by yourself!).

There are many code snippets by default in RStudio. Here are the code snippets I use most often:

  • lib to call library()
library(package)
  • mat to create a matrix
matrix(data, nrow = rows, ncol = cols)
  • if, el, and ei to create conditional expressions such as if() {}, else {} and else if () {}
if (condition) {
  
}

else {
  
}

else if (condition) {
  
}
  • fun to create a function
name <- function(variables) {
  
}
  • for to create for loops
for (variable in vector) {
  
}
  • ts to insert a comment with the current date and time (useful if you have very long code and share it with others so they see when it has been edited)
# Tue Jan 21 20:20:14 2020 ------------------------------
  • shinyapp every time I create a new shiny app
library(shiny)

ui <- fluidPage(
  
)

server <- function(input, output, session) {
  
}

shinyApp(ui, server)

You can see all default code snippets and add yours by clicking on Tools > Global Options… > Code (left sidebar) > Edit Snippets…

Ordered list in R Markdown

In R Markdown, when creating an ordered list such as this one:

  1. Item 1
  2. Item 2
  3. Item 3

Instead of bothering with the numbers and typing

1. Item 1
2. Item 2
3. Item 3

you can simply type

1. Item 1
1. Item 2
1. Item 3

for the exact same result (try it yourself or check the code of this article!). This way you do not need to bother which number is next when creating a new item.

To go even further, any numeric will actually render the same result as long as the first item is the number you want to start from. For example, you could type:

1. Item 1
7. Item 2
3. Item 3

which renders

  1. Item 1
  2. Item 2
  3. Item 3

However, I suggest always using the number you want to start from for all items because if you move one item at the top, the list will start with this new number. For instance, if we move 7. Item 2 from the previous list at the top, the list becomes:

7. Item 2
1. Item 1
3. Item 3

which incorrectly renders

  1. Item 2
  2. Item 1
  3. Item 3

New code chunk in R Markdown

When editing R Markdown documents, you will need to insert a new R code chunk many times. The following shortcuts will make your life easier:

command + option + I on Mac (or command + alt + I depending on your keyboard)
Ctrl + ALT + I on Windows
New R code chunk in R Markdown

New R code chunk in R Markdown

Reformat code

A clear and readable code is always easier and faster to read (and look more professional when sharing it to collaborators). To automatically apply the most common coding guidelines such as whitespaces, indents, etc., use:

cmd + Shift + A on Mac
Ctrl + Shift + A on Windows

So for example the following code which does not respect the guidelines (and which is not easy to read):

1+1
  for(i in 1:10){if(!i%%2){next}
print(i)
 }

becomes much more neat and readable:

1 + 1
for (i in 1:10) {
  if (!i %% 2) {
    next
  }
  print(i)
}

RStudio addins

RStudio addins are extensions which provide a simple mechanism for executing advanced R functions from within RStudio. In simpler words, when executing an addin (by clicking a button in the Addins menu), the corresponding code is executed without you having to write the code. RStudio addins have the advantage that they allow you to execute complex and advanced code much more easily than if you would have to write it yourself.

The addin I use most often is probably the {esquisse} addin, which allows to draw plots from the {ggplot2} package in a user-friendly and interactive way, and without having to write the code myself.

RStudio addins are quite diverse and require a more detailed explanation, so I wrote an article focusing on these addins. See the article here.

{pander} for aesthetics

The pander() function from the {pander} package is very useful for R Markdown documents and reporting. It is not actually a shortcut but it greatly improves the aesthetics of R outputs.

For instance, see below the difference between the default output of a Chi-square test of independence and the output from the same test with the pander() function (using the diamonds dataset from the {ggplot2} package):

library(ggplot2)
dat <- diamonds

test <- chisq.test(table(dat$cut, dat$color))
test
## 
##  Pearson's Chi-squared test
## 
## data:  table(dat$cut, dat$color)
## X-squared = 310.32, df = 24, p-value < 2.2e-16
library(pander)
pander(test)
Pearson’s Chi-squared test: table(dat$cut, dat$color)
Test statistic df P value
310.3 24 1.395e-51 * * *

All information that you need are displayed in an elegant table. The pander() function works on many statistical tests (not to say all of them, but I have not tried it on all available tests in R) and on regression models:

# Linear model with lm()
model <- lm(price ~ carat + x + y + z, data = dat)
model
## 
## Call:
## lm(formula = price ~ carat + x + y + z, data = dat)
## 
## Coefficients:
## (Intercept)        carat            x            y            z  
##      1921.2      10233.9       -884.2        166.0       -576.2
pander(model)
Fitting linear model: price ~ carat + x + y + z
  Estimate Std. Error t value Pr(>|t|)
(Intercept) 1921 104.4 18.41 1.977e-75
carat 10234 62.94 162.6 0
x -884.2 40.47 -21.85 2.317e-105
y 166 25.86 6.421 1.365e-10
z -576.2 39.28 -14.67 1.277e-48

The pander function also makes datasets, tables, vectors, etc. more readable in R Markdown output. For example, see the differences below:

head(diamonds) # first 6 observations of a dataset
## # A tibble: 6 x 10
##   carat cut       color clarity depth table price     x     y     z
##   <dbl> <ord>     <ord> <ord>   <dbl> <dbl> <int> <dbl> <dbl> <dbl>
## 1 0.23  Ideal     E     SI2      61.5    55   326  3.95  3.98  2.43
## 2 0.21  Premium   E     SI1      59.8    61   326  3.89  3.84  2.31
## 3 0.23  Good      E     VS1      56.9    65   327  4.05  4.07  2.31
## 4 0.290 Premium   I     VS2      62.4    58   334  4.2   4.23  2.63
## 5 0.31  Good      J     SI2      63.3    58   335  4.34  4.35  2.75
## 6 0.24  Very Good J     VVS2     62.8    57   336  3.94  3.96  2.48
pander(head(diamonds))
carat cut color clarity depth table price x y z
0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
0.29 Premium I VS2 62.4 58 334 4.2 4.23 2.63
0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75
0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48
summary(diamonds) # main descriptive statistics
##      carat               cut        color        clarity          depth      
##  Min.   :0.2000   Fair     : 1610   D: 6775   SI1    :13065   Min.   :43.00  
##  1st Qu.:0.4000   Good     : 4906   E: 9797   VS2    :12258   1st Qu.:61.00  
##  Median :0.7000   Very Good:12082   F: 9542   SI2    : 9194   Median :61.80  
##  Mean   :0.7979   Premium  :13791   G:11292   VS1    : 8171   Mean   :61.75  
##  3rd Qu.:1.0400   Ideal    :21551   H: 8304   VVS2   : 5066   3rd Qu.:62.50  
##  Max.   :5.0100                     I: 5422   VVS1   : 3655   Max.   :79.00  
##                                     J: 2808   (Other): 2531                  
##      table           price             x                y         
##  Min.   :43.00   Min.   :  326   Min.   : 0.000   Min.   : 0.000  
##  1st Qu.:56.00   1st Qu.:  950   1st Qu.: 4.710   1st Qu.: 4.720  
##  Median :57.00   Median : 2401   Median : 5.700   Median : 5.710  
##  Mean   :57.46   Mean   : 3933   Mean   : 5.731   Mean   : 5.735  
##  3rd Qu.:59.00   3rd Qu.: 5324   3rd Qu.: 6.540   3rd Qu.: 6.540  
##  Max.   :95.00   Max.   :18823   Max.   :10.740   Max.   :58.900  
##                                                                   
##        z         
##  Min.   : 0.000  
##  1st Qu.: 2.910  
##  Median : 3.530  
##  Mean   : 3.539  
##  3rd Qu.: 4.040  
##  Max.   :31.800  
## 
pander(summary(diamonds))
Table continues below
carat cut color clarity depth
Min. :0.2000 Fair : 1610 D: 6775 SI1 :13065 Min. :43.00
1st Qu.:0.4000 Good : 4906 E: 9797 VS2 :12258 1st Qu.:61.00
Median :0.7000 Very Good:12082 F: 9542 SI2 : 9194 Median :61.80
Mean :0.7979 Premium :13791 G:11292 VS1 : 8171 Mean :61.75
3rd Qu.:1.0400 Ideal :21551 H: 8304 VVS2 : 5066 3rd Qu.:62.50
Max. :5.0100 NA I: 5422 VVS1 : 3655 Max. :79.00
NA NA J: 2808 (Other): 2531 NA
table price x y z
Min. :43.00 Min. : 326 Min. : 0.000 Min. : 0.000 Min. : 0.000
1st Qu.:56.00 1st Qu.: 950 1st Qu.: 4.710 1st Qu.: 4.720 1st Qu.: 2.910
Median :57.00 Median : 2401 Median : 5.700 Median : 5.710 Median : 3.530
Mean :57.46 Mean : 3933 Mean : 5.731 Mean : 5.735 Mean : 3.539
3rd Qu.:59.00 3rd Qu.: 5324 3rd Qu.: 6.540 3rd Qu.: 6.540 3rd Qu.: 4.040
Max. :95.00 Max. :18823 Max. :10.740 Max. :58.900 Max. :31.800
NA NA NA NA NA
table(dat$cut, dat$color) # contingency table
##            
##                D    E    F    G    H    I    J
##   Fair       163  224  312  314  303  175  119
##   Good       662  933  909  871  702  522  307
##   Very Good 1513 2400 2164 2299 1824 1204  678
##   Premium   1603 2337 2331 2924 2360 1428  808
##   Ideal     2834 3903 3826 4884 3115 2093  896
pander(table(dat$cut, dat$color))
  D E F G H I J
Fair 163 224 312 314 303 175 119
Good 662 933 909 871 702 522 307
Very Good 1513 2400 2164 2299 1824 1204 678
Premium 1603 2337 2331 2924 2360 1428 808
Ideal 2834 3903 3826 4884 3115 2093 896
names(dat) # variable names
##  [1] "carat"   "cut"     "color"   "clarity" "depth"   "table"   "price"  
##  [8] "x"       "y"       "z"
pander(names(dat))

carat, cut, color, clarity, depth, table, price, x, y and z

rnorm(4) # generates 4 observations from a standard normal distribution
## [1]  1.4742574 -0.3038638  1.5244488  1.1083355
pander(rnorm(4))

-0.4801, 2.016, -0.4474 and -0.662

Pipe operator %>%

If you are using the {dplyr}, {tidyverse} or {magrittr} packages often, here is a shortcut for the pipe operator %>%:

command + Shift + M on Mac
Ctrl + Shift + M on Windows

Others

Similar to many other programs, you can also use:

  • command + Shift + N on Mac and Ctrl + Shift + N on Windows to open a new R Script
  • command + S on Mac and Ctrl + S on Windows to save your current script or R Markdown document

Thanks for reading. I hope you find these tips and tricks useful. If you are using others, feel free to share them in the comment section. See this starting guide in R Markdown if you are unfamiliar with it.

As always, if you have a question or a suggestion related to the topic covered in this article, please add it as a comment so other readers can benefit from the discussion. If you find a mistake or bug, you can inform me by raising an issue on GitHub. For all other requests, you can contact me here.

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