???? R Coding Style Guide

Iegor Rudnytskyi

3 years ago

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Language is a tool that allows human beings to interact and communicate with each other. The clearer we express ourselves, the better the idea is transferred from our mind to the other. The same applies to programming languages: concise, clear and consistent codes are easier to read and edit. It is especially important, if you have collaborators, which depend on your code. However, even if you don’t, keep in mind that at some point in time, you might come back to your code, for example, to fix an error. And if you did not follow consistently your coding style, reviewing your code can take much longer, than expected. In this context, taking care of your audience means to make your code as readable as possible.

Good coding style is like using correct punctuation. You can manage without it, but it sure makes things easier to read. Hadley Wickham

There is no such thing as a “correct” coding style, as there is no such thing as the best color. At the end of the day, coding style is a set of developers’ preferences. If you are coding alone, sticking to your coding style and being consistent is more than enough. The story is a bit different if you are working in a team: it is crucial to agree on a convention beforehand and make sure that everyone follows it.

Even though there is no official style guide, R is mature and steady enough to have an “unofficial” convention. In this post, you will learn these “unofficial” rules, their deviations, and most common styles.

Naming

Naming files

The convention actually depends on whether you develop a file for a package, or as a part of data analysis process. There are, however, common rules:

File names should use .R extension.
```
  # Good
  read.R

  # Bad 
  read
```

File names should be meaningful.

  # Good 
  model.R
    
  # Bad
  Untitled1.R

File names should not contain / and spaces. Instead, a dash (-) or underscore (_) should be used.

  # Good 
  fir_regression.R
  fir-regression.R
    
  # Bad
  fit regression.R

If the file is a part of data analysis, then it makes sense to follow the following recommendations:

File names should be lowercase. There is nothing bad in having capital case names, just bear in mind UNIX systems are case insensitive, meaning that test.R and Test.R do not differ.
```
  # Good
  analyse.R
    
  # Bad
  Analyse.R
```

Use meaningful verbs for file names.

  # Good 
  validate-vbm.R
    
  # Bad
  regression.R

If files should be run in a particular order, then use ascending names.
```
  01-read.R
  02-clean.R
  02-plot.R
```

If the file is used in a package, then slightly different rules should be folowed:

Mind special names:
- AllClasses.R (or AllClass.R), a file that stores all S4 classes definitions.
- AllGenerics.R (or AllGeneric.R), a file that stores all S4 generic functions.
- zzz.R, a file that contains .onLoad() and friends.
If the file contains only one function, name it by the function name.
Use methods- prefix for S4 class methods.

Naming variables

Generally, names should be as short as possible, still meaningful nouns.

  # Good 
  fit_rt
  split_1
  imdb_page
    
  # Bad
  fit_regression_tree
  cross_validation_split_one
  foo

Variable names should be typically lowercase.
```
  # Good 
  event
    
  # Bad 
  Event
```
NEVER separate words within the name by . (reserved for an S3 dispatch) or use CamelCase (reserved for S4 classes definitions). Instead, use an underscore (_).
```
  # Good 
  event_window
    
  # Bad 
  event.window
  EventWindow
```
DO NOT use names of existing function and variables (especially, built-in ones).
```
  # Bad
  T <- 10 # T is a shortcut of TRUE in R
  c <- "constant"
```

Naming functions

Many points of naming variables are similar for naming functions:

Generally, function names should be verbs.

  # Good
  add()
    
  # Bad
  addition()

Use . ONLY for dispatching S3 generic.

  # Good 
  bw_test()
    
  # Bad
  bw.test()

Add the underscore (_) prefix to a standard evaluation (SE) equivalent of a function (summarize vs summarize_ ).

Naming S4 classes

Class names should be nouns in CamelCase with initial capital case letter.

Syntax

Line length

The maximum length of lines is limited to 80 characters (thanks to IBM Punch Card).

It is possible to display the margin in RStudio Source editor:

Go to Tools -> Global Options… -> Code -> Display
Click on “Show margin”
Set “Margin column” to 80

Spacing

Put spaces around all infix binary operators (=, +, *, ==, &&, <-, %*%, etc.).
```
  # Good 
  x == y
  a <- a ^ 2 + 1
    
  # Bad
  x==y
  a<-a^2+1
```

Put spaces around “=” in function calls (except for Bioconductor).

  # Good 
  mean(x = c(1, NA, 2), na.rm = TRUE)
    
  # Bad
  mean(x=c(1, NA, 2), na.rm=TRUE)

Do NOT place space for subsetting ($ and @), namespace manipulation (:: and :::), and for sequence generation (:).
```
  # Good 
  car$cyl
  dplyr::select
  1:10
    
  # Bad
  car $cyl
  dplyr:: select
  1: 10
```

Put a space after a coma.

  # Good 
  mtcars[, "cyl"]
  mtcars[1, ]
  mean(x = c(1, NA, 2), na.rm = TRUE)
    
  # Bad
  mtcars[,"cyl"]
  mtcars[1 ,]
  mean(x = c(1, NA, 2),na.rm = TRUE)

Use a space before left parentheses, except in a function call.

  # Good 
  for (element in element_list)
  if (grade == 5.5)
  sum(1:10)
    
  # Bad
  for(element in element_list)
  if(grade == 5.5)
  sum (1:10)

No spacing around code in parenthesis or square brackets.

  # Good 
  if (debug) message("debug mode")
  species["tiger", ]
    
  # Bad
  if ( debug ) message("debug mode")
  species[ "tiger" ,]

Curly braces

An opening curly brace should NEVER go on its own line and should always be followed by a new line.

  # Good 
  if (is_used) {
      # do something
  }
    
  if (is_used) {
      # do something
  } else {
      # do something else
  }
    
  # Bad
  if (is_used)
  {
      # do something
  }
    
  if (is_used) { # do something }
  else { # do something else }

A closing curly brace should always go on its own line, unless it’s followed by else.

  # Good 
  if (is_used) {
      # do something
  } else {
      # do something else
  }
    
  # Bad
  if (is_used) {
      # do something
  }
  else {
      # do something else 
  }

Always indent the code inside curly braces (see next section).

  # Good 
  if (is_used) {
      # do something
      # and then something else
  }
    
  # Bad
  if (is_used) {
  # do something
  # and then something else
  }

Curly braces and new lines can be avoided, if a statement after if is very short.
```
  # Good 
  if (is_used) return(rval)
```

Indentation

ALWAYS indent your code!

No tabs or mixes of tabs and spaces.
There are two common number of spaces for indentation: two (Hadley and others) and four (Bioconductor). My own rule of thumb: I use four spaces indentation for data analyses scripts, and two spaces while developing packages.
Choose the number of spaces of indentation upfront and stick to it. Never mix different number of spaces in one project.
To set the number of spaces in the project, go to Tools -> Global options… -> Code -> Editing. Check the following boxes: “Insert spaces for tab” (with “Tab width” equal to chosen number), “Auto-indent code after paste”, and “Vertically align arguments in auto-indent”.

Magic shortcut: Command+I (Ctrl+I for Windows/Linux) will indent a selected chunk of code. Together with Command+A (select all) it is a very powerful tool, which saves time.

Try a little exercise: paste the following code in your RStudio source editor, select it, and hit Command+I:

for(i in 1:10) {
if(i %% 2 == 0)
print(paste(i, "is even"))
}

New line

Very often function definition does not fit into one line. In this case, excessive arguments should be moved to a new line, starting with the opening parenthesis.
```
  long_function_name <- function(arg1, arg2, arg3, arg4, 
                                 long_argument_name1 = TRUE)
```

If arguments expand more than into two lines, then each argument should be placed on a separate line.

  long_function_name <- function(long_argument_name1 = c("value1", "value2"),
                                 long_argument_name2 = TRUE,
                                 long_argument_name3 = NULL,
                                 long_argument_name4 = FALSE)

The same applies to a function call: excessive arguments should be indented where the closing parenthesis is located, if only two lines are sufficient.
```
  plot(table(rpois(100, 5)), type = "h", col = "red", lwd = 10, 
       main = "rpois(100, lambda = 5)")
```

Otherwise, each argument can go into a separate line, starting with a new line after the opening parenthesis.

  list(
      mean = mean(x),
      sd = sd(x),
      var = var(x),
      min = min(x),
      max = max(x),
      median = median(x)
  )

If the condition in if statement expands into several lines, than each condition should end with a logical operator, NOT start with it.

  # Good
  if (some_very_long_name_1 == 1 &&
      some_very_long_name_2 == 1 ||
      some_very_long_name_3 %in% some_very_long_name_4)
        
  # Bad
  if (some_very_long_name_1 == 1
      && some_very_long_name_2 == 1
      || some_very_long_name_3 %in% some_very_long_name_4)

I know some people who are completely against it. See the next item why I believe it is better.

If the statement, which contains operators, expands into several lines, then each line should end with an operator and not begin with it. Sometimes, it makes sense to split a formula into meaningful chunks.
```
  # Good 
  normal_pdf <- 1 / sqrt(2 * pi * d_sigma ^ 2) *
      exp(-(x - d_mean) ^ 2 / 2 / s ^ 2)
    
  # Bad
  normal_pdf <- 1 / sqrt(2 * pi * d_sigma ^ 2)
      * exp(-(x - d_mean) ^ 2 / 2 / d_sigma ^ 2)
```
Not only it is ugly, but also syntactically wrong. In the second case, R will consider these two lines as two distinct statements: the first line will assign the value of 1 / sqrt(2 * pi * d_sigma ^ 2) to normal_pdf, and the second line will throw an error, since * does not have the first argument.

Each grammar statement of dplyr (after %>%) and ggplot2 (after +) should start with a new line.

  mtcars %>%
      filter(cyl == 4) %>% 
      group_by(am) %>% 
      summarize(avg_mpg = mean(mpg))
        
  ggplot(mtcars) + 
      geom_point(aes(x = mpg, y = qsec, color = factor(am))) + 
      geom_line(aes(x = mpg, y = qsec, color = factor(am)))

Comments

Comment your code. Always. Your collaborators and future-you will be very grateful. Comments start with # followed by space and text of the comment.
```
  # This is a comment. 
```
Comments should explain the why, not the what. Comments should not replicate the code by a plain langue, but rather explain the overall intention of the command.
```
  # Good
  # define iterator
  i <- 1
    
  # Bad
  # set i to 1
  i <- 1
```

Short comments can be placed on the same line of the code.

  plot(price, weight) # plot a scatter chart of price and weight

To comment/uncomment selected chunk, use Command+Shift+C.
Use roxygen2 comments for a package development (i.e., #') to comment functions.

It makes sense to split the source into logical chunks by # followed by - or =.

  # Read data
  #---------------------------------------------------------------------------
    
  # Tidy data
  #---------------------------------------------------------------------------

Other recommendations

Use <- for assignment, NOT =.
Use library() instead of require(), unless it is a conscious choice. Package names should be characters (avoid NSE – non-standard evaluation).
```
  # Good
  library("dplyr")
    
  # Bad
  require(dplyr)
```
In a function call, arguments can be specified by position, complete name, or partial name. Never specify by partial name and never mix by position and complete name.
```
  # Good 
  mean(x, na.rm = TRUE)
  rnorm(10, 0.2, 0.3)
    
  # Bad
  mean(x, na = TRUE)
  rnorm(mean = 0.2, 10, 0.3)
```
While developing a package, specify arguments by name.
The required (with no default value) arguments should be first, followed by optional arguments.
```
  # Good
  raise_to_power(x, power = 2.7)
    
  # Bad
  raise_to_power(power = 2.7, x)
```

The ... argument should either be in the beginning or in the end.

  # Good
  standardize(..., scale = TRUE, center = TRUE)
  save_chart(chart, file, width, height, ...)
    
  # Bad
  standardize(scale = TRUE, ..., center = TRUE)
  save_chart(chart, ..., file, width, height)

Good practice rule is to set default arguments inside the function using NULL idiom, and avoid dependence between arguments:

  # Good
  histogram <- function(x, bins = NULL) {
      if (is.null(bins)) bins <- nclass.Sturges(x)
      ...
  }
    
  # Bad
  histogram <- function(x, bins = nclass.Sturges(x)) {
      ...
  }

Always validate arguments in a function.
While developing a package, specify the namespace of each used function, except if it is from base package.
Do NOT put more than one statement (command) per line. Do NOT use semicolon as termination of the command.
```
  # Good
  x <- 1
  x <- x + 1
    
  # Bad 
  x <- 1; x <- x + 1
```
Avoid using setwd("/Users/irudnyts/path/that/only/I/have"). Almost surely your collaborators will have different paths, which makes the project not portable. Instead, use here::here() function from here() package.
Avoid using rm(list = ls()). This statement deletes all objects from the global environment, and gives you an illusion of a fresh R start.

If you have read until this moment, you deserve a treat. There is a magic key combination Command+Shift+A that reformats selected code: add spaces and indents it. Do not use it excessively though!

References

Advanced R
Google’s R Style Guide
Bioconductor Coding Style
Efficient R programming
Colin Gillespie’s R style guide
The State of Naming Conventions in R
Consistent naming conventions in R
Project-oriented workflow
Picture is taken from R Memes For Statistical Fiends Facebook page.

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