Creating Functions
Last updated on 2024-10-02 | Edit this page
Overview
Questions
- How do I make a function?
- How can I test my functions?
- How should I document my code?
Objectives
- Define a function that takes arguments.
- Return a value from a function.
- Test a function.
- Set default values for function arguments.
- Explain why we should divide programs into small, single-purpose functions.
If we only had one data set to analyze, it would probably be faster to load the file into a spreadsheet and use that to plot some simple statistics. But we have twelve files to check, and may have more in the future. In this lesson, we’ll learn how to write a function so that we can repeat several operations with a single command.
Defining a Function
You can write your own functions in order to make repetitive operations using a single command. Let’s start by defining your function “my_function” and the input parameter(s) that the user will feed to the function. Afterwards you will define the operation that you desire to program in the body of the function within curly braces ({}). Finally, you need to assign the result (or output) of your function in the return statement.
Now let’s see this process with an example. We are going to define a
function fahrenheit_to_celsius
that converts temperatures
from Fahrenheit
to Celsius:
R
fahrenheit_to_celsius <- function(temp_F) {
temp_C <- (temp_F - 32) * 5 / 9
return(temp_C)
}
We define fahrenheit_to_celsius
by assigning it to the
output of function
. The list of argument names are
contained within parentheses. Next, the body of the function–the
statements that are executed when it runs–is contained within curly
braces ({}
). The statements in the body are indented by two
spaces, which makes the code easier to read but does not affect how the
code operates.
When we call the function, the values we pass to it are assigned to those variables so that we can use them inside the function. Inside the function, we use a return statement to send a result back to whoever asked for it.
Automatic Returns
In R, it is not necessary to include the return statement. R automatically returns whichever variable is on the last line of the body of the function. While in the learning phase, we will explicitly define the return statement.
Let’s try running our function. Calling our own function is no different from calling any other function:
R
# freezing point of water
fahrenheit_to_celsius(32)
OUTPUT
[1] 0
R
# boiling point of water
fahrenheit_to_celsius(212)
OUTPUT
[1] 100
We’ve successfully called the function that we defined, and we have access to the value that we returned.
Composing Functions
Now that we’ve seen how to turn Fahrenheit into Celsius, we can also turn Celsius into Kelvin:
R
celsius_to_kelvin <- function(temp_C) {
temp_K <- temp_C + 273.15
return(temp_K)
}
# freezing point of water in Kelvin
celsius_to_kelvin(0)
OUTPUT
[1] 273.15
What about converting Fahrenheit to Kelvin? We could write out the formula, but we don’t need to. Instead, we can compose the two functions we have already created:
R
fahrenheit_to_kelvin <- function(temp_F) {
temp_C <- fahrenheit_to_celsius(temp_F)
temp_K <- celsius_to_kelvin(temp_C)
return(temp_K)
}
# freezing point of water in Kelvin
fahrenheit_to_kelvin(32.0)
OUTPUT
[1] 273.15
This is our first taste of how larger programs are built: we define basic operations, then combine them in ever-larger chunks to get the effect we want. Real-life functions will usually be larger than the ones shown here–typically half a dozen to a few dozen lines–but they shouldn’t ever be much longer than that, or the next person who reads it won’t be able to understand what’s going on.
Nesting Function Calls
This example showed the output of fahrenheit_to_celsius
assigned to temp_C
, which is then passed to
celsius_to_kelvin
to get the final result. It is also
possible to perform this calculation in one line of code, by “nesting”
one function call inside another, like so:
R
# freezing point of water in Fahrenheit
celsius_to_kelvin(fahrenheit_to_celsius(32.0))
OUTPUT
[1] 273.15
Here, we call fahrenheit_to_celsius
to convert
32.0
from Fahrenheit to Celsius, and immediately pass the
value returned from fahrenheit_to_celsius
to
celsius_to_kelvin
to convert from Celsius to Kelvin. Our
conversion from Fahrenheit to Kelvin is done, all in one go!
This is convenient, but you should be careful not to nest too many function calls at once - it can become confusing and difficult to read!
Create a Function
In the last lesson, we learned to combine elements
into a vector using the c
function,
e.g. x <- c("A", "B", "C")
creates a vector
x
with three elements. Furthermore, we can extend that
vector again using c
, e.g. y <- c(x, "D")
creates a vector y
with four elements. Write a function
called highlight
that takes two vectors as arguments,
called content
and wrapper
, and returns a new
vector that has the wrapper vector at the beginning and end of the
content:
R
best_practice <- c("Write", "programs", "for", "people", "not", "computers")
asterisk <- "***" # R interprets a variable with a single value as a vector
# with one element.
highlight(best_practice, asterisk)
OUTPUT
[1] "***" "Write" "programs" "for" "people" "not"
[7] "computers" "***"
R
highlight <- function(content, wrapper) {
answer <- c(wrapper, content, wrapper)
return(answer)
}
Create a Function (continued)
If the variable v
refers to a vector, then
v[1]
is the vector’s first element and
v[length(v)]
is its last (the function length
returns the number of elements in a vector). Write a function called
edges
that returns a vector made up of just the first and
last elements of its input:
R
dry_principle <- c("Don't", "repeat", "yourself", "or", "others")
edges(dry_principle)
OUTPUT
[1] "Don't" "others"
R
edges <- function(v) {
first <- v[1]
last <- v[length(v)]
answer <- c(first, last)
return(answer)
}
The Call Stack
For a deeper understanding of how functions work, you’ll need to learn how they create their own environments and call other functions. Function calls are managed via the call stack. For more details on the call stack, have a look at the supplementary material.
Named Variables and the Scope of Variables
Functions can accept arguments explicitly assigned to a variable name
in the function call functionName(variable = value)
, as
well as arguments by order:
R
input_1 <- 20
mySum <- function(input_1, input_2 = 10) {
output <- input_1 + input_2
return(output)
}
- Given the above code was run, which value does
mySum(input_1 = 1, 3)
produce?- 4
- 11
- 23
- 30
- If
mySum(3)
returns 13, why doesmySum(input_2 = 3)
return an error?
The solution is
a.
.Read the error message:
argument "input_1" is missing, with no default
means that no value forinput_1
is provided in the function call, and neither in the function’s definition. Thus, the addition in the function body can not be completed.
Testing, Error Handling, and Documenting
Once we start putting things in functions so that we can re-use them, we need to start testing that those functions are working correctly. To see how to do this, let’s write a function to center a dataset around a particular midpoint:
R
center <- function(data, midpoint) {
new_data <- (data - mean(data)) + midpoint
return(new_data)
}
We could test this on our actual data, but since we don’t know what the values ought to be, it will be hard to tell if the result was correct. Instead, let’s create a vector of 0s and then center that around 3. This will make it simple to see if our function is working as expected:
R
z <- c(0, 0, 0, 0)
z
OUTPUT
[1] 0 0 0 0
R
center(z, 3)
OUTPUT
[1] 3 3 3 3
That looks right, so let’s try center on our real data. We’ll center the inflammation data from day 4 around 0:
R
dat <- read.csv(file = "data/inflammation-01.csv", header = FALSE)
centered <- center(dat[, 4], 0)
head(centered)
OUTPUT
[1] 1.25 -0.75 1.25 -1.75 1.25 0.25
It’s hard to tell from the default output whether the result is correct, but there are a few simple tests that will reassure us:
R
# original mean
mean(dat[, 4])
OUTPUT
[1] 1.75
R
# centered mean
mean(centered)
OUTPUT
[1] 0
That seems right: the original mean was about 1.75 and the mean of the centered data is 0. We can even go further and check that the standard deviation hasn’t changed:
R
# original standard deviation
sd(dat[, 4])
OUTPUT
[1] 1.067628
R
# centered standard deviation
sd(centered)
OUTPUT
[1] 1.067628
Those values look the same, but we probably wouldn’t notice if they were different in the sixth decimal place. Let’s do this instead:
R
# difference in standard deviations before and after
sd(dat[, 4]) - sd(centered)
OUTPUT
[1] 0
Sometimes, a very small difference can be detected due to rounding at
very low decimal places. R has a useful function for comparing two
objects allowing for rounding errors, all.equal
:
R
all.equal(sd(dat[, 4]), sd(centered))
OUTPUT
[1] TRUE
It’s still possible that our function is wrong, but it seems unlikely enough that we should probably get back to doing our analysis. However, there are two other important tasks to consider: 1) we should ensure our function can provide informative errors when needed, and 2) we should write some documentation for our function to remind ourselves later what it’s for and how to use it.
Error Handling
What happens if we have missing data (NA values) in the
data
argument we provide to center
?
R
# new data object and set one value in column 4 to NA
datNA <- dat
datNA[10,4] <- NA
# returns all NA values
center(datNA[,4], 0)
OUTPUT
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA
This is likely not the behavior we want, and is caused by the
mean
function returning NA when the na.rm=TRUE
is not provided. We may wish to not consider NA values in our
center
function. We can provide the na.rm=TRUE
argument and solve this issue.
R
center <- function(data, midpoint) {
new_data <- (data - mean(data, na.rm=TRUE)) + midpoint
return(new_data)
}
center(datNA[,4], 0)
OUTPUT
[1] 1.2542373 -0.7457627 1.2542373 -1.7457627 1.2542373 0.2542373
[7] 0.2542373 0.2542373 1.2542373 NA -1.7457627 -1.7457627
[13] -0.7457627 -1.7457627 -0.7457627 -1.7457627 -1.7457627 -0.7457627
[19] -0.7457627 -1.7457627 1.2542373 1.2542373 1.2542373 -0.7457627
[25] -0.7457627 -0.7457627 0.2542373 -0.7457627 0.2542373 -0.7457627
[31] -1.7457627 1.2542373 0.2542373 -0.7457627 0.2542373 1.2542373
[37] 0.2542373 0.2542373 1.2542373 1.2542373 0.2542373 1.2542373
[43] 1.2542373 1.2542373 1.2542373 0.2542373 1.2542373 1.2542373
[49] 1.2542373 0.2542373 -0.7457627 0.2542373 0.2542373 -0.7457627
[55] -0.7457627 1.2542373 0.2542373 -0.7457627 -0.7457627 -1.7457627
However, what happens if the user were to accidentally hand this
function a factor
or character
vector?
R
datNA[,1] <- as.factor(datNA[,1])
datNA[,2] <- as.character(datNA[,2])
center(datNA[,1], 0)
WARNING
Warning in mean.default(data, na.rm = TRUE): argument is not numeric or
logical: returning NA
WARNING
Warning in Ops.factor(data, mean(data, na.rm = TRUE)): '-' not meaningful for
factors
OUTPUT
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA
R
center(datNA[,2], 0)
WARNING
Warning in mean.default(data, na.rm = TRUE): argument is not numeric or
logical: returning NA
ERROR
Error in data - mean(data, na.rm = TRUE): non-numeric argument to binary operator
Both of these attempts result in errors. Luckily, the errors are
quite informative. In other cases, we may need to add in error handling
using the warning
and stop
functions.
For instance, the center
function only works on numeric
vectors. Recognizing this and adding warnings and errors provides
feedback to the user and makes sure the output of the function is what
the user wanted.
Documentation
A common way to put documentation in software is to add comments like this:
R
center <- function(data, midpoint) {
# return a new vector containing the original data centered around the
# midpoint.
# Example: center(c(1, 2, 3), 0) => c(-1, 0, 1)
new_data <- (data - mean(data)) + midpoint
return(new_data)
}
Writing Documentation
Formal documentation for R functions is written in separate
.Rd
using a markup language similar to LaTeX. You see the result of
this documentation when you look at the help file for a given function,
e.g. ?read.csv
. The roxygen2
package allows R coders to write documentation alongside the function
code and then process it into the appropriate .Rd
files.
You will want to switch to this more formal method of writing
documentation when you start writing more complicated R projects.
Functions to Create Graphs
Write a function called analyze
that takes a filename as
an argument and displays the three graphs produced in the previous lesson (average, min and
max inflammation over time).
analyze("data/inflammation-01.csv")
should produce the
graphs already shown, while
analyze("data/inflammation-02.csv")
should produce
corresponding graphs for the second data set. Be sure to document your
function with comments.
R
analyze <- function(filename) {
# Plots the average, min, and max inflammation over time.
# Input is character string of a csv file.
dat <- read.csv(file = filename, header = FALSE)
avg_day_inflammation <- apply(dat, 2, mean)
plot(avg_day_inflammation)
max_day_inflammation <- apply(dat, 2, max)
plot(max_day_inflammation)
min_day_inflammation <- apply(dat, 2, min)
plot(min_day_inflammation)
}
Rescaling
Write a function rescale
that takes a vector as input
and returns a corresponding vector of values scaled to lie in the range
0 to 1. (If L
and H
are the lowest and highest
values in the original vector, then the replacement for a value
v
should be (v-L) / (H-L)
.) Be sure to
document your function with comments.
Test that your rescale
function is working properly
using min
, max
, and plot
.
R
rescale <- function(v) {
# Rescales a vector, v, to lie in the range 0 to 1.
L <- min(v)
H <- max(v)
result <- (v - L) / (H - L)
return(result)
}
Defining Defaults
We have passed arguments to functions in two ways: directly, as in
dim(dat)
, and by name, as in
read.csv(file = "data/inflammation-01.csv", header = FALSE)
.
In fact, we can pass the arguments to read.csv
without
naming them:
R
dat <- read.csv("data/inflammation-01.csv", FALSE)
However, the position of the arguments matters if they are not named.
R
dat <- read.csv(header = FALSE, file = "data/inflammation-01.csv")
dat <- read.csv(FALSE, "data/inflammation-01.csv")
ERROR
Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection
To understand what’s going on, and make our own functions easier to
use, let’s re-define our center
function like this:
R
center <- function(data, midpoint = 0) {
# return a new vector containing the original data centered around the
# midpoint (0 by default).
# Example: center(c(1, 2, 3), 0) => c(-1, 0, 1)
new_data <- (data - mean(data)) + midpoint
return(new_data)
}
The key change is that the second argument is now written
midpoint = 0
instead of just midpoint
. If we
call the function with two arguments, it works as it did before:
R
test_data <- c(0, 0, 0, 0)
center(test_data, 3)
OUTPUT
[1] 3 3 3 3
But we can also now call center()
with just one
argument, in which case midpoint
is automatically assigned
the default value of 0
:
R
more_data <- 5 + test_data
more_data
OUTPUT
[1] 5 5 5 5
R
center(more_data)
OUTPUT
[1] 0 0 0 0
This is handy: if we usually want a function to work one way, but occasionally need it to do something else, we can allow people to pass an argument when they need to but provide a default to make the normal case easier.
The example below shows how R matches values to arguments
R
display <- function(a = 1, b = 2, c = 3) {
result <- c(a, b, c)
names(result) <- c("a", "b", "c") # This names each element of the vector
return(result)
}
# no arguments
display()
OUTPUT
a b c
1 2 3
R
# one argument
display(55)
OUTPUT
a b c
55 2 3
R
# two arguments
display(55, 66)
OUTPUT
a b c
55 66 3
R
# three arguments
display(55, 66, 77)
OUTPUT
a b c
55 66 77
As this example shows, arguments are matched from left to right, and any that haven’t been given a value explicitly get their default value. We can override this behavior by naming the value as we pass it in:
R
# only setting the value of c
display(c = 77)
OUTPUT
a b c
1 2 77
Matching Arguments
To be precise, R has three ways that arguments supplied by you are matched to the formal arguments of the function definition:
- by complete name,
- by partial name (matching on initial n characters of the argument name), and
- by position.
Arguments are matched in the manner outlined above in that order: by complete name, then by partial matching of names, and finally by position.
With that in hand, let’s look at the help for
read.csv()
:
R
?read.csv
There’s a lot of information there, but the most important part is the first couple of lines:
R
read.csv(file, header = TRUE, sep = ",", quote = "\"",
dec = ".", fill = TRUE, comment.char = "", ...)
This tells us that read.csv()
has one argument,
file
, that doesn’t have a default value, and six others
that do. Now we understand why the following gives an error:
R
dat <- read.csv(FALSE, "data/inflammation-01.csv")
ERROR
Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection
It fails because FALSE
is assigned to file
and the filename is assigned to the argument header
.
A Function with Default Argument Values
Rewrite the rescale
function so that it scales a vector
to lie between 0 and 1 by default, but will allow the caller to specify
lower and upper bounds if they want. Compare your implementation to your
neighbor’s: Do your two implementations produce the same results when
both are given the same input vector and parameters?
R
rescale <- function(v, lower = 0, upper = 1) {
# Rescales a vector, v, to lie in the range lower to upper.
L <- min(v)
H <- max(v)
result <- (v - L) / (H - L) * (upper - lower) + lower
return(result)
}
Key Points
- Define a function using
name <- function(...args...) {...body...}
. - Call a function using
name(...values...)
. - R looks for variables in the current stack frame before looking for them at the top level.
- Use
help(thing)
to view help for something. - Put comments at the beginning of functions to provide help for that function.
- Annotate your code!
- Specify default values for arguments when defining a function using
name = value
in the argument list. - Arguments can be passed by matching based on name, by position, or by omitting them (in which case the default value is used).