Programming with R

Creating functions

Learning Objectives

  • Define a function that takes arguments.
  • Return a value from a function.
  • Test a function.
  • Explain what a call stack is, and trace changes to the call stack as functions are called.
  • 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

Let’s start by defining a function fahr_to_kelvin that converts temperatures from Fahrenheit to Kelvin:

fahr_to_kelvin <- function(temp) {
  kelvin <- ((temp - 32) * (5 / 9)) + 273.15

We define fahr_to_kelvin by assigning it to the output of function. The list of argument names are containted 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. This 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.

Let’s try running our function. Calling our own function is no different from calling any other function:

# freezing point of water
[1] 273.15
# boiling point of water
[1] 373.15

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 Kelvin, it’s easy to turn Kelvin into Celsius:

kelvin_to_celsius <- function(temp) {
  celsius <- temp - 273.15

#absolute zero in Celsius
[1] -273.15

What about converting Fahrenheit to Celsius? We could write out the formula, but we don’t need to. Instead, we can compose the two functions we have already created:

fahr_to_celsius <- function(temp) {
  temp_k <- fahr_to_kelvin(temp)
  result <- kelvin_to_celsius(temp_k)

# freezing point of water in Celsius
[1] 0

This is our first taste of how larger programs are built: we define basic operations, then combine them in ever-large 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.

Challenge - Create a function

  • In the last lesson, we learned to concatenate 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 fence that takes two vectors as arguments, called original and wrapper, and returns a new vector that has the wrapper vector at the beginning and end of the original:
best_practice <- c("Write", "programs", "for", "people", "not", "computers")
asterisk <- "***"  # R interprets a variable with a single value as a vector
                   # with one element.
fence(best_practice, asterisk)
[1] "***"       "Write"     "programs"  "for"       "people"    "not"      
[7] "computers" "***"      
  • 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 outside that returns a vector made up of just the first and last elements of its input:
dry_principle <- c("Don't", "repeat", "yourself", "or", "others")
[1] "Don't"  "others"

The Call Stack

Let’s take a closer look at what happens when we call fahr_to_celsius(32). To make things clearer, we’ll start by putting the initial value 32 in a variable and store the final result in one as well:

original <- 32
final <- fahr_to_celsius(original)

The diagram below shows what memory looks like after the first line has been executed:

Call Stack (Initial State)

When we call fahr_to_celsius, R doesn’t create the variable temp right away. Instead, it creates something called a stack frame to keep track of the variables defined by fahr_to_kelvin. Initially, this stack frame only holds the value of temp:

Call Stack Immediately After First Function Call

When we call fahr_to_kelvin inside fahr_to_celsius, R creates another stack frame to hold fahr_to_kelvin’s variables:

Call Stack During First Nested Function Call

It does this because there are now two variables in play called temp: the argument to fahr_to_celsius, and the argument to fahr_to_kelvin. Having two variables with the same name in the same part of the program would be ambiguous, so R (and every other modern programming language) creates a new stack frame for each function call to keep that function’s variables separate from those defined by other functions.

When the call to fahr_to_kelvin returns a value, R throws away fahr_to_kelvin’s stack frame and creates a new variable in the stack frame for fahr_to_celsius to hold the temperature in Kelvin:

Call Stack After Return From First Nested Function Call

It then calls kelvin_to_celsius, which means it creates a stack frame to hold that function’s variables:

Call Stack During Call to Second Nested Function

Once again, R throws away that stack frame when kelvin_to_celsius is done and creates the variable result in the stack frame for fahr_to_celsius:

Call Stack After Second Nested Function Returns

Finally, when fahr_to_celsius is done, R throws away its stack frame and puts its result in a new variable called final that lives in the stack frame we started with:

Call Stack After All Functions Have Finished

This final stack frame is always there; it holds the variables we defined outside the functions in our code. What it doesn’t hold is the variables that were in the various stack frames. If we try to get the value of temp after our functions have finished running, R tells us that there’s no such thing:

Error in eval(expr, envir, enclos): object 'temp' not found

Why go to all this trouble? Well, here’s a function called span that calculates the difference between the minimum and maximum values in an array:

span <- function(a) {
  diff <- max(a) - min(a)

dat <- read.csv(file = "data/inflammation-01.csv", header = FALSE)
# span of inflammation data
[1] 20

Notice span assigns a value to variable called diff. We might very well use a variable with the same name (diff) to hold the inflammation data:

diff <- read.csv(file = "data/inflammation-01.csv", header = FALSE)
# span of inflammation data
[1] 20

We don’t expect the variable diff to have the value 20 after this function call, so the name diff cannot refer to the same variable defined inside span as it does in as it does in the main body of our program (which R refers to as the global environment). And yes, we could probably choose a different name than diff for our variable in this case, but we don’t want to have to read every line of code of the R functions we call to see what variable names they use, just in case they change the values of our variables.

The big idea here is encapsulation, and it’s the key to writing correct, comprehensible programs. A function’s job is to turn several operations into one so that we can think about a single function call instead of a dozen or a hundred statements each time we want to do something. That only works if functions don’t interfere with each other; if they do, we have to pay attention to the details once again, which quickly overloads our short-term memory.

Challenge - Following the call stack

  • We previously wrote functions called fence and outside. Draw a diagram showing how the call stack changes when we run the following:
inner_vec <- "carbon"
outer_vec <- "+"
result <- outside(fence(inner_vec, outer_vec))

Testing 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 value:

center <- function(data, desired) {
  new_data <- (data - mean(data)) + desired

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:

z <- c(0, 0, 0, 0)
[1] 0 0 0 0
center(z, 3)
[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:

dat <- read.csv(file = "data/inflammation-01.csv", header = FALSE)
centered <- center(dat[, 4], 0)
[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:

# original min
min(dat[, 4])
[1] 0
# original mean
mean(dat[, 4])
[1] 1.75
# original max
max(dat[, 4])
[1] 3
# centered min
[1] -1.75
# centered mean
[1] 0
# centered max
[1] 1.25

That seems almost right: the original mean was about 1.75, so the lower bound from zero is now about -1.75. The mean of the centered data is 0. We can even go further and check that the standard deviation hasn’t changed:

# original standard deviation
sd(dat[, 4])
[1] 1.067628
# centerted standard deviation
[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:

# difference in standard deviations before and after
sd(dat[, 4]) - sd(centered)
[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:

all.equal(sd(dat[, 4]), sd(centered))
[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. We have one more task first, though: we should write some documentation for our function to remind ourselves later what it’s for and how to use it.

A common way to put documentation in software is to add comments like this:

center <- function(data, desired) {
  # return a new vector containing the original data centered around the
  # desired value.
  # Example: center(c(1, 2, 3), 0) => c(-1, 0, 1)
  new_data <- (data - mean(data)) + desired

Challenge - A more advanced function

  • Write a function called analyze that takes a filename as a 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.
  • 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.

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:

dat <- read.csv("data/inflammation-01.csv", FALSE)

However, the position of the arguments matters if they are not named.

dat <- read.csv(header = FALSE, file = "data/inflammation-01.csv")
dat <- read.csv(FALSE, "data/inflammation-01.csv")
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:

center <- function(data, desired = 0) {
  # return a new vector containing the original data centered around the
  # desired value (0 by default).
  # Example: center(c(1, 2, 3), 0) => c(-1, 0, 1)
  new_data <- (data - mean(data)) + desired

The key change is that the second argument is now written desired = 0 instead of just desired. If we call the function with two arguments, it works as it did before:

test_data <- c(0, 0, 0, 0)
center(test_data, 3)
[1] 3 3 3 3

But we can also now call center() with just one argument, in which case desired is automatically assigned the default value of 0:

more_data <- 5 + test_data
[1] 5 5 5 5
[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

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

# no arguments
a b c 
1 2 3 
# one argument
 a  b  c 
55  2  3 
# two arguments
display(55, 66)
 a  b  c 
55 66  3 
# three arguments
display (55, 66, 77)
 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:

# only setting the value of c
display(c = 77)
 a  b  c 
 1  2 77 

With that in hand, let’s look at the help for read.csv():


There’s a lot of information there, but the most important part is the first couple of lines:

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:

dat <- read.csv(FALSE, "data/inflammation-01.csv")
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.

Challenge - 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 the two functions always behave the same way?