Functions Explained

Overview

Teaching: 45 min
Exercises: 15 min

Questions

How can I write a new function in R?

Objectives

Define a function that takes arguments.

Return a value from a function.

Check argument conditions with stopifnot() in functions.

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 simple statistics. However, the gapminder data is updated periodically, and we may want to pull in that new information later and re-run our analysis again. We may also obtain similar data from a different source 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.

What is a function?

Functions gather a sequence of operations into a whole, preserving it for ongoing use. Functions provide:

a name we can remember and invoke it by

relief from the need to remember the individual operations

a defined set of inputs and expected outputs

rich connections to the larger programming environment

As the basic building block of most programming languages, user-defined functions constitute “programming” as much as any single abstraction can. If you have written a function, you are a computer programmer.

Defining a function

Let’s open a new R script file in the functions/ directory and call it functions-lesson.R.

Let’s define a function fahr_to_kelvin() that converts temperatures from Fahrenheit to Kelvin:

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

We define fahr_to_kelvin() 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. This makes the code easier to read but does not affect how the code operates.

It is useful to think of creating functions like writing a cookbook. First you define the “ingredients” that your function needs. In this case, we only need one ingredient to use our function: “temp”. After we list our ingredients, we then say what we will do with them, in this case, we are taking our ingredient and applying a set of mathematical operators to it.

When we call the function, the values we pass to it as arguments 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.

Tip

One feature unique to R is that the return statement is not required. R automatically returns whichever variable is on the last line of the body of the function. But for clarity, 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:

# freezing point of water
fahr_to_kelvin(32)

[1] 273.15

# boiling point of water
fahr_to_kelvin(212)

[1] 373.15

Challenge 1

Write a function called kelvin_to_celsius() that takes a temperature in Kelvin and returns that temperature in Celsius.

Hint: To convert from Kelvin to Celsius you subtract 273.15
Solution to challenge 1

Write a function called kelvin_to_celsius that takes a temperature in Kelvin and returns that temperature in Celsius
kelvin_to_celsius <- function(temp) {
 celsius <- temp - 273.15
 return(celsius)
}

Combining functions

The real power of functions comes from mixing, matching and combining them into ever-larger chunks to get the effect we want.

Let’s define two functions that will convert temperature from Fahrenheit to Kelvin, and Kelvin to Celsius:

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

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

Challenge 2

Define the function to convert directly from Fahrenheit to Celsius, by reusing the two functions above (or using your own functions if you prefer).
Solution to challenge 2

Define the function to convert directly from Fahrenheit to Celsius, by reusing these two functions above
fahr_to_celsius <- function(temp) {
  temp_k <- fahr_to_kelvin(temp)
  result <- kelvin_to_celsius(temp_k)
  return(result)
}

Interlude: Defensive Programming

Now that we’ve begun to appreciate how writing functions provides an efficient way to make R code re-usable and modular, we should note that it is important to ensure that functions only work in their intended use-cases. Checking function parameters is related to the concept of defensive programming. Defensive programming encourages us to frequently check conditions and throw an error if something is wrong. These checks are referred to as assertion statements because we want to assert some condition is TRUE before proceeding. They make it easier to debug because they give us a better idea of where the errors originate.

Checking conditions with `stopifnot()`

Let’s start by re-examining fahr_to_kelvin(), our function for converting temperatures from Fahrenheit to Kelvin. It was defined like so:

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

For this function to work as intended, the argument temp must be a numeric value; otherwise, the mathematical procedure for converting between the two temperature scales will not work. To create an error, we can use the function stop(). For example, since the argument temp must be a numeric vector, we could check for this condition with an if statement and throw an error if the condition was violated. We could augment our function above like so:

fahr_to_kelvin <- function(temp) {
  if (!is.numeric(temp)) {
    stop("temp must be a numeric vector.")
  }
  kelvin <- ((temp - 32) * (5 / 9)) + 273.15
  return(kelvin)
}

If we had multiple conditions or arguments to check, it would take many lines of code to check all of them. Luckily R provides the convenience function stopifnot(). We can list as many requirements that should evaluate to TRUE; stopifnot() throws an error if it finds one that is FALSE. Listing these conditions also serves a secondary purpose as extra documentation for the function.

Let’s try out defensive programming with stopifnot() by adding assertions to check the input to our function fahr_to_kelvin().

We want to assert the following: temp is a numeric vector. We may do that like so:

fahr_to_kelvin <- function(temp) {
  stopifnot(is.numeric(temp))
  kelvin <- ((temp - 32) * (5 / 9)) + 273.15
  return(kelvin)
}

It still works when given proper input.

# freezing point of water
fahr_to_kelvin(temp = 32)

[1] 273.15

But fails instantly if given improper input.

# Metric is a factor instead of numeric
fahr_to_kelvin(temp = as.factor(32))

Error in fahr_to_kelvin(temp = as.factor(32)): is.numeric(temp) is not TRUE

Challenge 3

Use defensive programming to ensure that our fahr_to_celsius() function throws an error immediately if the argument temp is specified inappropriately.
Solution to challenge 3

Extend our previous definition of the function by adding in an explicit call to stopifnot(). Since fahr_to_celsius() is a composition of two other functions, checking inside here makes adding checks to the two component functions redundant.
fahr_to_celsius <- function(temp) {
  stopifnot(is.numeric(temp))
  temp_k <- fahr_to_kelvin(temp)
  result <- kelvin_to_celsius(temp_k)
  return(result)
}

More on combining functions

Now, we’re going to define a function that calculates the Gross Domestic Product of a nation from the data available in our dataset:

# Takes a dataset and multiplies the population column
# with the GDP per capita column.
calcGDP <- function(dat) {
  gdp <- dat$pop * dat$gdpPercap
  return(gdp)
}

We define calcGDP() 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 executed when you call the function – is contained within curly braces ({}).

We’ve indented the statements in the body by two spaces. This makes the code easier to read but does not affect how it operates.

When we call the function, the values we pass to it are assigned to the arguments, which become variables inside the body of the function.

Inside the function, we use the return() function to send back the result. This return() function is optional: R will automatically return the results of whatever command is executed on the last line of the function.

calcGDP(head(gapminder))

[1]  6567086330  7585448670  8758855797  9648014150  9678553274 11697659231

That’s not very informative. Let’s add some more arguments so we can extract that per year and country.

# Takes a dataset and multiplies the population column
# with the GDP per capita column.
calcGDP <- function(dat, year=NULL, country=NULL) {
  if(!is.null(year)) {
    dat <- dat[dat$year %in% year, ]
  }
  if (!is.null(country)) {
    dat <- dat[dat$country %in% country,]
  }
  gdp <- dat$pop * dat$gdpPercap

  new <- cbind(dat, gdp=gdp)
  return(new)
}

If you’ve been writing these functions down into a separate R script (a good idea!), you can load in the functions into our R session by using the source() function:

source("functions/functions-lesson.R")

Ok, so there’s a lot going on in this function now. In plain English, the function now subsets the provided data by year if the year argument isn’t empty, then subsets the result by country if the country argument isn’t empty. Then it calculates the GDP for whatever subset emerges from the previous two steps. The function then adds the GDP as a new column to the subsetted data and returns this as the final result. You can see that the output is much more informative than a vector of numbers.

Let’s take a look at what happens when we specify the year:

head(calcGDP(gapminder, year=2007))

       country year      pop continent lifeExp  gdpPercap          gdp
Afghanistan 2007 31889923      Asia  43.828   974.5803  31079291949
   Albania 2007  3600523    Europe  76.423  5937.0295  21376411360
   Algeria 2007 33333216    Africa  72.301  6223.3675 207444851958
    Angola 2007 12420476    Africa  42.731  4797.2313  59583895818
 Argentina 2007 40301927  Americas  75.320 12779.3796 515033625357
 Australia 2007 20434176   Oceania  81.235 34435.3674 703658358894

Or for a specific country:

calcGDP(gapminder, country="Australia")

     country year      pop continent lifeExp gdpPercap          gdp
Australia 1952  8691212   Oceania  69.120  10039.60  87256254102
Australia 1957  9712569   Oceania  70.330  10949.65 106349227169
Australia 1962 10794968   Oceania  70.930  12217.23 131884573002
Australia 1967 11872264   Oceania  71.100  14526.12 172457986742
Australia 1972 13177000   Oceania  71.930  16788.63 221223770658
Australia 1977 14074100   Oceania  73.490  18334.20 258037329175
Australia 1982 15184200   Oceania  74.740  19477.01 295742804309
Australia 1987 16257249   Oceania  76.320  21888.89 355853119294
Australia 1992 17481977   Oceania  77.560  23424.77 409511234952
Australia 1997 18565243   Oceania  78.830  26997.94 501223252921
Australia 2002 19546792   Oceania  80.370  30687.75 599847158654
Australia 2007 20434176   Oceania  81.235  34435.37 703658358894

Or both:

calcGDP(gapminder, year=2007, country="Australia")

     country year      pop continent lifeExp gdpPercap          gdp
72 Australia 2007 20434176   Oceania  81.235  34435.37 703658358894

Let’s walk through the body of the function:

calcGDP <- function(dat, year=NULL, country=NULL) {

Here we’ve added two arguments, year, and country. We’ve set default arguments for both as NULL using the = operator in the function definition. This means that those arguments will take on those values unless the user specifies otherwise.

  if(!is.null(year)) {
    dat <- dat[dat$year %in% year, ]
  }
  if (!is.null(country)) {
    dat <- dat[dat$country %in% country,]
  }

Here, we check whether each additional argument is set to null, and whenever they’re not null overwrite the dataset stored in dat with a subset given by the non-null argument.

Building these conditionals into the function makes it more flexible for later. Now, we can use it to calculate the GDP for:

The whole dataset;
A single year;
A single country;
A single combination of year and country.

By using %in% instead, we can also give multiple years or countries to those arguments.

Tip: Pass by value

Functions in R almost always make copies of the data to operate on inside of a function body. When we modify dat inside the function we are modifying the copy of the gapminder dataset stored in dat, not the original variable we gave as the first argument.

This is called “pass-by-value” and it makes writing code much safer: you can always be sure that whatever changes you make within the body of the function, stay inside the body of the function.

Tip: Function scope

Another important concept is scoping: any variables (or functions!) you create or modify inside the body of a function only exist for the lifetime of the function’s execution. When we call calcGDP(), the variables dat, gdp and new only exist inside the body of the function. Even if we have variables of the same name in our interactive R session, they are not modified in any way when executing a function.

  gdp <- dat$pop * dat$gdpPercap
  new <- cbind(dat, gdp=gdp)
  return(new)
}

Finally, we calculated the GDP on our new subset, and created a new data frame with that column added. This means when we call the function later we can see the context for the returned GDP values, which is much better than in our first attempt where we got a vector of numbers.

Challenge 4

Test out your GDP function by calculating the GDP for New Zealand in 1987. How does this differ from New Zealand’s GDP in 1952?
Solution to challenge 4
  calcGDP(gapminder, year = c(1952, 1987), country = "New Zealand")
GDP for New Zealand in 1987: 65050008703

GDP for New Zealand in 1952: 21058193787

Challenge 5

The paste() function can be used to combine text together, e.g:
best_practice <- c("Write", "programs", "for", "people", "not", "computers")
paste(best_practice, collapse=" ")
[1] "Write programs for people not computers"
Write a function called fence() that takes two vectors as arguments, called text and wrapper, and prints out the text wrapped with the wrapper:
fence(text=best_practice, wrapper="***")
Note: the paste() function has an argument called sep, which specifies the separator between text. The default is a space: “ “. The default for paste0() is no space “”.
Solution to challenge 5

Write a function called fence() that takes two vectors as arguments, called text and wrapper, and prints out the text wrapped with the wrapper:
fence <- function(text, wrapper){
  text <- c(wrapper, text, wrapper)
  result <- paste(text, collapse = " ")
  return(result)
}
best_practice <- c("Write", "programs", "for", "people", "not", "computers")
fence(text=best_practice, wrapper="***")
[1] "*** Write programs for people not computers ***"

Tip

R has some unique aspects that can be exploited when performing more complicated operations. We will not be writing anything that requires knowledge of these more advanced concepts. In the future when you are comfortable writing functions in R, you can learn more by reading the R Language Manual or this chapter from Advanced R Programming by Hadley Wickham.

Tip: Testing and documenting

It’s important to both test functions and document them: Documentation helps you, and others, understand what the purpose of your function is, and how to use it, and its important to make sure that your function actually does what you think.

When you first start out, your workflow will probably look a lot like this:

Write a function

Comment parts of the function to document its behaviour

Load in the source file

Experiment with it in the console to make sure it behaves as you expect

Make any necessary bug fixes

Rinse and repeat.

Formal documentation for functions, written in separate .Rd files, gets turned into the documentation you see in help files. 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.

Formal automated tests can be written using the testthat package.

Key Points

Use function to define a new function in R.

Use parameters to pass values into functions.

Use stopifnot() to flexibly check function arguments in R.

Load functions into programs using source().

previous episode

Software Carpentry: Introduction to Scientific Reproducibility with R

next episode

Functions Explained

Overview

What is a function?

Defining a function

Tip

Challenge 1

Solution to challenge 1

Combining functions

Challenge 2

Solution to challenge 2

Interlude: Defensive Programming

Checking conditions with `stopifnot()`

Challenge 3

Solution to challenge 3

More on combining functions

Tip: Pass by value

Tip: Function scope

Challenge 4

Solution to challenge 4

Challenge 5

Solution to challenge 5

Tip

Tip: Testing and documenting

Key Points

previous episode

next episode

previous episode

Software Carpentry: Introduction to Scientific Reproducibility with R

next episode

Functions Explained

Overview

What is a function?

Defining a function

Tip

Challenge 1

Solution to challenge 1

Combining functions

Challenge 2

Solution to challenge 2

Interlude: Defensive Programming

Checking conditions with stopifnot()

Challenge 3

Solution to challenge 3

More on combining functions

Tip: Pass by value

Tip: Function scope

Challenge 4

Solution to challenge 4

Challenge 5

Solution to challenge 5

Tip

Tip: Testing and documenting

Key Points

previous episode

next episode

Checking conditions with `stopifnot()`