In the following five chapters you’ll learn about object oriented programming (OOP) in R. OOP in R is a little more challenging than in other languages, because:
There are multiple OOP systems to choose from. In this book, I’ll focus on the three that I believe are most important: S3, S4, and R6.
S3 and S4 come from a very different heritage than the OOP found in most other popular languages. This means your existing OOP skills are unlikely to be of much help.
Indeed, in day-to-day use FP is much more important than OOP in R. Nevertheless, there are three main reasons to learn OOP:
S3 allows your functions to return richer results that are displayed in a user friendly way and that have programmer friendly internals. It also conforms to syntactic standards that apply across multiple packages. This is why S3 is used throughout base R.
S4 can be helpful for building up large systems that will evolve over time and will be written by many programmers. This is why the Bioconductor project uses S4 as its fundamental infrastructure.
R6 gives you a standardized way to escape R’s copy-on-modify semantics. This is particularly important if you want to model real-world objects that change over time.
This chapter will give you a rough lay of the land, and a field guide to help you identify OOP systems in the wild. The following four chapters (Base types, S3, S4, and R6) will dive into the details, starting with R’s base types. These are not technically an OOP system, but they’re important to understand because they’re the fundamental building block of the true OOP systems.
12.6 OOP Systems
We’ll begin with an info dump of vocabulary and terminology. Don’t worry if it doesn’t stick. We’ll come back to these ideas multiple times in the subsequent chapters.
Central to any OOP system are the concepts of class and method. A class defines the behaviour of a set of objects, or instances, by describing their attributes and their relationship to other classes. The class is also used when selecting methods, functions that behave differently depending on the class of their input. A class defines what something is and methods describe what something can do.
Classes are usually organised in a hierarchy: if a method does not exist for a child, then the parent’s method is used instead. This means that a child class will inherit behaviour from the parent class. Inheritance is one of the most important parts of OOP because it allows you to reduce the amount of code you have to write.
Following the notation of Extending R, there are two main styles of OOP:
In encapsulated OOP, methods belong to objects or classes. This is the most common paradigm in modern programming languages, and method calls typically look like
object.method. This is called encapsulated because the object encapsulates all its metadata.
In functional OOP, methods belong to functions called generics. Method calls look like ordinary function calls:
generic(object). This is called functional because from the outside it just looks like function calls.
12.7 OOP in R
Base R provides three OOP systems: S3, S4, and reference classes (RC):
S3 is R’s first OOP system, and is described Statistical Models in S (1991). It informally implements the functional style. It provides no ironclad guarantees but instead relies on a set of conventions. This makes it easy to get started with, and a low cost way of solving many simple problems.
S4 is similar to S3, but much more formal. It was introduced in Programming with Data (1998). It requires more upfront work and in return provides greater consistency. S4 is implemented in the methods package, which is attached by default. The only package in base R to make use of S4 is stats4.
(You might wonder if S1 and S2 exist. They don’t: S3 and S4 were named according to the versions of S that they accompanied.)
RC implements encapsulated OO. RC objects are also mutable: they don’t use R’s usual copy-on-modify semantics, but are modified in place. This makes them harder to reason about, but allows them to solve problems that are difficult to solve with S3 or S4.
There are a number other OOP systems provided by packages. Three of the most popular are:
R6 implements encapsulated OOP like RC, but resolves some important issues. You’ll learn R6 instead of RC in this book. More on why later.
R.oo provides some formalism on top of S3, and makes it possible to have mutable S3 objects.
proto implements another style of OOP, called prototype based. It blurs the distinctions between classes and instances of classes (objects). There is some more information about prototype based programming http://vita.had.co.nz/papers/mutatr.html.
Most OO systems in external packages are primarily of academic interest: they will help you understand the spectrum of OOP better, and can make it easier to solve certain classes of problems. However, they come with a big drawback: few R users know and understand them, so it is hard for others to read and contribute to your code.
12.8 Field guide
Before we go on to discuss base types, S3, S4, and R6 in more detail I want to introduce the sloop package:
The sloop package (think sail the seas of OOP in R) provides a number of helpers to fill in missing pieces in base R. The first helper to know about is
sloop::otype(). It makes it easy to figure what OOP system an object found in the wild uses:
otype(), you need to work your way through the base functions:
is.object()distinguishes between base types (
FALSE) and everything else (
isS4()distinguishes between S3 and S4.
inherits()lets you figure out if you have an R6 object (an S3 object that inherits from “R6”) or an RC object (an S4 object that inherits from “refClass”).