๐Ÿ’ฐ 15 S4 | Advanced R

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Other Resources; S3 and S4 classes; Constructors and getting help; Slots and In standard R, an S3 object is essentially a list with a class attribute on it.


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representation: a list of slots (or attributes), giving their names and classes. For example, a person class might be represented by a character name and a numeric.


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The first is the slotNames command. This command can take either an object or the name of a class. It returns the names of the slots associated with the class asโ€‹.


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By convention, S4 class names use UpperCamelCase. A named list of slots (โ€‹fields), which defines slot names and permitted classes. For example, a person.


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You define an S4 class by calling setClass() with the class name and a definition of its slots, and the names and classes of the class data: setClass("Person".


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While defining a class, we need to set the name and the slots (along with class of the slot) it is going to have. Example 1: Definition of S4 class. setClass("student",โ€‹.


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Other Resources; S3 and S4 classes; Constructors and getting help; Slots and In standard R, an S3 object is essentially a list with a class attribute on it.


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This makes method dispatch in S4 substantially more complicated, but avoids having to implement double-dispatch as a special case. If the slot is also writeable, you should provide a setter function. There is one other important argument to setClass : contains. The Person class is so simple so a helper is almost superfluous, but we can use it to clearly define the contract: age is optional but name is required. You should always include validObject in the setter to prevent the user from creating invalid objects. The fallback ANY method still exists but the rules are little more complex. A helper should always:. These features make S4 very powerful, but can also make it hard to understand which method will get selected for a given combination of inputs. If signature is not supplied, all arguments apart from It is occasionally useful to remove arguments from dispatch. There are two pseudo-classes that you can define methods for. A prototype , a list of default values for each slot. To define a method for an existing generic, you must first determine the arguments. The job of a generic is to perform method dispatch, i. NB: while the method graph is a powerful metaphor for understanding method dispatch, implementing it in this way would be rather inefficient, so the actual approach that S4 uses is somewhat different. If you do want to use it in practice, there are two main challenges:. The underlying ideas are similar to S3 the topic of Chapter 13 , but implementation is much stricter and makes use of specialised functions for creating classes setClass , generics setGeneric , and methods setMethod. What class is each slot? NB: The validity method is only called automatically by new , so you can still create an invalid object by modifying it:. Once the class is defined, you can construct new objects from it by calling new with the name of the class and a value for each slot:. What happens if methods are the same distance? The bottom part is the method graph and displays all the possible methods that could be defined. Martin Morgan is a member of R-core and the project lead of Bioconductor. You will need to implement more complicated checks i. The pseudo-class ANY allows a slot to accept objects of any type. To get help for a method, put? For example, we might want to make it clear that the Person class is a vector class, and can store data about multiple people. As you move towards more advanced usage, you will need to piece together needed information by carefully reading the documentation, asking questions on StackOverflow, and performing experiments. The Bioconductor community is a long-term user of S4 and has produced much of the best material about its effective use. Have a thoughtfully crafted user interface with carefully chosen default values and useful conversions. To test if an object inherits from a specific class, use the second argument of is :. As with all state-modifying functions you need to use setClass with care. This means that it will never contribute to ambiguity.{/INSERTKEYS}{/PARAGRAPH} If no method is found, method dispatch has failed and an error is thrown. Sketch out the setClass calls that you would use to define the classes. This allows you to control the arguments that are used for method dispatch. The code below illustrates the three arguments by creating a Person class with character name and numeric age slots. As the developer of a class, you should also provide your own accessor functions. The most commonly defined S4 method that controls printing is show , which controls how the object appears when it is printed. The first pseudo-class is ANY which matches any class If you define a method for this pseudo-class, it will match whenever the argument is missing. The basic process remains the same: you start from the actual class supplied to the generic, then follow the arrows until you find a defined method. When you discover ambiguity you should always resolve it by providing a more precise method:. Methods that exist, i. The wrinkle is that now there are multiple arrows to follow, so you might find multiple methods. Generally, you should only use in your methods. Additionally, S4 provides both multiple inheritance i. Emoji give us very compact class names that evoke the relationships between the classes. What accessors does it provide? There are three important arguments: the name of the generic, the name of the class, and the method itself. {PARAGRAPH}{INSERTKEYS}S4 provides a formal approach to functional OOP. In S4, unlike S3, the signature can include multiple arguments. The set of slots, and their classes, forms an important part of the definition of an S4 class. What other ways can you find help for a method? An important new component of S4 is the slot , a named component of the object that is accessed using the specialised subsetting operator pronounced at. A named character vector that describes the names and classes of the slots fields. Why does the show method defined in Section Hint: try printing the employee subclass. This specifies a class or classes to inherit slots and behaviour from. The top part, f Here we have a generic with one argument, that has a class hierarchy that is three levels deep. Section The basic idea is simple, then it rapidly gets more complex once multiple inheritance and multiple dispatch are combined. This can cause confusion during interactive creation of new classes. John Chambers is the author of the S4 system, and provides an overview of its motivation and historical context in Object-oriented programming, functional programming and R Chambers All functions related to S4 live in the methods package. In Section Extend the Person class with fields to match utils::person. Slots should be considered an internal implementation detail: they can change without warning and user code should avoid accessing them directly. Hint: read about virtual classes in? To create a new S4 generic, call setGeneric with a function that calls standardGeneric :. Imagine you were going to reimplement factors, dates, and data frames in S4. When you call setClass , you are registering a class definition in a hidden global variable. In R, however, both definition and construction occur at run time. There is only one that you need to know about: signature. In practice, this means that you should alway define methods defined for the terminal nodes, i. R6 classes have the same problem, as described in Section User-facing classes should always be paired with a user-friendly helper. Technically, the prototype is optional 55 , but you should always provide it. To find the method that gets called, you start with the most specific class of the actual arguments, then follow the arrows until you find a method that exists. It takes a class and a function that returns TRUE if the input is valid, and otherwise returns a character vector describing the problem s :. Instead, all user-accessible slots should be accompanied by a pair of accessors. What slots does it have? Think about appropriate slots and prototype. Like the other OO chapters, the focus here will be on how S4 works, not how to deploy it most effectively. You can get those from the documentation or by looking at the args of the generic:. In practice, keep method dispatch as simple as possible by avoiding multiple inheritance, and reserving multiple dispatch only for where it is absolutely necessary. In most programming languages, class definition occurs at compile-time and object construction occurs later, at run-time. As indicated by the wavy dotted lines, the ANY method is always considered further away than a method for a real class. If that happens, you pick the method that is closest, i. You define an S4 class by calling setClass with the class name and a definition of its slots, and the names and classes of the class data:. Some recommendations:. If the slot is unique to the class, this can just be a function:. More formally, the second argument to setMethod is called the signature. To enforce these additional constraints we write a validator with setValidity. Like setClass , setGeneric has many other arguments. Accessors are typically S4 generics allowing multiple classes to share the same external interface. You can read the details in? For example, we can create an Employee class that inherits from the Person class, adding an extra slot that describes their boss.