Chapter 15 S4

15.2 Basics

Broadly, what is a generic and method in S4 and what is their relationship?

setClass("Person", 
  slots = c(
    name = "character", 
    age = "numeric"
  )
)

setGeneric("age", function(x) standardGeneric("age"))
setGeneric("age<-", function(x, value) standardGeneric("age<-"))

setMethod("age", "Person", function(x) x@age)
setMethod("age<-", "Person", function(x, value) {
  x@age <- value
  x
})

john <- new("Person", name = "John Smith", age = 12)
age(john)

[1] 12

A generic is a function that will dispatch differently based on the class it is applied to. Above we apply the age generic to Person using setMethod but we could create an age method that behaves differently for another class, like dogs (which will add 7 to the supplied age)

setClass("Person", slots = c(name = "character",age = "numeric"))

setGeneric("age", function(x) standardGeneric("age"))
setGeneric("age<-", function(x, value) standardGeneric("age<-"))

setMethod("age", "Person", function(x) x@age)
setMethod("age<-", "Person", function(x, value) {
  x@age <- value
  x
})

setClass("Dog", slots = c(name = "character",  age = "numeric"))

# You want the age generic to automatically return 7x the slot in human years
setMethod("age", "Dog", function(x) {x@age*7} ) 
setMethod("age<-", "Dog", function(x, value) {
  x@age <- value
  x
})


spot <- new("Dog", name = "Spot Smith", age = 12)
age(spot)

[1] 84

What is standardGeneric doing in the example above?

It’s the same thing as UseMethod but for S4

15.3.6.2 Exercises

What is a virtual class and how does it relate to setClassUnion [see ?setClass]

A virtual class is a class that cannot be instanciated. Rather than define two of the same methods for two classes, give them both a virtual parent class with the shared method.

Signature

In our own words what exactly is a signature? Are there any signatures within our Person example? If not can we add one?

15.5.1 Single dispatch

What’s a use case in the wild for ANY?