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Advanced R

Chapters 15 & 16, S4 and Trade-offs

Erick Knackstedt

@Eknackstedt

2020-11-12

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Outline

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Outline

  • Introducing S4
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Outline

  • Introducing S4
  • Classes, generics, & methods
4 / 62

Outline

  • Introducing S4
  • Classes, generics, & methods
  • Prototypes, constructors, helpers, & validators
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Outline

  • Introducing S4
  • Classes, generics, & methods
  • Prototypes, constructors, helpers, & validators
  • Creating & accessing generics and methods
6 / 62

Outline

  • Introducing S4
  • Classes, generics, & methods
  • Prototypes, constructors, helpers, & validators
  • Creating & accessing generics and methods
  • Method dispatch, multiple inheritance, & multiple dispatch
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Outline

  • Introducing S4
  • Classes, generics, & methods
  • Prototypes, constructors, helpers, & validators
  • Creating & accessing generics and methods
  • Method dispatch, multiple inheritance, & multiple dispatch
  • Interaction of S4 & S3
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Outline

  • Introducing S4
  • Classes, generics, & methods
  • Prototypes, constructors, helpers, & validators
  • Creating & accessing generics and methods
  • Method dispatch, multiple inheritance, & multiple dispatch
  • Interaction of S4 & S3
  • Trade-offs
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Introducing S4

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Introducing S4

Why S4?

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Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
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Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
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Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
  • Much of the code is written by John Chambers himself
14 / 62

Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
  • Much of the code is written by John Chambers himself
  • Used extensively in the Bioconductor project
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Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
  • Much of the code is written by John Chambers himself
  • Used extensively in the Bioconductor project
  • Fairly independent of S3, separate systems
16 / 62

Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
  • Much of the code is written by John Chambers himself
  • Used extensively in the Bioconductor project
  • Fairly independent of S3, separate systems
  • Provides multiple inheritance and multiple dispatch
17 / 62

Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
  • Much of the code is written by John Chambers himself
  • Used extensively in the Bioconductor project
  • Fairly independent of S3, separate systems
  • Provides multiple inheritance and multiple dispatch
  • Has the slot and a specialized subsetting operator @
18 / 62

Introducing S4

Why S4?

  • Like S3, uses function overloading to throttle the number of functions required to interact with objects
  • A more formal and rigorous update to S3
  • Much of the code is written by John Chambers himself
  • Used extensively in the Bioconductor project
  • Fairly independent of S3, separate systems
  • Provides multiple inheritance and multiple dispatch
  • Has the slot and a specialized subsetting operator @
  • Implemented using the methods package
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Classes, generics, & methods

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Classes, generics, & methods

How do you create a class?

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Classes, generics, & methods

How do you create a class?

setClass("myClass", slots= ...., contains =...., prototype =....)

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Classes, generics, & methods

How do you create a class?

setClass("myClass", slots= ...., contains =...., prototype =....)

How do you create a generic for the class?

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Classes, generics, & methods

How do you create a class?

setClass("myClass", slots= ...., contains =...., prototype =....)

How do you create a generic for the class?

setGeneric(name, def)

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Classes, generics, & methods

How do you create a class?

setClass("myClass", slots= ...., contains =...., prototype =....)

How do you create a generic for the class?

setGeneric(name, def)

How do you create a method for the generic?

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Classes, generics, & methods

How do you create a class?

setClass("myClass", slots= ...., contains =...., prototype =....)

How do you create a generic for the class?

setGeneric(name, def)

How do you create a method for the generic?

setMethod(f, signature, definition)

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Prototypes, constructors, helpers, & validators

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Prototypes, constructors, helpers, & validators

If the prototype is optional, why should we use it?

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Prototypes, constructors, helpers, & validators

If the prototype is optional, why should we use it?

This allows you to pass in default values for class slots (attributes)

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Prototypes, constructors, helpers, & validators

If the prototype is optional, why should we use it?

This allows you to pass in default values for class slots (attributes)

I want to build on top of another class. Is there a workaround to copy and pasting attributes from one class to another?

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Prototypes, constructors, helpers, & validators

If the prototype is optional, why should we use it?

This allows you to pass in default values for class slots (attributes)

I want to build on top of another class. Is there a workaround to copy and pasting attributes from one class to another?

Why, yes there is! The contains argument in setClass allows you to specify the class to inherit from

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Prototypes, constructors, helpers, & validators

If the prototype is optional, why should we use it?

This allows you to pass in default values for class slots (attributes)

I want to build on top of another class. Is there a workaround to copy and pasting attributes from one class to another?

Why, yes there is! The contains argument in setClass allows you to specify the class to inherit from

If I can use new() to construct an object, why do I bother to create a constructor?

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Prototypes, constructors, helpers, & validators

If the prototype is optional, why should we use it?

This allows you to pass in default values for class slots (attributes)

I want to build on top of another class. Is there a workaround to copy and pasting attributes from one class to another?

Why, yes there is! The contains argument in setClass allows you to specify the class to inherit from

If I can use new() to construct an object, why do I bother to create a constructor?

Apparently programmers want other people to use their stuff. Constructors politely define the slots (attributes) that require data, which you then assign to new() in the body of the constructor

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Prototypes, constructors, helpers, & validators cont.

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Prototypes, constructors, helpers, & validators cont.

I don't want this use of my class to break, how do I validate that an object has the correct attributes?

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Prototypes, constructors, helpers, & validators cont.

I don't want this use of my class to break, how do I validate that an object has the correct attributes?

setValidity(Class, method), where the method is a function that contains the validity checks. You define this once and it is associated with object construction going forward. It is not triggered if an object is modified

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Prototypes, constructors, helpers, & validators cont.

I don't want this use of my class to break, how do I validate that an object has the correct attributes?

setValidity(Class, method), where the method is a function that contains the validity checks. You define this once and it is associated with object construction going forward. It is not triggered if an object is modified

Well, if I can't validate on modificaiton, what do I do?

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Prototypes, constructors, helpers, & validators cont.

I don't want this use of my class to break, how do I validate that an object has the correct attributes?

setValidity(Class, method), where the method is a function that contains the validity checks. You define this once and it is associated with object construction going forward. It is not triggered if an object is modified

Well, if I can't validate on modificaiton, what do I do?

This is where we build on the idea of helpers and wrap an accessor in a function that also validates the inputs to underlying attributes

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Creating & accessing generics and methods

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Creating & accessing generics and methods

What was the point of a generic again?

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Creating & accessing generics and methods

What was the point of a generic again?

Generics are functions that describe behavior found across multiple classes of objects. By decomposing functions into generics and methods we solve the issue of function overpopulation

41 / 62

Creating & accessing generics and methods

What was the point of a generic again?

Generics are functions that describe behavior found across multiple classes of objects. By decomposing functions into generics and methods we solve the issue of function overpopulation

And the S4 syntax for creating one?

42 / 62

Creating & accessing generics and methods

What was the point of a generic again?

Generics are functions that describe behavior found across multiple classes of objects. By decomposing functions into generics and methods we solve the issue of function overpopulation

And the S4 syntax for creating one?

setGeneric(name, def)
# Example
setGeneric("myGeneric", function(x) standardGeneric("myGeneric"))
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Creating & accessing generics and methods cont.

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Creating & accessing generics and methods cont.

What was the point of a method again?

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Creating & accessing generics and methods cont.

What was the point of a method again?

A method is a function for a specific class of object. Which means as a programmer you are still writing up functions for every class but for the user the interface is standardized through the generic

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Creating & accessing generics and methods cont.

What was the point of a method again?

A method is a function for a specific class of object. Which means as a programmer you are still writing up functions for every class but for the user the interface is standardized through the generic

And the S4 syntax for creating one?

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Creating & accessing generics and methods cont.

What was the point of a method again?

A method is a function for a specific class of object. Which means as a programmer you are still writing up functions for every class but for the user the interface is standardized through the generic

And the S4 syntax for creating one?

setMethod(f, signature, definition)
#Example
setMethod("myGeneric", "Person", function(x) {
  # method implementation
})
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Method dispatch, multiple inheritance, & multiple dispatch

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Method dispatch, multiple inheritance, & multiple dispatch

I've overloaded generic functions with a bunch of class specific methods. Now what?

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Method dispatch, multiple inheritance, & multiple dispatch

I've overloaded generic functions with a bunch of class specific methods. Now what?

The generic function looks at the class and lookups up the method!

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Method dispatch, multiple inheritance, & multiple dispatch

I've overloaded generic functions with a bunch of class specific methods. Now what?

The generic function looks at the class and lookups up the method!

What if I built up classes one on top of the other? You know, like evolution or something?

--

Well, the generic will search for the methods assigned to the classes and use the one that is "closest". If there there is not a closest, then it picks the method that comes earliest in the alphabet.

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Interaction of S4 & S3

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Interaction of S4 & S3

How exactly do these two system allow interactions?

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Interaction of S4 & S3

How exactly do these two system allow interactions?

Well, you can assign an S3 object to a S4 slot or build on top of an S3 object by using contains.

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Interaction of S4 & S3

How exactly do these two system allow interactions?

Well, you can assign an S3 object to a S4 slot or build on top of an S3 object by using contains.

Sounds easy! Really glad there isn't a fancy function required to allow this to work!!

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Interaction of S4 & S3

How exactly do these two system allow interactions?

Well, you can assign an S3 object to a S4 slot or build on top of an S3 object by using contains.

Sounds easy! Really glad there isn't a fancy function required to allow this to work!!

Silly, of course there is a fancy function required! Seems painless though

setOldClass(Classes)

setClass("factor",
  contains = "integer",
  slots = c(
    levels = "character"
  ),
  prototype = structure(
    integer(),
    levels = character()
  )
)
setOldClass("factor", S4Class = "factor")

Interaction of S4 & S3 cont.

57 / 62

Interaction of S4 & S3

How exactly do these two system allow interactions?

Well, you can assign an S3 object to a S4 slot or build on top of an S3 object by using contains.

Sounds easy! Really glad there isn't a fancy function required to allow this to work!!

Silly, of course there is a fancy function required! Seems painless though

setOldClass(Classes)

setClass("factor",
  contains = "integer",
  slots = c(
    levels = "character"
  ),
  prototype = structure(
    integer(),
    levels = character()
  )
)
setOldClass("factor", S4Class = "factor")

Interaction of S4 & S3 cont.

Ok, we've got a way to inherit attributes from S3 Objects. What about importing S3 generics to S4?

58 / 62

Interaction of S4 & S3

How exactly do these two system allow interactions?

Well, you can assign an S3 object to a S4 slot or build on top of an S3 object by using contains.

Sounds easy! Really glad there isn't a fancy function required to allow this to work!!

Silly, of course there is a fancy function required! Seems painless though

setOldClass(Classes)

setClass("factor",
  contains = "integer",
  slots = c(
    levels = "character"
  ),
  prototype = structure(
    integer(),
    levels = character()
  )
)
setOldClass("factor", S4Class = "factor")

Interaction of S4 & S3 cont.

Ok, we've got a way to inherit attributes from S3 Objects. What about importing S3 generics to S4?

setGeneric(name, def)

Does this break its use for S3 methods?

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Trade-offs

S4 vs S3

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Trade-offs

S4 vs S3

  • S3 and S4 solve similar problems with solutions pointed towards the entire R ecosystem
  • S4 has conventions by design, while S3 allows the same conventions, others, or none
  • S3 seems more like the self-service friendly tool-set
  • S3 is more generally used, S4 is used by large projects like bioconductor
61 / 62

Trade-offs

S4 vs S3

  • S3 and S4 solve similar problems with solutions pointed towards the entire R ecosystem
  • S4 has conventions by design, while S3 allows the same conventions, others, or none
  • S3 seems more like the self-service friendly tool-set
  • S3 is more generally used, S4 is used by large projects like bioconductor

R6 vs S3

  • R6 seems to allow by nature the build up of a mini-ecosystem of functionality
  • R6 reference semantics seem cool
  • Something about using the $ to pipe method calls
  • R6 seems to have some nice features to prevent breaking changes when improvements to classes or methods are made
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Outline

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