How to combine or modify S4 objects? - r

I am struggling to find an easy way to modify S4 objects having many slots. A toy example is:
setClass(
Class = "First",
slots = c(foo = "numeric")
)
setClass(
Class = "Second",
slots = c(bar = "numeric"),
contains = "First"
)
dog <- new(Class="First",
foo = 1)
cat <- new(Class="Second",
foo = dog#foo,
bar = 1)
str(cat)
This is trivial because class First contains only one slot (foo). Is there an easy way to combine/modify S4 objects which contain many slots?

Looks like you're trying to instantiate a sub-class with the values of a parent class instance. I don't think there is an easy way to do this, but it can be done. Here, we retrieve the parent class instance slot values, and use do.call to instantiate a child class object:
par.slots <- sapply(slotNames(dog), slot, object=dog, simplify=F)
do.call("new", c("Second", bar=1, par.slots))
## An object of class "Second"
## Slot "bar":
## [1] 1
##
## Slot "foo":
## [1] 1

Yes, most people who create S4 objects create a variety of methods to work on them in the ways you would be most inclined manipulate data for your given purpose.
Sometimes that is by creating a whole new class-specific method to accomplish a specific task and others it is by creating a do that instructs R to apply the class-specific implementation of an existing generic function (such as rbind or summary) You can read about it here:
Bioconductor S4 Tutorial
This should get you headed in the right direction creating your own functions or customizing existing generics to work with your objects.

Related

R methods for custom S3 class

I have my s3 class student
# a constructor function for the "student" class
student <- function(n,a,g) {
# we can add our own integrity checks
if(g>4 || g<0) stop("GPA must be between 0 and 4")
value <- list(name = n, age = a, GPA = g)
# class can be set using class() or attr() function
attr(value, "class") <- "student"
value
}
stud <- student("name", 10, 3.5)
Now I would like to create a method similar to stud.doubleGPA() which would double the GPA of the student. I know I can achieve this using
stud$GPA <- stud$GPA*2
stud$GPA # 7
However trying to define a function doesn't seem to work.
doubleGPA <- function(student) {
if(!class(student)=="student") stop("nope")
student$GPA <- student$GPA*2
}
doubleGPA(stud)
stud$GPA # 7 again (didn't work)
And replacing <- with <<- in the above function gives
Error in student$GPA <<- student$GPA * 2 :
object of type 'closure' is not subsettable
How can I define such a method which would belong to an s3 class and therefore be inherited by children ?
Cheers
You are thinking of a different kind of object oriented programming than the S3 style, something more like C++ or Java. You can do that in R, just not in the S3 system.
In the S3 system, methods "belong to" generic functions, not to classes. Like most functions in R, generic functions don't modify their arguments, they calculate new values and return those. So you might define a generic function doubleGPA(), and have it work on the "student" class using
doubleGPA <- function(x) UseMethod("doubleGPA")
doubleGPA.student <- function(x) {
x$GPA <- x$GPA*2
x
}
and then use it as
stud <- student("name", 10, 3.5)
stud <- doubleGPA(stud)
If you actually want something more like C++ or Java, there are a couple of choices: "reference classes" from the methods package (see ?methods::setRefClass) and "R6 classes" from the R6 package. There are also several prototype-based styles in packages proto, ggplot2, R.oo, and are probably more that I've forgotten to mention.

R: Named lists and description lists

R has two classes not so commonly used: "Dlist" and "namedList".
As regard the first, it is mentioned with respect to Sys.getenv(), which returns a result of class "Dlist" if its argument is missing, for nice printing. There is in fact a print.Dlist method for the class. There is also an apparently related formatDL function to format description lists. However I do not know how to create an object of class "Dlist".
As regards "namedList", it is defined by the manual:
the alternative to "list" that preserves the names attribute
In this case I am unable to create an object of this type and I have not found any instance where it is used.
How do you create a "Dlist" or a "namedList"?
Can you provide an example where the "namedList" is more convenient of an ordinary named list? (intended as a list L, where names(L) is not NULL)
A Dlist is an informal class defined in R's Base package that exists for the sole purpose of pretty-printing a named character vector. It's not a list at all, but a type of character vector:
a <- Sys.getenv()
class(a)
# [1] "Dlist"
typeof(a)
# [1] "character"
You can make one just by writing Dlist to a named character vector's class attribute:
hello_world <- c(Hello = "World", Hi = "Earth", Greetings = "planet");
class(hello_world) <- "Dlist"
hello_world
# Hello World
# Hi Earth
# Greetings planet
You can select formatting options with formatDL:
cat(formatDL(hello_world, style = "list", width = 20), sep = "\n")
# Hello: World
# Hi: Earth
# Greetings: planet
The Dlist is only used in base R for printing environmental variables to the console. Unless you wanted to have a named character vector printed this way, you don't need a Dlist.
On the other hand, a namedList is a formal S4 object as defined in the methods package (also preloaded in R). It inherits its attributes from list and defines a single method - its own version of the generic S4 show.
You might use it as a base class from which to make new S4 classes that inherit the properties of a named list (i.e. a normal list with a names attribute), although it's not clear why a user advanced enough to create S4 classes wouldn't just do that themselves. It's defined here.
You can create a namedList with new:
n <- new("namedList", list(a=1, b=2))
n
# An object of class “namedList”
# $`a`
# [1] 1
#
# $b
# [1] 2
isS4(n)
# [1] TRUE

How to find the default construstor methods for a class

Problems comes from experimenting a package and find using new(Class = 'ddmatrix', Data = X) and ddmatrix(Data = X) yields different results, in which X is a matrix(one can think class ddmatrix is a transformed Class matrix).
Document
In the package, a S4 class ddmatrix is defined. A generic constructor function by setGeneric(name = 'ddmatrix'). Further, the pacakge defines setMethod('ddmatrix', signature = 'matrix', ...) as below:
setMethod("ddmatrix", signature(data="matrix"),
function(data, nrow=1, ncol=1, byrow=FALSE, ...
bldim=.pbd_env$BLDIM, ICTXT=.pbd_env$ICTXT)
{
dim(data) <- NULL
ret <- ddmatrix(data=data, nrow=nrow, ncol=ncol, byrow=byrow, bldim=bldim, ICTXT=ICTXT)
return( ret )
}
)
I am confused how a method ddmatrix is used in the above setMethod('ddmatrix', signature = 'matrix') step. Is this ddmatrix method the default method for the generic ddmatrix?
Meanwhile, when call new('ddmatrix', Data = X), which method it will call to build a new ddmatrix object from a matrix object? new function is:
function (Class, ...)
{
ClassDef <- getClass(Class, where = topenv(parent.frame()))
value <- .Call(C_new_object, ClassDef)
initialize(value, ...)
}
Question
To answer the discrepancy between new('ddmatrix') and ddmatrix(), I think one way is to find the default constructor. Meanwhile, the package also defines setMethod('ddmatrix', signature = 'vector',...), is this the default one?
At some level this is up to the author. Many people view new() and # or slot() (for slot access) as strictly for the package developer -- these expose the implementation details directly to the user -- and prefer to write constructors and accessors that place an interface on top of the implementation. This appears to be the case for the package that you are considering, where ddmatrix() is meant to be the user-oriented constructor.
The author appears to have implemented a facade pattern, where several different methods make relatively minor data transformations before calling another function / method to do the actual object construction. From what you show, it seems ddmatrix,matrix-method invokes ddmatrix,vector-method (because inside ddmatrix,matrix-method the function sets dim(data) <- NULL, turning the matrix into a vector, and then calls ddmatrix() which now dispatches to the vector method), and this constructs the object via new() at https://github.com/RBigData/pbdDMAT/blob/master/R/constructors.r#L191. A different package author could have adopted a different design, where several methods separately call new().
The documentation often also helps, e.g., ?ddmatrix does not discuss direct object construction via new().
Here's a simpler example. I create a class "A", with a single slot containing a numeric vector
setClass("A", slots=c(x="numeric"))
Here I create a constructor, because I want the user to see the interface to the class, rather than it's implementation
A = function(x=numeric())
new("A", x=x)
So far, A() and new("A") return an object with the same structure, e.g.,
> new("A")
An object of class "A"
Slot "x":
numeric(0)
> A()
An object of class "A"
Slot "x":
numeric(0)
Maybe as the developer of the "A" class, I want an uninitialized object of class 'A' to have 'NA' as the value of the slot x, so I modify
A = function(x = NA_real_)
new("A", x=x)
now a direct call to new() returns a different object from a call to A()
> new("A")
An object of class "A"
Slot "x":
numeric(0)
> A()
An object of class "A"
Slot "x":
[1] NA
Which one is 'correct'? Well, both are correct, but as the creator of the class I intend for the user to create an object of class "A" by calling the function A().
A typical reason for separating the interface (using A() to construct an object) from the implementation (using new() to construct an object) is because the implementation is not obvious to the user. This seems to be the case with the ddmatrix() function -- for reasons that only the package author needs to know about, it is convenient to store an R matrix as a vector with information about dimensions. I guess a simple equivalent might be
setClass("A", slots=c(data="numeric", nrow="integer", ncol="integer"))
A = function(m=matrix(0, 0, 0)) {
stopifnot(is(m, "matrix"))
new("A", data=as.vector(m), nrow=nrow(m), ncol=ncol(m))
}
for instance
> A(matrix(1:10, 5))
An object of class "A"
Slot "data":
[1] 1 2 3 4 5 6 7 8 9 10
Slot "nrow":
[1] 5
Slot "ncol":
[1] 2
Why does the author want to do this? It doesn't matter to us as users. Why can't we create the same object by calling m = matrix(1:10, 5); new("A", data=as.vector(m), nrow=nrow(m), ncol(m))? We could, but then when the author decided to change their implementation such that the offsets to the start of each row were to be stored, we'd have to understand what the author had done and update our code.

Extent S4 class, how to use superclass' constructor

In my package, I want to subclass a class TheBaseClass from a contributed package (so it is out of my reach). There is a function for creating objects of this class. Here is a minimal example for that code.
setClass("TheBaseClass", representation(a="numeric"))
initBase <- function() new("TheBaseClass", a=1) # in reality more complex
Now I want simply use initBase as constructor for my subclass, but I do not know how
to set the new class
setClass("MyInheritedClass", contains="TheBaseClass")
initInher <- function() {
res <- initBase()
class(res) <- "MyInheritedClass" # this does not work for S4
}
How can I alter the last line to make it work? Copy & paste the initBase function is not an option, since it involves a .C call. I read about setIs, but this seems not to be the right function here.
Any hint appreciated!
Perhaps this answer provides more extensive explanation. One pattern is to provide an instance of the base class as an unnamed argument to your class constructor
.MyInheritedClass <- setClass("MyInheritedClass", contains="TheBaseClass")
.MyInheritedClass(initBase())
(setClass returns a generator function, which is really no different from calling new but seems cleaner; I use . in front, because generators are maybe a little too crude for "end users", e.g., there is no hint about what the arguments are supposed to be, just ...). This assumes that you have not written an initialize method for your class, or that your initialize method has been constructed in a way that is consistent with the contract of initialize,ANY-method, with a slightly more complicated class
.A <- setClass("A", contains="TheBaseClass",
representation=representation(x="numeric"))
setMethod(initialize, "A",
function(.Object, ..., x)
{
x <- log(x) # your class-specific initialization...
callNextMethod(.Object, ..., x = x) # passed to parent constructor
})
This pattern requires that the initialize method of the base class has been designed correctly. In action:
> .A(initBase(), x=1:2)
An object of class "A"
Slot "x":
[1] 0.0000000 0.6931472
Slot "a":
numeric(0)

R public method in S4 class

I want to subclass an S4 class and add a special method to that subclass.
The method should work only for the subclass, it does not make sense for any other class in my application.
setClass("MySpecies", contains="Species", ##Species is an S4 class
representation(x="numeric"))
setMethod("initialize", "MySpecies", function(.Object, x, ...){
.Object#x <- x
args <- list(...)
for(i in seq_len(length(args))){
attr(.Object, names(args)[i]) <- args[[i]]
}
.Object
})
##CalcMatrix <- function(.Object, y){
## x <- .Object#x
## matrix(x, x*2, y*3)
##}
setGeneric("CalcMatrix", function(object, y){standardGeneric("CalcMatrix")})
setMethod("CalcMatrix", "MySpecies",function(object, y){
x <- object#x
matrix(x, x*2, y*3)
})
With the setGeneric it works, but do I really have to define a generic function although it will be used only with this object? The commented out part works, but then there is no check if the function is called with the right arguments. What is the correct way to do this?
Thanks in advance.
You're wanting to use method dispatch, and every method needs to be associated with a generic, so yes, setGeneric is required.
And for a little unasked-for advice... It's a bit weird to use a formal class system (presumably because the well-defined classes help in writing more complicated programs) and then to subvert the structure by adding arbitrary attributes; these should really be additional, well-defined slots in your class.
Let's make your example reproducible by defining Species
setClass("Species", representation(y="numeric"))
setClass("MySpecies", contains="Species", ##Species is an S4 class
representation(x="numeric"))
An implicit requirement for S4 classes is that new("MySpecies") works; your initialize method fails this test (because x does not have a default value). In addition, it's common practice to expect that initializing MySpecies calls the initialize methods for the classes it contains. One could write
setMethod("initialize", "MySpecies", function(.Object, ..., x=numeric()) {
callNextMethod(.Object, x=x, ...)
})
Note callNextMethod, so that the base class gets initialized properly. Using ... and passing it to callNextMethod means that slots that might be defined in Species would also be initialized correctly. Also, x needs to be after ..., because initialize is defined to take unnamed arguments that represent contained classes -- new("MySpecies", new("Species")) is required to work, even if it is a way of constructing arguments that you do not use directly. The initialize method above doesn't actually do anything more than the default initialize method, so in reality (and this is often the case) it makes sense not to write an initialize method at all.
And then in more recent R, setClass returns a default constructor so
MySpecies <- setClass("MySpecies", contains="Species", ##Species is an S4 class
representation(x="numeric"))
and then
> MySpecies(x=1:5, y=5:1)
An object of class "MySpecies"
Slot "x":
[1] 1 2 3 4 5
Slot "y":
[1] 5 4 3 2 1

Resources