Question

How do I test if an object is a instance of an S4 class (not sure if this is the right terminology)? I know about the function isS4 however, this also returns true for class definitions, etc. E.g.:

traj <- setClass(
  Class="Trajectories",
  representation=representation(
    times = "numeric",
    traj = "matrix"
  )
)

trajclass <- getClass("Trajectories")
trajobject <- new(Class="Trajectories",times=c(1,3),traj=matrix(1:4,ncol=2))

isS4(traj)
isS4(trajclass)
isS4(trajobject)

I am only interested in objects containing data, trajobject in this case; not so much in methods or class definitions. Is there a native function that I can use to test if an S4 object is an actual object? I.e. when using print(object) the output starts with:

An object of class “foo”…..

Answer 1

S4 classes (and reference classes, for that matter and perhaps to the chagrin of some) are defined using S4 classes (cool (?) eh?)

> class(trajclass)
[1] "classRepresentation"
attr(,"package")
[1] "methods"
> getClass(class(trajclass))
Class "classRepresentation" [package "methods"]

Slots:

Name:             slots         contains          virtual        prototype
Class:             list             list          logical              ANY

Name:          validity           access        className          package
Class: OptionalFunction             list        character        character

Name:        subclasses       versionKey           sealed
Class:             list      externalptr          logical

Known Subclasses: "ClassUnionRepresentation", "refClassRepresentation"

I think the best you could do is along the lines of

isS4(trajclass) && !is(trajclass, "classRepresentation")

S4 uses show as a synonym (sort of) for print; there is an S4 show method for classRepresentation that is

> selectMethod(show, class(traj))
Method Definition:

function (object) 
{
    cat(gettextf("Class generator function for class \"%s\" from package \"%s\"\n", 
        object@className, object@package))
    show(as(object, "function"))
}
<bytecode: 0x1522d40>
<environment: 0xf1d808>

Signatures:
        object                  
target  "classGeneratorFunction"
defined "classGeneratorFunction"

whereas the show method for trajobject is the default, which is

> selectMethod(show, class(trajobject))
Method Definition (Class "derivedDefaultMethod"):

function (object) 
showDefault(object, FALSE)
<bytecode: 0x1516d08>
<environment: namespace:methods>

Signatures:
        object        
target  "Trajectories"
defined "ANY"         

with the meat in methods::showDefault. I guess you could implement

setGeneric("isNotS4ClassDef",
    function(object) standardGeneric("isNotS4ClassDef"))

setMethod(isNotS4ClassDef, "ANY",
    function(object) TRUE)

setMethod(isNotS4ClassDef, "classRepresentation",
    function(object) FALSE)