s4

I've seen some discussions in SO and other places regarding how this should be or will be done in future versions of Roxygen2. However, I am stuck. How should I go about documenting a S4 generic, as well as its methods, using Roxygen2? A working example for a brand new generic/methods, as well as an example for extending base S4 generic would be incredibly useful. I do not want to have to make separate (mostly) redundant documentation for each S4 method of the same generic. Due dilligence: I have tracked down a useful example for the "extract" method. However, it appears to be outdated and

I have written some functions in R using S4 classes. Now I want to build an R package out of these functions. How should I proceed? Is there anything that I should do differently because I have used S4 classes? Andrie Consult the following reference material: Chapter 1, Creating R packages , of the Writing R extensions manual. This is the canonical source. It's the ultimate reference point, but not necessarily the best starting point. A short presentation outlining the key ideas in package development and using the devtools package for development Hadley's devtools wiki , particular the

In packages like marray and limma , when complex objects are loaded, they contain "members variables" that are accessed using the @ symbol. What does this mean and how does it differ from the $ symbol? See ?'@' : Description: Extract the contents of a slot in a object with a formal (S4) class structure. Usage: object@name ... The S language has two object systems, known informally as S3 and S4. S3 objects, classes and methods have been available in R from the beginning, they are informal, yet very interactive . S3 was first described in the White Book (Statistical Models in S). S3 is not a

For documenting classes with roxygen(2), specifying a title and description/details appears to be the same as for functions, methods, data, etc. However, slots and inheritance are their own sort of animal. What is the best practice -- current or planned -- for documenting S4 classes in roxygen2? Due Diligence: I found mention of an @slot tag in early descriptions of roxygen. A 2008 R-forge mailing list post seems to indicate that this is dead, and there is no support for @slot in roxygen: Is this true of roxygen2? The previously-mentioned post suggests a user should instead make their own

As I'm often confronted with situations where S4 programming is needed to keep an overview, I've collected quite some sources on S4 objects, methods and programming. I've listed them here as a reference. Please add your own sources as well. On the web The methods help files : help files from the package methods, where much of the necessary information can be found S4 classes in 15 pages : Short introduction on the programming with S4 objects. How S4 methods work : more explanation about the underlying mechanisms. Not so short introduction to S4 : with practical examples of how to construct the

What is a good way of defining a general purpose function which should have implementations for both S3 and S4 classes? I have been using something like this: setGeneric("myfun", function(x, ...){ standardGeneric("myfun"); }); setMethod("myfun", "ANY", function(x, ...) { if(!isS4(x)) { return(UseMethod("myfun")); } stop("No implementation found for class: ", class(x)); }); This succeeds: myfun.bar <- function(x, ...){ return("Object of class bar successfully dispatched."); } object <- structure(123, class=c("foo", "bar")); myfun(object) Is there a move "native" way to accomplish this? I know

I am having trouble figuring out the proper way to define the [ , $ , and [[ subset operators for an S4 class. Can anyone provide me with a basic example of defining these three for an S4 class? Discover the generic so that we know what we are aiming for > getGeneric("[") standardGeneric for "[" defined from package "base" function (x, i, j, ..., drop = TRUE) standardGeneric("[", .Primitive("[")) <bytecode: 0x32e25c8> <environment: 0x32d7a50> Methods may be defined for arguments: x, i, j, drop Use showMethods("[") for currently available ones. Define a simple class setClass("A", representation