S3 methods for S4 classes not properly documented

[JoFAM]

Per the methods manual , the following construct should be used when creating S3 methods for S4 classes. This is eg needed when having a model framework in S4, but one needs to provide predict(), fitted(), coef() , ... methods.

setClass("uncased", contains = "character")
unique.uncased <- function(x, incomparables = FALSE, ...) nextMethod(tolower(x))
setMethod("unique", "uncased", unique.uncased)

And the namespace should contain

S3method(unique, uncased)
exportMethods(unique)

When I try the following :

#' @rdname unique
#' @export
unique.uncased <- function(x, incomparables = FALSE, ...) nextMethod(tolower(x))
#' @rdname unique
#' @export
setMethod("unique", "uncased", unique.uncased)

Then :

• in the namespace export(unique.uncased) is added.
• R CMD check gives a note about a possible S3 method being refered to in the manual with its full name.

S3 methods shown with full name in documentation object 'unique':
'unique.uncased'
The \usage entries for S3 methods should use the \method markup and not their full name.

If I use the (deprecated) tag @S3method instead, I have the correct entry in the namespace but still the same note in R CMD check.

[hadley]

This is a case where you should use @method.

[JoFAM]

Checked it, and @method doesn't do anything for the NAMESPACE. I need

S3method(unique, uncased)

in the NAMESPACE file instead of export(unique.uncased) as I get now. @method only adds the correct entry in the Rd file, not in the NAMESPACE file.

[hadley]

@method tells roxygen that it's a method, @export will then export it correctly.

[JoFAM]

Ah, so I need both tags together. Tried it, seems to work. Thx.