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 itemized list with LaTeX markup. E.g. a new S4 class that extends the "character" class would be coded and documented like this:
#' The title for my S4 class that extends \code{"character"} class.
#'
#' Some details about this class and my plans for it in the body.
#'
#' \describe{
#' \item{myslot1}{A logical keeping track of something.}
#'
#' \item{myslot2}{An integer specifying something else.}
#'
#' \item{myslot3}{A data.frame holding some data.}
#' }
#' @name mynewclass-class
#' @rdname mynewclass-class
#' @exportClass mynewclass
setClass("mynewclass",
representation(myslot1="logical",
myslot2="integer",
myslot3="data.frame"),
contains = "character"
)
However, although this works, this \describe , \item approach for documenting the slots seems inconsistent with the rest of roxygen(2), in that there are no @-delimited tags and slots could go undocumented with no objection from roxygenize(). It also says nothing about a consistent way to document inheritance of the class being defined. I imagine dependency still generally works fine (if a particular slot requires a non-base class from another package) using the @import tag.
So, to summarize, what is the current best-practice for roxygen(2) slots?
There seem to be three options to consider at the moment:
- A -- Itemized list (as example above).
- B --
@slot... but with extra tags/implementation I missed. I was unable to get @slot to work with roxygen / roxygen2 in versions where it was included as a replacement for the itemized list in the example above. Again, the example above does work with roxygen(2).- C -- Some alternative tag for specifying slots, like
@param, that would accomplish the same thing.
I'm borrowing/extending this question from a post I made to the roxygen2 development page on github.
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Updated answer for Roxygen2 5.0.1, current as of 7.2.0
For S4, the best practice now is documenting using the @slot tag:
#' The title for my S4 class that extends \code{"character"} class.
#'
#' Some details about this class and my plans for it in the body.
#'
#' @slot myslot1 A logical keeping track of something.
#' @slot myslot2 An integer specifying something else.
#' @slot myslot3 A data.frame holding some data.
#'
#' @name mynewclass-class
#' @rdname mynewclass-class
#' @export
On a sidenote, @exportClass is only necessary in some cases, the general way to export a function is using @export now. You also don't have to export a class, unless you want other packages to be able to extend the class.
See also http://r-pkgs.had.co.nz/namespace.html#exports
Updated answer for Roygen2 3.0.0, current as of 5.0.1.
For S4, the best practice is documentation in the form:
#' \section{Slots}{
#' \describe{
#' \item{\code{a}:}{Object of class \code{"numeric"}.}
#' \item{\code{b}:}{Object of class \code{"character"}.}
#' }
#' }
This is consistent with the internal representation of slots as a list inside the object. As you point out, this syntax is different than other lines, and we may hope for a more robust solution in the future that incorporates knowledge of inheritance -- but today that does not exist.
As pointed out by @Brian Diggs, this feature was pulled into 3.0.0, further discussion at https://github.com/klutometis/roxygen/pull/85