classrr-s4slotroxygen2

How to properly document S4 class slots using Roxygen2?


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.


Solution

  • roxygen2 v4.1+ and Hadley's latest doc for doing this:

    http://r-pkgs.had.co.nz/man.html#man-classes

    I have not tried it yet for RC, but it works for me for S4 now.

    Previously

    It looks like S4 class slots are fully supported under Roxygen2 version 3.0+:

    http://blog.rstudio.org/2013/12/09/roxygen2-3-0-0/

    "document your S4 classes, S4 methods and RC classes with roxygen2 – you can safely remove workarounds that used @alias and @usage, and simply rely on roxygen2 to do the right thing."