From lawrence.michael at gene.com  Thu Jan 29 15:17:23 2015
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Thu, 29 Jan 2015 06:17:23 -0800
Subject: [Rd] [Q] Get formal arguments of my implemented S4 method
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Message-ID: <CAOQ5NycBgy2BFU4eTw=bDHauTJgoXx4reXXy9KTjheUaid+Euw@mail.gmail.com>

On Thu, Jan 29, 2015 at 5:57 AM, John Chambers <jmc at r-project.org> wrote:

>
> On Jan 28, 2015, at 6:37 PM, Michael Lawrence <lawrence.michael at gene.com>
> wrote:
>
> At this point I would just due:
>
> formals(body(method)[[2L]])
>
> At some point we need to figure out what to do with this .local()
> confusion.
>
>
> Agreed, definitely.  The current hack is to avoid re-matching arguments on
> method dispatch, so a fix would need to be fairly deep in the
> implementation.
>
> But I don't think the expression above is quite right. body(method)[[2L]]
> is the assignment.  You need to evaluate the rhs.
>
>
Sorry, thanks for the catch.


> Here is a function that does the same sort of thing, and returns the
> standard formals for the generic if this method does not have nonstandard
> arguments.  We should probably add a version of this function for 3.3.0, so
> user code doesn't have hacks around the current hack.
>
> methodFormals <- function(f, signature = character()) {
>     fdef <- getGeneric(f)
>     method <- selectMethod(fdef, signature)
>     genFormals <- base::formals(fdef)
>     b <- body(method)
>     if(is(b, "{") && is(b[[2]], "<-") && identical(b[[2]][[2]], as.name(".local")))
> {
>         local <- eval(b[[2]][[3]])
>         if(is.function(local))
>             return(formals(local))
>         warning("Expected a .local assignment to be a function. Corrupted
> method?")
>     }
>     genFormals
> }
>
>
Yea, I had thought about having that, or a more general getMethodFunction()
on which formals() could be called. I held back though, because I thought
it might be best to address the .local issue, instead of introducing
additional API components that would otherwise be unnecessary.


>
>
>
> On Wed, Jan 28, 2015 at 10:07 AM, Roebuck,Paul L <PLRoebuck at mdanderson.org
> >
> wrote:
>
> I'm attempting to reflect the information for use with corresponding
> fields in GUI (in a different package), to provide default values,
> argname as key for UI label lookups, etc.
>
> So I want something much more like the formals of the implementation:
>
> {
>    "object",
>    "method":             c("median", "vs", "tukey"),
>    "calc.medians":       TRUE,
>    "sweep.cols":         calc.medians,
>    "recalc.after.sweep": sweep.cols,
>    "?"
> }
>
> not those of the generic:
>
> {
>    "object",
>    "?"
> }
>
>
> From:  Michael Lawrence <lawrence.michael at gene.com>
> Date:  Wednesday, January 28, 2015 11:28 AM
> To:  "Roebuck,Paul L" <PLRoebuck at mdanderson.org>
> Cc:  R-devel <r-devel at r-project.org>
> Subject:  Re: [Rd] [Q] Get formal arguments of my implemented S4 method
>
>
> Would you please clarify your exact use case?
>
>
> Thanks,
> Michael
>
>
> On Wed, Jan 28, 2015 at 9:02 AM, Roebuck,Paul L
> <PLRoebuck at mdanderson.org> wrote:
>
> Interrogating some (of my own) code in another package.
>
> norm.meth <- getMethod("normalize", "MatrixLike")
> message("str(norm.meth)")
> str(norm.meth)
>
>
> message("show(norm.meth at .Data)")
> show(norm.meth at .Data)
>
>
>
> Last show() displays this:
>
> function (object, ...)
> {
>    .local <- function (object, method = c("median", "vs", "tukey"),
>        calc.medians = TRUE, sweep.cols = calc.medians,
>        recalc.after.sweep = sweep.cols, ...)
>    {
>        .do_normalize(object,
>            method = match.arg(method),
>            calc.medians = calc.medians,
>            sweep.cols = sweep.cols,
>            recalc.after.sweep = recalc.after.sweep,
>            ...)
>    }
>    .local(object, ...)
> }
>
>
> Desire to be able to access formals() for the .local() function definition,
> not the generic one. Have seen information desired available via "defined"
> slot of returned 'MethodDefinition' object, but not using the code below.
>
>
>
> ====================
>
> library(methods)
>
> if (!isGeneric("normalize")) {
>    ## Other packages also define this generic...
>    setGeneric("normalize",
>               function(object, ...) standardGeneric("normalize"))
> }
>
> setClassUnion("MatrixLike", c("matrix", "data.frame"))
>
> .do_normalize <- function(concs,
>                          method,
>                          calc.medians,
>                          sweep.cols,
>                          recalc.after.sweep,
>                          ...) {
>    message("internal routine called!")
>    NULL
> }
>
> setMethod("normalize", signature(object="MatrixLike"),
>          function(object,
>                   method=c("median", "vs", "tukey"),
>                   calc.medians=TRUE,
>                   sweep.cols=calc.medians,
>                   recalc.after.sweep=sweep.cols,
>                   ...) {
>
>    .do_normalize <- function(object,
>                            method=match.arg(method),
>                            calc.medians=calc.medians,
>                            sweep.cols=sweep.cols,
>                            recalc.after.sweep=recalc.after.sweep,
>                            ...)
> }
>
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[Rd] [Q] Get formal arguments of my implemented S4 method
Michael Lawrence