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Roebuck,Paul L

2015-Jan-28 18:07 UTC

[Rd] [Q] Get formal arguments of my implemented S4 method

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,
                            ...)
}

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Michael Lawrence

2015-Jan-29 02:37 UTC

head link

[Rd] [Q] Get formal arguments of my implemented S4 method

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.




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,
>                             ...)
> }
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
>
>
>
	[[alternative HTML version deleted]]

John Chambers

2015-Jan-29 13:57 UTC

head link

[Rd] [Q] Get formal arguments of my implemented S4 method

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.

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
}
> 
> 
> 
> 
> 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,
>>                            ...)
>> }
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

	[[alternative HTML version deleted]]

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