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Roebuck,Paul L

2015-Jan-28 17:02 UTC

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

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,
                            ...)
}

Michael Lawrence

2015-Jan-28 17:28 UTC

head link

[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]]

Roebuck,Paul L

2015-Jan-28 18:07 UTC

head link

[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,
                            ...)
}

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