From renaud at mancala.cbio.uct.ac.za  Wed Jul  8 15:57:49 2015
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Wed, 8 Jul 2015 15:57:49 +0200
Subject: [Rd] List S3 methods and defining packages
In-Reply-To: <CAKFxdiRPwvOWrHOHYKnJyrV8M-h2qq_tzMTaKUga-eDZ9DG5bQ@mail.gmail.com>
References: <CAHavPHE_A=Ynngg41MnUnWxDUvq47LwT4HYwPGiJYXoSLO5BKw@mail.gmail.com>
	<559C2200.4070305@fredhutch.org>
	<CAHavPHFZgOQTMuyXcu-Zn39Yo2y_xn=o=V0yuONGm_3qTjaduQ@mail.gmail.com>
	<CAKFxdiRPwvOWrHOHYKnJyrV8M-h2qq_tzMTaKUga-eDZ9DG5bQ@mail.gmail.com>
Message-ID: <CAHavPHFLNR=dMhn7vyDM=qo4CZe7bi7Gakr48e+__6T9LY2sGQ@mail.gmail.com>

Thanks Kevin, this indeed clarifies a bit the S3 method registration universe.

On 8 July 2015 at 15:48, Kevin Wright <kw.stat at gmail.com> wrote:
> Not sure if this answers your question, but you can't unregister a method.  See
>
> http://tolstoy.newcastle.edu.au/R/help/06/07/30791.html
>
> Kevin Wright
>
>
> On Wed, Jul 8, 2015 at 5:09 AM, Renaud Gaujoux
> <renaud at mancala.cbio.uct.ac.za> wrote:
>> Thank you for your reply Martin.
>> Your code made me realize that S3 methods are added to the
>> .__S3MethodsTable__. of the package that defines the generic, not to
>> the ones defining the method itself.
>> How does things work in the case of a method from one package B
>> masking the one from another package A? I don't get any warning
>> message and there seems to be only one entry in the relevant
>> .__S3MethodsTable__.
>> Aren't these tables updated when the masking package B is detached?
>>
>> On 7 July 2015 at 21:01, Martin Morgan <mtmorgan at fredhutch.org> wrote:
>>> On 07/07/2015 02:05 AM, Renaud Gaujoux wrote:
>>>>
>>>> Hi,
>>>>
>>>> from the man page ?methods, I expected to be able to build pairs
>>>> (class,package) for a given S3 method, e.g., print, using
>>>>
>>>> attr(methods(print), 'info').
>>>>
>>>> However all the methods, except the ones defined in base or S4
>>>> methods, get the 'from' value "registered S3method for print", instead
>>>> of the actual package name (see below for the first rows).
>>>>
>>>> Is this normal behaviour? If so, is there a way to get what I want: a
>>>> character vector mapping class to package (ideally in loading order,
>>>> but this I can re-order from search()).
>>>
>>>
>>> It's the way it has always been, so normal in that sense.
>>>
>>> There could be two meanings of 'from' -- the namespace in which the generic
>>> to which the method belongs is defined, and the namespace in which the
>>> method is defined. I think the former is what you're interested in, but the
>>> latter likely what methods() might be modified return.
>>>
>>> For your use case, maybe something like
>>>
>>>     .S3methodsInNamespace <- function(envir, pattern) {
>>>         mtable <- get(".__S3MethodsTable__.", envir = asNamespace(envir))
>>>         methods <- ls(mtable, pattern = pattern)
>>>         env <- vapply(methods, function(x) {
>>>             environmentName(environment(get(x, mtable)))
>>>         }, character(1))
>>>         setNames(names(env), unname(env))
>>>     }
>>>
>>>
>>> followed by
>>>
>>>   nmspc = loadedNamespaces()
>>>   lapply(setNames(nmspc, nmspc), .S3methodsInNamespace, "^plot.")
>>>
>>> which reveals the different meanings of 'from', e.g.,
>>>
>>>> lapply(setNames(nmspc, nmspc), .S3methodsInNamespace,
>>>> "^plot.")["graphics"]
>>> $graphics
>>>                stats             graphics                stats
>>>           "plot.acf"    "plot.data.frame" "plot.decomposed.ts"
>>>             graphics                stats                stats
>>>       "plot.default"    "plot.dendrogram"       "plot.density"
>>>                stats             graphics             graphics
>>>          "plot.ecdf"        "plot.factor"       "plot.formula"
>>>             graphics                stats             graphics
>>>      "plot.function"        "plot.hclust"     "plot.histogram"
>>>                stats                stats                stats
>>>   "plot.HoltWinters"        "plot.isoreg"            "plot.lm"
>>>                stats                stats                stats
>>>     "plot.medpolish"           "plot.mlm"           "plot.ppr"
>>>                stats                stats                stats
>>>        "plot.prcomp"      "plot.princomp"   "plot.profile.nls"
>>>             graphics                stats                stats
>>>        "plot.raster"          "plot.spec"       "plot.stepfun"
>>>                stats             graphics                stats
>>>           "plot.stl"         "plot.table"            "plot.ts"
>>>                stats                stats
>>>      "plot.tskernel"      "plot.TukeyHSD"
>>>
>>> Also this is for loaded, rather than attached, namespaces.
>>>
>>> Martin Morgan
>>>
>>>> Thank you.
>>>>
>>>> Bests,
>>>> Renaud
>>>>
>>>>                                               visible
>>>>         from generic  isS4
>>>> print.abbrev                                   FALSE registered
>>>> S3method for print   print FALSE
>>>> print.acf                                      FALSE registered
>>>> S3method for print   print FALSE
>>>> print.AES                                      FALSE registered
>>>> S3method for print   print FALSE
>>>> print.agnes                                    FALSE registered
>>>> S3method for print   print FALSE
>>>> print.anova                                    FALSE registered
>>>> S3method for print   print FALSE
>>>> print.Anova                                    FALSE registered
>>>> S3method for print   print FALSE
>>>> print.anova.loglm                              FALSE registered
>>>> S3method for print   print FALSE
>>>> print,ANY-method                                TRUE
>>>>         base   print  TRUE
>>>> print.aov                                      FALSE registered
>>>> S3method for print   print FALSE
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>>
>>> --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> Kevin Wright
>



[Rd] List S3 methods and defining packages
Renaud Gaujoux