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 <mtmor...@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
>>
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>>
>
>
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