[Rd] as.list method for by Objects
Michael Lawrence
lawrence.michael at gene.com
Tue Jan 30 23:50:10 CET 2018
by() does not always return a list. In Gabe's example, it returns an
integer, thus it is coerced to a list. as.list() means that it should be a
VECSXP, not necessarily with "list" in the class attribute.
Michael
On Tue, Jan 30, 2018 at 2:41 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Gabe,
>
> Interestingly the behavior of as.list() on by objects seem to
> depend on the object itself:
>
> > b1 <- by(1:2, 1:2, identity)
> > class(as.list(b1))
> [1] "list"
>
> > b2 <- by(warpbreaks[, 1:2], warpbreaks[,"tension"], summary)
> > class(as.list(b2))
> [1] "by"
>
> This is with R 3.4.3 and R devel (2017-12-11 r73889).
>
> H.
>
> On 01/30/2018 02:33 PM, Gabriel Becker wrote:
>
>> Dario,
>>
>> What version of R are you using. In my mildly old 3.4.0 installation and
>> in the version of Revel I have lying around (also mildly old...) I don't
>> see the behavior I think you are describing
>>
>> > b = by(1:2, 1:2, identity)
>>
>> > class(as.list(b))
>>
>> [1] "list"
>>
>> > sessionInfo()
>>
>> R Under development (unstable) (2017-12-19 r73926)
>>
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>
>> Running under: OS X El Capitan 10.11.6
>>
>>
>> Matrix products: default
>>
>> BLAS:
>> /Users/beckerg4/local/Rdevel/R.framework/Versions/3.5/Resour
>> ces/lib/libRblas.dylib
>>
>> LAPACK:
>> /Users/beckerg4/local/Rdevel/R.framework/Versions/3.5/Resour
>> ces/lib/libRlapack.dylib
>>
>>
>> locale:
>>
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] compiler_3.5.0
>>
>> >
>>
>>
>> As for by not having a class definition, no S3 class has an explicit
>> definition, so this is somewhat par for the course here...
>>
>> did I misunderstand something?
>>
>>
>> ~G
>>
>> On Tue, Jan 30, 2018 at 2:24 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>> I agree that it makes sense to expect as.list() to perform
>> a "strict coercion" i.e. to return an object of class "list",
>> *even* on a list derivative. That's what as( , "list") does
>> by default:
>>
>> # on a data.frame object
>> as(data.frame(), "list") # object of class "list"
>> # (but strangely it drops the names)
>>
>> # on a by object
>> x <- by(warpbreaks[, 1:2], warpbreaks[,"tension"], summary)
>> as(x, "list") # object of class "list"
>>
>> More generally speaking as() is expected to perform "strict
>> coercion" by default, unless called with 'strict=FALSE'.
>>
>> That's also what as.list() does on a data.frame:
>>
>> as.list(data.frame()) # object of class "list"
>>
>> FWIW as.numeric() also performs "strict coercion" on an integer
>> vector:
>>
>> as.numeric(1:3) # object of class "numeric"
>>
>> So an as.list.env method that does the same as as(x, "list")
>> would bring a small touch of consistency in an otherwise
>> quite inconsistent world of coercion methods(*).
>>
>> H.
>>
>> (*) as(data.frame(), "list", strict=FALSE) doesn't do what you'd
>> expect (just one of many examples)
>>
>>
>> On 01/29/2018 05:00 PM, Dario Strbenac wrote:
>>
>> Good day,
>>
>> I'd like to suggest the addition of an as.list method for a by
>> object that actually returns a list of class "list". This would
>> make it safer to do type-checking, because is.list also returns
>> TRUE for a data.frame variable and using class(result) == "list"
>> is an alternative that only returns TRUE for lists. It's also
>> confusing initially that
>>
>> class(x)
>>
>> [1] "by"
>>
>> is.list(x)
>>
>> [1] TRUE
>>
>> since there's no explicit class definition for "by" and no
>> mention if it has any superclasses.
>>
>> --------------------------------------
>> Dario Strbenac
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>>
>> ______________________________________________
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>>
>> -- Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>> ______________________________________________
>> R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
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>>
>>
>>
>>
>> --
>> Gabriel Becker, PhD
>> Scientist (Bioinformatics)
>> Genentech Research
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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