From hpages at fredhutch.org  Wed Jan 31 00:47:33 2018
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Date: Tue, 30 Jan 2018 15:47:33 -0800
Subject: [Rd] as.list method for by Objects
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On 01/30/2018 02:50 PM, Michael Lawrence wrote:
> 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.

The documentation is not particularly clear about what as.list()
means for list derivatives. IMO clarifications should stick to
simple concepts and formulations like "is.list(x) is TRUE" or
"x is a list or a list derivative" rather than "x is a VECSXP".
Coercion is useful beyond the use case of implementing a .C entry
point and calling as.numeric/as.list/etc... on its arguments.

This is why I was hoping that we could maybe discuss the possibility
of making the as.list() contract less vague than just "as.list()
must return a list or a list derivative".

Again, I think that 2 things weight quite a lot in that discussion:
   1) as.list() returns an object of class "data.frame" on a
      data.frame (strict coercion). If all what as.list() needed to
      do was to return a VECSXP, then as.list.default() already does
      this on a data.frame so why did someone bother adding an
      as.list.data.frame method that does strict coercion?
   2) The S4 coercion system based on as() does strict coercion by
      default.

H.

> 
> Michael
> 
> On Tue, Jan 30, 2018 at 2:41 PM, Herv? Pag?s <hpages at fredhutch.org 
> <mailto: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/Resources/lib/libRblas.dylib
> 
>          ? ? LAPACK:
>             
>         /Users/beckerg4/local/Rdevel/R.framework/Versions/3.5/Resources/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, Herv? Pag?s
>         <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>         <mailto: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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> 
>          ? ? --? ? ?Herv? Pag?s
> 
>          ? ? 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>
>         <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
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>         <tel:%28206%29%20667-5791>
>          ? ? Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>         <tel:%28206%29%20667-1319>
> 
> 
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> 
> 
> 
>         -- 
>         Gabriel Becker, PhD
>         Scientist (Bioinformatics)
>         Genentech Research
> 
> 
>     -- 
>     Herv? Pag?s
> 
>     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>
> 
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> 
> 

-- 
Herv? Pag?s

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



[Rd] as.list method for by Objects
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