From hpages at fredhutch.org  Tue Jan 30 23:41:03 2018
From: hpages at fredhutch.org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 30 Jan 2018 14:41:03 -0800
Subject: [Rd] as.list method for by Objects
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References: <SY3PR01MB07474F9CEBBC61FD2A152E58CDE40@SY3PR01MB0747.ausprd01.prod.outlook.com>
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 <CADwqtCO98pTE6G4xOva3pVEEA0jSMND9zepcR19B-8rZ6mhYRg@mail.gmail.com>
Message-ID: <f2080a27-71e0-4f52-61cd-2c2a8bb8e8cd@fredhutch.org>

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>> 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
> 
>         ______________________________________________
>         R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
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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>
>     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
>     https://stat.ethz.ch/mailman/listinfo/r-devel
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JIjTy48pWmEOxpHYM6DUHbRRSVwvOXOkgEFuoMhNkm0&s=x29ogWxfEnr2uKDcVEtKDWtB0USw8Xwm4f18WKBO-Dg&e=>
> 
> 
> 
> 
> -- 
> 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
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] as.list method for by Objects
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