as.list method for by Objects
On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
Michael Lawrence <lawrence.michael at gene.com>
on Tue, 30 Jan 2018 15:57:42 -0800 writes:
> I just meant that the minimal contract for as.list() appears to be that it
> returns a VECSXP. To the user, we might say that is.list() will always
> return TRUE.
Indeed. I also agree with Herv'e that the user level documentation should rather mention is.list(.) |--> TRUE than VECSXP, and interestingly for the experts among us, the is.list() primitive gives not only TRUE for VECSXP but also of LISTSXP (the good ole' pairlists).
> I'm not sure we can expect consistency across methods
> beyond that, nor is it feasible at this point to match the
> semantics of the methods package. It deals in "class
> space" while as.list() deals in "typeof() space".
> Michael
Yes, and that *is* the extra complexity we have in R (inherited
from S, I'd say) which ideally wasn't there and of course is
not there in much younger languages/systems such as julia.
And --- by the way let me preach, for the "class space" ---
do __never__ use
if(class(obj) == "<classname>")
in your code (I see this so often, shockingly to me ...) but rather use
if(inherits(obj, "<classname>"))
instead.
Second this one. But, soon (*) the former will at least give the correct answer when length(class(obj)) == 1 and produce an error otherwise. So, several of these cases will be caught at run-time in a near future. (*) When _R_CHECK_LENGTH_1_CONDITION_=true becomes the default behavior - hopefully by R 3.5.0.
Martin
> On Tue, Jan 30, 2018 at 3:47 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:
>> 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
.............
>>> -- 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
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