From mehmet.suzen at gmail.com  Wed Nov 29 21:21:44 2017
From: mehmet.suzen at gmail.com (Suzen, Mehmet)
Date: Wed, 29 Nov 2017 21:21:44 +0100
Subject: [Rd] binary form of is() contradicts its unary form
In-Reply-To: <5A1F0EB3.7090508@fredhutch.org>
References: <5A1EF8DB.6080401@fredhutch.org>
 <CAPtbhHzXe3=EBW6wwyx1Hh158qjBrC0vfFbh4+o3bRZTC+c5Kw@mail.gmail.com>
 <5A1F0EB3.7090508@fredhutch.org>
Message-ID: <CAPtbhHws5Fydk0AHeq3Urh9qEZ4XM0C-BJtoRvUpnStb33G=mg@mail.gmail.com>

Hi Herve,

Interesting observation with `setClass` but it is for S4.  It looks
like `data.frame()` is not an S4 class.

> isS4(data.frame())
[1] FALSE

And in your case this might help:

> is(asS4(data.frame()), "list")
[1] TRUE

Looks like `is` is designed for S4 classes, I am not entirely sure.

Best,
-Mehmet

On 29 November 2017 at 20:46, Herv? Pag?s <hpages at fredhutch.org> wrote:
> Hi Mehmet,
>
> On 11/29/2017 11:22 AM, Suzen, Mehmet wrote:
>>
>> Hi Herve,
>>
>> I think you are confusing subclasses and classes. There is no
>> contradiction. `is` documentation
>> is very clear:
>>
>> `With one argument, returns all the super-classes of this object's class.`
>
>
> Yes that's indeed very clear. So if "list" is a super-class
> of "data.frame" (as reported by is(data.frame())), then
> is(data.frame(), "list") should be TRUE.
>
> With S4 classes:
>
>   setClass("A")
>   setClass("B", contains="A")
>
>   ## Get all the super-classes of B.
>   is(new("B"))
>   # [1] "B" "A"
>
>   ## Does a B object inherit from A?
>   is(new("B"), "A")
>   # [1] TRUE
>
> Cheers,
> H.
>
>>
>> Note that object class is always `data.frame` here, check:
>>
>>  > class(data.frame())
>> [1] "data.frame"
>>  > is(data.frame(), "data.frame")
>> [1] TRUE
>>
>> Best,
>> Mehmet
>>
>>
>>
>>
>>
>> On 29 Nov 2017 19:13, "Herv? Pag?s" <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>>     Hi,
>>
>>     The unary forms of is() and extends() report that data.frame
>>     extends list, oldClass, and vector:
>>
>>        > is(data.frame())
>>        [1] "data.frame" "list"       "oldClass"   "vector"
>>
>>        > extends("data.frame")
>>        [1] "data.frame" "list"       "oldClass"   "vector"
>>
>>     However, the binary form of is() disagrees:
>>
>>        > is(data.frame(), "list")
>>        [1] FALSE
>>        > is(data.frame(), "oldClass")
>>        [1] FALSE
>>        > is(data.frame(), "vector")
>>        [1] FALSE
>>
>>     while the binary form of extends() agrees:
>>
>>        > extends("data.frame", "list")
>>        [1] TRUE
>>        > extends("data.frame", "oldClass")
>>        [1] TRUE
>>        > extends("data.frame", "vector")
>>        [1] TRUE
>>
>>     Who is right?
>>
>>     Shouldn't 'is(object, class2)' be equivalent
>>     to 'class2 %in% is(object)'? Furthermore, is there
>>     any reason why 'is(object, class2)' is not implemented
>>     as 'class2 %in% is(object)'?
>>
>>     Thanks,
>>     H.
>>
>>     --
>>     Herv? Pag?s
>>
>>     Program in Computational Biology
>>     Division of Public Health Sciences
>>     Fred Hutchinson Canc
>>
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>>
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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] binary form of is() contradicts its unary form
Suzen, Mehmet