Re: [Rd] as.list method for by Objects

[Henrik Bengtsson]

On Fri, Feb 2, 2018 at 12:07 AM, Martin Maechler
 wrote:
>> Henrik Bengtsson 
>> on Thu, 1 Feb 2018 10:26:23 -0800 writes:
>
> > On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler
> >  wrote:
> >>> Michael Lawrence 
> >>> 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) == "")
> >>
> >> in your code (I see this so often, shockingly to me ...) but rather use
> >>
> >> if(inherits(obj, ""))
> >>
> >> 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.
>
> Not quite; I think you you did not get the real danger in using
> 'class(.) == *':
> What you say above would only be true if there were only S3 classes!
> Try the following small R snippet
>
> myDate <- setClass("myDate", contains = "Date")
> ## Object of class "myDate"
> ## [1] "2018-02-02"
> (d <- myDate(Sys.Date()))
> class(d) == "Date"  # is FALSE (hence of length 1)
> inherits(d, "Date") # is TRUE
>
> > So, several of these cases will be caught at run-time in a
> > near future.
>
> Maybe.  But all the others are  still wrong, as I show above.

Oh my, thanks for clarifying/emphasizing.  I hope I didn't mislead too
many people.  I've been away from S4 for too long - I like to stay in
the cozy S3 world :)

/Henrik

> Martin
>
> > (*) When _R_CHECK_LENGTH_1_CONDITION_=true becomes the default
> > behavior - hopefully by R 3.5.0.
>
> >>
> >> Martin

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Re: [Rd] as.list method for by Objects

[Martin Maechler]

> Henrik Bengtsson 
> on Thu, 1 Feb 2018 10:26:23 -0800 writes:

> On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler
>  wrote:
>>> Michael Lawrence 
>>> 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) == "")
>> 
>> in your code (I see this so often, shockingly to me ...) but rather use
>> 
>> if(inherits(obj, ""))
>> 
>> 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.

Not quite; I think you you did not get the real danger in using
'class(.) == *':
What you say above would only be true if there were only S3 classes!
Try the following small R snippet

myDate <- setClass("myDate", contains = "Date")
## Object of class "myDate"
## [1] "2018-02-02"
(d <- myDate(Sys.Date()))
class(d) == "Date"  # is FALSE (hence of length 1)
inherits(d, "Date") # is TRUE

> So, several of these cases will be caught at run-time in a
> near future.

Maybe.  But all the others are  still wrong, as I show above.
Martin

> (*) When _R_CHECK_LENGTH_1_CONDITION_=true becomes the default
> behavior - hopefully by R 3.5.0.

>> 
>> Martin

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Re: [Rd] as.list method for by Objects

[Henrik Bengtsson]

On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler
 wrote:
>> Michael Lawrence 
>> 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) == "")
>
> in your code (I see this so often, shockingly to me ...) but rather use
>
>   if(inherits(obj, ""))
>
> 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, Hervé Pagès  
> 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, Hervé Pagès  >>> > 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:
> 

Re: [Rd] as.list method for by Objects

[Martin Maechler]

> Michael Lawrence 
> on Thu, 1 Feb 2018 06:12:20 -0800 writes:

> On Thu, Feb 1, 2018 at 1:21 AM, Martin Maechler 

> wrote:

>> > Michael Lawrence 
>> > on Tue, 30 Jan 2018 10:37:38 -0800 writes:
>> 
>> > I agree that it would make sense for the object to have c("by",
>> "list") as
>> > its class attribute, since the object is known to behave as a list.
>> 
>> Well, but that (list behavior) applies to most non-simple S3
>> classed objects, say "data.frame", say "lm" to start with real basic 
ones.
>> 
>> The later part of the discussion, seems more relevant to me.
>> Adding "list" to the class attribute seems as wrong to me as
>> e.g. adding "double" to "Date" or "POSIXct" (and many more such cases).
>> 
>> 
> There's a distinction though. Date and POSIXct should not really behave as
> double values (an implementation detail), but "by" is expected to behave 
as
> a list (when it is one).

yes, you are right  As I'm "never"(*) using by(), I'm glad
to leave this issue to you.

Martin

---
*) Never  [James Bond, 1983]

> For the present case, we should stay with focusing on  is.list()
>> being true after as.list() .. the same we would do with
>> as.numeric() and is.numeric().
>> 
>> Martin
>> 
>> > However, it would may be too disruptive to make this change at this
>> point.
>> > Hard to predict.
>> 
>> > Michael
>> 
>> > On Mon, Jan 29, 2018 at 5:00 PM, Dario Strbenac <
>> dstr7...@uni.sydney.edu.au>
>> > 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@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>> >>
>> >>
>> 
>> > [[alternative HTML version deleted]]
>> 
>> > __
>> > R-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>> 

> [[alternative HTML version deleted]]

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Re: [Rd] as.list method for by Objects

[Michael Lawrence]

On Thu, Feb 1, 2018 at 1:21 AM, Martin Maechler 
wrote:

> > Michael Lawrence 
> > on Tue, 30 Jan 2018 10:37:38 -0800 writes:
>
> > I agree that it would make sense for the object to have c("by",
> "list") as
> > its class attribute, since the object is known to behave as a list.
>
> Well, but that (list behavior) applies to most non-simple S3
> classed objects, say "data.frame", say "lm" to start with real basic ones.
>
> The later part of the discussion, seems more relevant to me.
> Adding "list" to the class attribute seems as wrong to me as
> e.g. adding "double" to "Date" or "POSIXct" (and many more such cases).
>
>
There's a distinction though. Date and POSIXct should not really behave as
double values (an implementation detail), but "by" is expected to behave as
a list (when it is one).

For the present case, we should stay with focusing on  is.list()
> being true after as.list() .. the same we would do with
> as.numeric() and is.numeric().
>
> Martin
>
> > However, it would may be too disruptive to make this change at this
> point.
> > Hard to predict.
>
> > Michael
>
> > On Mon, Jan 29, 2018 at 5:00 PM, Dario Strbenac <
> dstr7...@uni.sydney.edu.au>
> > 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@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
>
> > [[alternative HTML version deleted]]
>
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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Re: [Rd] as.list method for by Objects

[Martin Maechler]

> Michael Lawrence 
> on Tue, 30 Jan 2018 10:37:38 -0800 writes:

> I agree that it would make sense for the object to have c("by", "list") as
> its class attribute, since the object is known to behave as a list.

Well, but that (list behavior) applies to most non-simple S3
classed objects, say "data.frame", say "lm" to start with real basic ones.

The later part of the discussion, seems more relevant to me.
Adding "list" to the class attribute seems as wrong to me as
e.g. adding "double" to "Date" or "POSIXct" (and many more such cases).

For the present case, we should stay with focusing on  is.list()
being true after as.list() .. the same we would do with
as.numeric() and is.numeric().

Martin

> However, it would may be too disruptive to make this change at this point.
> Hard to predict.

> Michael

> On Mon, Jan 29, 2018 at 5:00 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@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>> 

> [[alternative HTML version deleted]]

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Re: [Rd] as.list method for by Objects

[Martin Maechler]

> Michael Lawrence 
> 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) == "")

in your code (I see this so often, shockingly to me ...) but rather use

  if(inherits(obj, ""))

instead.

Martin



> On Tue, Jan 30, 2018 at 3:47 PM, Hervé Pagès  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, Hervé Pagès >> > 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
>>> 

Re: [Rd] as.list method for by Objects

[Michael Lawrence]

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. 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

On Tue, Jan 30, 2018 at 3:47 PM, Hervé Pagès  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, Hervé Pagès > > 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, Hervé Pagès
>> 
>> >>
>> 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 

Re: [Rd] as.list method for by Objects

[Michael Lawrence]

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  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 > > 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@r-project.org  mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAfqt84V
>> tBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=8nXbM
>> rKus1XsG7MluCRy3sluJKKhMVwOPHtudDpYJ4o=qDnEZOWalov3E9h1daj
>> p8RLURfRz0-nbwH721jFAcEo=
>> > ethz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAf
>> qt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=
>> 8nXbMrKus1XsG7MluCRy3sluJKKhMVwOPHtudDpYJ4o=qDnEZOWalov3E9
>> h1dajp8RLURfRz0-nbwH721jFAcEo=>
>>
>>
>> -- Hervé Pagès
>>
>> Program in Computational Biology
>> 

Re: [Rd] as.list method for by Objects

[Hervé Pagès]

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, Hervé Pagès > 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: hpa...@fredhutch.org 
Phone: (206) 667-5791 
Fax: (206) 667-1319 


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Re: [Rd] as.list method for by Objects

[Gabriel Becker]

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, Hervé Pagès  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@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAfqt84V
>> tBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=8nXbM
>> rKus1XsG7MluCRy3sluJKKhMVwOPHtudDpYJ4o=qDnEZOWalov3E9h1daj
>> p8RLURfRz0-nbwH721jFAcEo=
>>
>>
> --
> 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: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



-- 
Gabriel Becker, PhD
Scientist (Bioinformatics)
Genentech Research

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Re: [Rd] as.list method for by Objects

[Hervé Pagès]

On 01/30/2018 02:24 PM, Hervé Pagès 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")

^^^
oops, I meant as.list.by, sorry...

H.


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: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Rd] as.list method for by Objects

[Hervé Pagès]

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: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Rd] as.list method for by Objects

[Michael Lawrence]

I agree that it would make sense for the object to have c("by", "list") as
its class attribute, since the object is known to behave as a list.
However, it would may be too disruptive to make this change at this point.
Hard to predict.

Michael

On Mon, Jan 29, 2018 at 5:00 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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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