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 <hpa...@fredhutch.org
<mailto:hpa...@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, Hervé Pagès
<hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>
<mailto:hpa...@fredhutch.org <mailto:hpa...@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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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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--
Gabriel Becker, PhD
Scientist (Bioinformatics)
Genentech Research
--
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 <mailto:hpa...@fredhutch.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
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