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Lenth, Russell V

2022-Jun-24 00:45 UTC

[Rd] [External] Re: svd() results should have a class

Duncan et al.,

The real example would be the estimability package, in which there is a generic
function nonest.basis and methods for classes lm, matrix, and qr. I wanted to
add a method for class svd except there is no such class.

I agree BTW that the safe thing to do would be to have the returned object be of
class c("svd", "list").

Best,

Russ

-----Original Message-----
From: Duncan Murdoch <murdoch.duncan at gmail.com> 
Sent: Thursday, June 23, 2022 7:23 PM
To: Lenth, Russell V <russell-lenth at uiowa.edu>; Robert Harlow
<rharlow86 at gmail.com>
Cc: r-devel at r-project.org
Subject: Re: [Rd] [External] Re: svd() results should have a class

On 23/06/2022 8:07 p.m., Lenth, Russell V wrote:> Bob,
> 
> I'm not talking about using svd as a generic method. I am talking 
> about a method FOR svd results, e.g. an S3 method like foo.svd(), for 
> which there already exist other methods, say foo.default and foo.qr. 
> Currently if I wanted to do
> 
>      svdobj <- svd(x)
>      foo(svdobj)
> 
> it would not dispatch correctly because there is no svd class. Instead, it
would be handled by foo.list if it exists, and it is certainly not clear that
foo.list would do the right thing.
I think this would be more convincing if you gave a real example.  You can see
the existing methods for the "qr" and "eigen" classes using

   methods(class = "qr")
   methods(class = "eigen")

When I do it, I think I'm only seeing methods from base packages, and they
are:

   kappa for qr
   solve for qr
   print for eigen

I think the default print method works fine for svd() results. 
kappa.svd would probably make sense, but would need some thought: 
calculating kappa on a matrix and using the help page for kappa to naively
calculate it from the svd() of that matrix give different results:

   > set.seed(123)
   > X <- matrix(rnorm(25), 5,5)
   > kappa(X)
   [1] 90.71283
   > s <- svd(X)
   > s$d[1]/s$d[length(s$d)]
   [1] 62.68048

Duncan Murdoch
> Russ
> 
> Sent from my iPad
> 
> On Jun 23, 2022, at 6:53 PM, Robert Harlow <rharlow86 at gmail.com>
wrote:
> 
> ?
> Don't have a view on whether it makes sense in base R or not, but WRE
section 7.1 may be helpful to you:
https://cran.r-project.org/doc/manuals/R-exts.html#Adding-new-generics.
> 
> It's not uncommon for packages to want to make base methods generic and
the above link provides advice on how to do so.
> 
> Bob
> 
> On Thu, Jun 23, 2022 at 12:07 PM Lenth, Russell V <russell-lenth at
uiowa.edu<mailto:russell-lenth at uiowa.edu>> wrote:
> Dear R-Devel,
> 
> I noticed that if we run base::svd(x), we obtain an object of class
"list". Shouldn't there be an "svd" class, in case
someone (e.g., me) wants to write methods for singular value decompositions?
Note that other matrix-decomposition routines like qr() and eigen() each return
objects having those names.
> 
> Thanks
> 
> Russ Lenth
> Russell-lenth at uiowa.edu<mailto:Russell-lenth at uiowa.edu>
> 
>          [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org<mailto:R-devel at r-project.org> mailing
list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Martin Maechler

2022-Jun-24 08:41 UTC

head link

[Rd] [External] Re: svd() results should have a class

>>>>> Lenth, Russell V 
>>>>>     on Fri, 24 Jun 2022 00:45:21 +0000 writes:
    > Duncan et al.,
    > The real example would be the estimability package, in which there is a
generic function nonest.basis and methods for classes lm, matrix, and qr. I
wanted to add a method for class svd except there is no such class.

    > I agree BTW that the safe thing to do would be to have the returned
object be of class c("svd", "list").

Well.. "safe" is relative here.
Practically *all* S3 classes are internally lists (notable
exceptions: "Date", "PosixCT") and we
never (AFAIR) append "list" to the class vector in such cases.

Martin

    > Best,

    > Russ

    > -----Original Message-----
    > From: Duncan Murdoch <murdoch.duncan at gmail.com> 
    > Sent: Thursday, June 23, 2022 7:23 PM
    > To: Lenth, Russell V <russell-lenth at uiowa.edu>; Robert Harlow
<rharlow86 at gmail.com>
    > Cc: r-devel at r-project.org
    > Subject: Re: [Rd] [External] Re: svd() results should have a class

    > On 23/06/2022 8:07 p.m., Lenth, Russell V wrote:
    >> Bob,
    >> 
    >> I'm not talking about using svd as a generic method. I am
talking
    >> about a method FOR svd results, e.g. an S3 method like foo.svd(),
for
    >> which there already exist other methods, say foo.default and
foo.qr.
    >> Currently if I wanted to do
    >> 
    >> svdobj <- svd(x)
    >> foo(svdobj)
    >> 
    >> it would not dispatch correctly because there is no svd class.
Instead, it would be handled by foo.list if it exists, and it is certainly not
clear that foo.list would do the right thing.

    > I think this would be more convincing if you gave a real example.  You
can see the existing methods for the "qr" and "eigen"
classes using

    > methods(class = "qr")
    > methods(class = "eigen")

    > When I do it, I think I'm only seeing methods from base packages,
and they are:

    > kappa for qr
    > solve for qr
    > print for eigen

    > I think the default print method works fine for svd() results. 
    > kappa.svd would probably make sense, but would need some thought: 
    > calculating kappa on a matrix and using the help page for kappa to
naively calculate it from the svd() of that matrix give different results:

    >> set.seed(123)
    >> X <- matrix(rnorm(25), 5,5)
    >> kappa(X)
    > [1] 90.71283
    >> s <- svd(X)
    >> s$d[1]/s$d[length(s$d)]
    > [1] 62.68048

    > Duncan Murdoch

    >> Russ
    >> 
    >> Sent from my iPad
    >> 
    >> On Jun 23, 2022, at 6:53 PM, Robert Harlow <rharlow86 at
gmail.com> wrote:
    >> 
    >> ?
    >> Don't have a view on whether it makes sense in base R or not,
but WRE section 7.1 may be helpful to you:
https://cran.r-project.org/doc/manuals/R-exts.html#Adding-new-generics.
    >> 
    >> It's not uncommon for packages to want to make base methods
generic and the above link provides advice on how to do so.
    >> 
    >> Bob
    >> 
    >> On Thu, Jun 23, 2022 at 12:07 PM Lenth, Russell V <russell-lenth
at uiowa.edu<mailto:russell-lenth at uiowa.edu>> wrote:
    >> Dear R-Devel,
    >> 
    >> I noticed that if we run base::svd(x), we obtain an object of class
"list". Shouldn't there be an "svd" class, in case
someone (e.g., me) wants to write methods for singular value decompositions?
Note that other matrix-decomposition routines like qr() and eigen() each return
objects having those names.
    >> 
    >> Thanks
    >> 
    >> Russ Lenth
    >> Russell-lenth at uiowa.edu<mailto:Russell-lenth at uiowa.edu>
    >> 
    >> [[alternative HTML version deleted]]
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org<mailto:R-devel at r-project.org>
mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel
    >> 
    >> [[alternative HTML version deleted]]
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

R devel - Jun 2022 - [External] Re: svd() results should have a class

[Rd] [External] Re: svd() results should have a class

[Rd] [External] Re: svd() results should have a class