Proposed Patch for poly.Rd
On 17/07/2017 2:57 AM, Martin Maechler wrote:
Duncan Murdoch <murdoch.duncan at gmail.com>
on Sat, 15 Jul 2017 19:27:57 -0400 writes:
> On 15/07/2017 11:37 AM, Martin Maechler wrote:
>>>>>>> Marc Schwartz <marc_schwartz at me.com>
>>>>>>> on Fri, 14 Jul 2017 11:01:03 -0500 writes:
>>
>> >> On Jul 14, 2017, at 9:50 AM, Martin Maechler
>> >> <maechler at stat.math.ethz.ch> wrote:
>> >>
>> >>>>>>> Martin Maechler <maechler at stat.math.ethz.ch> on Fri,
>> >>>>>>> 14 Jul 2017 16:30:50 +0200 writes:
>> >>
>> >>>>>>> Marc Schwartz <marc_schwartz at me.com> on Fri, 14 Jul
>> >>>>>>> 2017 06:57:26 -0500 writes:
>> >>
>> >>>>> On Jul 13, 2017, at 5:07 PM, Marc Schwartz
>> >>>>> <marc_schwartz at me.com> wrote:
>> >>>>>
>> >>>>>
>>>>>>> On Jul 13, 2017, at 3:37 PM, Marc Schwartz
>> >>>>> <marc_schwartz at me.com> wrote:
>>>>>>>
>>>>>>>
>> >>>>>>> On Jul 13, 2017, at 3:22 PM, Duncan Murdoch
>> >>>>>>> <murdoch.duncan at gmail.com> wrote:
>> >>>>>>>
>> >>>>>>> On 13/07/2017 4:08 PM, Marc Schwartz wrote:
>> >>>>>>>> Hi All,
>> >>>>>>>>
>> >>>>>>>> As per the discussion today on R-Help:
>> >>>>>>>>
>> >>>>>>>> https://stat.ethz.ch/pipermail/r-help/2017-July/448132.html
>> >>>>>>>>
>> >>>>>>>> I am attaching a proposed patch for poly.Rd to
>> >>>>>>>> provide clarifying wording relative to naming the
>> >>>>>>>> 'degree' argument explicitly, in the case where the
>> >>>>>>>> 'x' argument is a matrix, rather than a vector.
>> >>>>>>>>
>> >>>>>>>> This is based upon the svn trunk version of
>> >>>>>>>> poly.Rd.
>> >>>>>>>
>> >>>>>>> I don't think this is the right fix. The use of the
>> >>>>>>> unnamed 2nd arg as degree happens whether the first
>> >>>>>>> arg is a matrix or not.
>> >>>>>>>
>> >>>>>>> I didn't read the whole thread in detail, but it
>> >>>>>>> appears there's a bug somewhere, in the report or in
>> >>>>>>> the poly() code or in the plsr() code. That bug
>> >>>>>>> should be reported on the bug list if it turns out
>> >>>>>>> to be in base R, and to the package maintainer if it
>> >>>>>>> is in plsr().
>> >>>>>>>
>> >>>>>>> Duncan Murdoch
>>>>>>>
>>>>>>>
>>>>>>> Duncan,
>>>>>>>
>>>>>>> Thanks for your reply. You only really need to read that
>> >>>>>>> last post in the thread linked to above.
>>>>>>>
>>>>>>> I won't deny the possibility of a bug in poly(), relative
>> >>>>>>> to the handling of 'x' as a matrix. The behavior
>> >>>>>>> occurs in the poly() function in a pure stand alone
>> >>>>>>> fashion, without the need for plsr():
>>>>>>>
>>>>>>> x1 <- runif(20)
>>>>>>> x2 <- runif(20)
>>>>>>> mx <- cbind(x1, x2)
>>>>>>>
>> >>>>>
>> >>>>> <snip>
>> >>>>>
>> >>>>> Duncan,
>> >>>>>
>> >>>>> Tracing through the code for poly() using debug once
>> >>>>> with:
>> >>>>>
>> >>>>> poly(mx, 2)
>> >>>>>
>> >>>>> and then with:
>> >>>>>
>> >>>>> poly(mx, degree = 2)
>> >>>>>
>> >>>>> there is a difference in the transformation of 'mx'
>> >>>>> internally by the use of:
>> >>>>>
>> >>>>> if (is.matrix(x)) { m <-
>> >>>>> unclass(as.data.frame(cbind(x, ...)))
>> >>>>> return(do.call(polym, c(m, degree = degree, raw = raw,
>> >>>>> list(coefs = coefs)))) }
>> >>>>>
>> >>>>>
>> >>>>> In the first case, 'mx' ends up being transformed to:
>> >>>>>
>> >>>>> Browse[2]> m $x1 [1] 0.99056941 0.13953093 0.38965567
>> >>>>> 0.35353514 0.90838486 0.97552474 [7] 0.01135743
>> >>>>> 0.06537047 0.56207834 0.50554056 0.96653391 0.69533973
>> >>>>> [13] 0.31333549 0.97488211 0.54952630 0.71747157
>> >>>>> 0.31164777 0.81694822 [19] 0.58641410 0.08858699
>> >>>>>
>> >>>>> $x2 [1] 0.6628658 0.9221436 0.3162418 0.8494452
>> >>>>> 0.4665010 0.3403719 [7] 0.4040692 0.4916650 0.9091161
>> >>>>> 0.2956006 0.3454689 0.3331070 [13] 0.8788974 0.5614636
>> >>>>> 0.7794396 0.2304009 0.6566537 0.6875646 [19] 0.5110733
>> >>>>> 0.4122336
>> >>>>>
>> >>>>> $V3 [1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
>> >>>>>
>> >>>>> attr(,"row.names") [1] 1 2 3 4 5 6 7 8 9 10 11 12 13
>> >>>>> 14 15 16 17 18 19 20
>> >>>>>
>> >>>>> Thus, when do.call() is used, m$V3 is passed as the
>> >>>>> 'x' argument on the third iteration, essentially
>> >>>>> resulting in:
>> >>>>>
>>>>>>> polym(rep(2, 20), degree = 2) Error in poly(dots[[1L]],
>> >>>>> degree, raw = raw, simple = raw && nd > 1) : 'degree'
>> >>>>> must be less than number of unique points
>> >>>>>
>> >>>>>
>> >>>>> Note also that in this case, 'dots', which is the
>> >>>>> result of using list(...) on the initial call, is:
>> >>>>>
>> >>>>> Browse[2]> dots [[1]] [1] 2
>> >>>>>
>> >>>>>
>> >>>>> In the second case:
>> >>>>>
>> >>>>> Browse[2]> m $x1 [1] 0.99056941 0.13953093 0.38965567
>> >>>>> 0.35353514 0.90838486 0.97552474 [7] 0.01135743
>> >>>>> 0.06537047 0.56207834 0.50554056 0.96653391 0.69533973
>> >>>>> [13] 0.31333549 0.97488211 0.54952630 0.71747157
>> >>>>> 0.31164777 0.81694822 [19] 0.58641410 0.08858699
>> >>>>>
>> >>>>> $x2 [1] 0.6628658 0.9221436 0.3162418 0.8494452
>> >>>>> 0.4665010 0.3403719 [7] 0.4040692 0.4916650 0.9091161
>> >>>>> 0.2956006 0.3454689 0.3331070 [13] 0.8788974 0.5614636
>> >>>>> 0.7794396 0.2304009 0.6566537 0.6875646 [19] 0.5110733
>> >>>>> 0.4122336
>> >>>>>
>> >>>>> attr(,"row.names") [1] 1 2 3 4 5 6 7 8 9 10 11 12 13
>> >>>>> 14 15 16 17 18 19 20
>> >>>>>
>> >>>>>
>> >>>>> So, there is no m$V3.
>> >>>>>
>> >>>>> Note also that 'dots' ends up being:
>> >>>>>
>> >>>>> Browse[2]> dots list()
>> >>>>>
>> >>>>>
>> >>>>> In both cases, 'degree' is indeed 2, but the result of
>> >>>>> 'list(...)' on the initial function call is quite
>> >>>>> different.
>> >>>>>
>> >>>>> So, I may be hypo-caffeinated, but if there is a bug
>> >>>>> here, it may be due to the way in which cbind() is
>> >>>>> being called in the code above, where the three dots
>> >>>>> are being used?
>> >>>>>
>> >>>>> I can replicate the presumably correct behavior by
>> >>>>> using:
>> >>>>>
>> >>>>> m <- unclass(as.data.frame(cbind(x)))
>> >>>>>
>> >>>>> instead of:
>> >>>>>
>> >>>>> m <- unclass(as.data.frame(cbind(x, ...)))
>> >>>>>
>> >>>>> But I am not sure if removing the three dots in the
>> >>>>> cbind() call may have other unintended consequences.
>> >>>>>
>> >>>>> Regards,
>> >>>>>
>> >>>>> Marc
>> >>
>> >>
>> >>>> Duncan,
>> >>
>> >>>> Some additional information here. Reviewing the source
>> >>>> code for the function in SVN:
>> >>
>> >>
>> >>>> there is a relevant comment in the code:
>> >>
>> >>>> if(is.matrix(x)) { ## FIXME: fails when combined with
>> >>>> 'unnamed degree' above m <-
>> >>>> unclass(as.data.frame(cbind(x, ...)))
>> >>>> return(do.call(polym, c(m, degree = degree, raw = raw,
>> >>>> list(coefs=coefs)))) }
>> >>
>> >>
>> >>>> A version review would suggest that the above comment
>> >>>> was added to the code back in 2015.
>> >>
>> >>> Yes, by me, possibly here :
>> >>
>> >>> $ svn log -v -c68727
>> >>> ------------------------------------------------------------------------
>> >>> r68727 | maechler | 2015-07-23 16:14:59 +0200 (Thu, 23
>> >>> Jul 2015) | 1 line Changed paths: M /trunk/doc/NEWS.Rd M
>> >>> /trunk/src/library/stats/R/contr.poly.R M
>> >>> /trunk/src/library/stats/man/poly.Rd M
>> >>> /trunk/tests/Examples/stats-Ex.Rout.save M
>> >>> /trunk/tests/reg-tests-1c.R
>> >>
>> >>> poly(), polym() now work better notably for prediction
>> >>> ------------------------------------------------------------------------
>> >>> $ svn-diffB -c68727 doc/NEWS.Rd Index: doc/NEWS.Rd
>> >>> ===================================================================
>> >>> 126a127,133
>> >>>>
>> >>>> \item \code{polym()} gains a \code{coefs = NULL}
>> >>>> argument and returns class \code{"poly"} just like
>> >>>> \code{poly()} which gets a new \code{simple=FALSE}
>> >>>> option. They now lead to correct \code{predict()}ions,
>> >>>> e.g., on subsets of the original data. %% see
>> >>>> https://stat.ethz.ch/pipermail/r-devel/2015-July/071532.html
>> >>
>> >>
>> >>>> So it would appear that the behavior being discussed
>> >>>> here is known.
>> >>
>> >>> Indeed! I remember to have spent quite a few hours with
>> >>> the code and its different uses before committing that
>> >>> patch.
>> >>
>> >>>> I am still confused by the need for the '...' in the
>> >>>> call to cbind(), which as far as I can tell, has been
>> >>>> in the code at least back to 2003, when the poly() code
>> >>>> was split from base.
>> >>
>> >>>> I am not sure why one would want to pass on other '...'
>> >>>> arguments to cbind(), but I am presumably missing
>> >>>> something here.
>> >>
>> >>> Yes, I think passing the '...' is important there...
>> >>> OTOH, I'm almost sure that I wrote the 'FIXME' because I
>> >>> thought one should be able to do things better. So, I'm
>> >>> happy to e-talk to you about how to get rid of the FIXME
>> >>> and still remain back-compatible: Notably with the
>> >>> paragraph in ?poly |> Details:
>> >>> |>
>> >>> |> Although formally ?degree? should be named (as it
>> >>> follows ?...?), |> an unnamed second argument of length
>> >>> 1 will be interpreted as the |> degree, such that
>> >>> ?poly(x, 3)? can be used in formulas.
>> >>
>> >> As a matter of fact, a patch seems very simple, and I am
>> >> testing it now.
>> >>
>> >> Won't have much more time today, but will return "on this
>> >> channel" later, maybe tomorrow.
>> >>
>> >> Martin
>>
>>
>> > Martin,
>> > Thanks for taking the time to look at this!
>>
>> > Marc
>>
>> Duncan had in the mean time filed a bug report about this,
>> but I had fixed the issue even before seeing the PR.
>> [currently fixed in R-devel only (svn r 72919)]
> I wrote to you the next day, when Marc pointed out the FIXME comment.
> Did you not receive my message?
> Duncan Murdoch
I'm sorry Duncan, there must have been messages crossing each other, possibly delayed on this end, where some (including me) are using a new spam/virus filtering service. Yes, I saw that too.. but also quite a bit *after* having replied on R-devel that I was the author of the FIXME and that I was going to look into the issue... ... and then I did look into the issue instead of checking my (almost always much too many) e-mails. But there's no problem about this, right? I'm sorry if I gave the impression in some way. It's good to have a bug report that we can quickly close isn't it?
No, there's no problem. I was just concerned because it sounded as though you hadn't received it; if messages were getting lost, that would be a problem. Duncan Murdoch