[Rd] Proposed Patch for poly.Rd
Duncan Murdoch
murdoch.duncan at gmail.com
Sun Jul 16 01:27:57 CEST 2017
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:
> >>
> >>>> https://svn.r-project.org/R/trunk/src/library/stats/R/contr.poly.R
> >>
> >>>> 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,
> --> https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17310
> 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
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