From maechler at stat.math.ethz.ch  Mon Jul 17 08:57:32 2017
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Mon, 17 Jul 2017 08:57:32 +0200
Subject: [Rd] Proposed Patch for poly.Rd
In-Reply-To: <5b7bfc31-2538-127c-b7d0-9e3b7e839024@gmail.com>
References: <DE3B9ECF-8CE2-460F-AAFC-4B6DFAAE958D@me.com>
 <600dfbc3-cfbc-110f-5ff7-965202c21a88@gmail.com>
 <5DD6CF21-E2D0-4475-8CF9-D05504279499@me.com>
 <3CCCE71C-B4A2-4C9D-A27F-18486AEA4F69@me.com>
 <C44434BD-CA2A-493C-8DBD-ED15CCB4C2B2@me.com>
 <22888.54682.928801.33074@stat.math.ethz.ch>
 <22888.55852.258809.522240@stat.math.ethz.ch>
 <0B38252A-6749-45F4-885E-73702CC32B53@me.com>
 <22890.13996.34531.687653@stat.math.ethz.ch>
 <5b7bfc31-2538-127c-b7d0-9e3b7e839024@gmail.com>
Message-ID: <22892.24540.802634.378981@stat.math.ethz.ch>

>>>>> 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:
    >> >>
    >> >>>> 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

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?

Best,
Martin



[Rd] Proposed Patch for poly.Rd
Martin Maechler