From maechler at stat.math.ethz.ch  Sat Jul 15 17:37:16 2017
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Sat, 15 Jul 2017 17:37:16 +0200
Subject: [Rd] Proposed Patch for poly.Rd
In-Reply-To: <0B38252A-6749-45F4-885E-73702CC32B53@me.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>
Message-ID: <22890.13996.34531.687653@stat.math.ethz.ch>

>>>>> 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)]

Martin



[Rd] Proposed Patch for poly.Rd
Martin Maechler