From maechler at stat.math.ethz.ch  Wed Mar 21 08:39:01 2007
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Wed, 21 Mar 2007 08:39:01 +0100
Subject: [Rd] wishlist -- Fix for major format.pval limitation (PR#9574)
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>>>>> "Gabor" == Gabor Grothendieck <ggrothendieck at gmail.com>
>>>>>     on Tue, 20 Mar 2007 22:10:27 -0400 writes:

    Gabor> On 3/20/07, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
    >> On 3/20/2007 1:40 PM, Gabor Grothendieck wrote:
    >> > On 3/20/07, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
    >> >> On 3/20/2007 12:44 PM, Gabor Grothendieck wrote:
    >> >> > On 3/20/07, murdoch at stats.uwo.ca <murdoch at stats.uwo.ca> wrote:
    >> >> >> On 3/20/2007 11:19 AM, charles.dupont at vanderbilt.edu wrote:
    >> >> >> > Full_Name: Charles Dupont
    >> >> >> > Version: 2.4.1
    >> >> >> > OS: linux 2.6.18
    >> >> >> > Submission from: (NULL) (160.129.129.136)
    >> >> >> >
    >> >> >> >
    >> >> >> > 'format.pval' has a major limitation in its implementation. For example
    >> >> >> > suppose a person had a vector like 'a' and the error being ?0.001.
    >> >> >> >
    >> >> >> >     > a <- c(0.1, 0.3, 0.4, 0.5, 0.3, 0.0001)
    >> >> >> >     > format.pval(a, eps=0.01)
    >> >> >> >
    >> >> >> > If that person wants to have the 'format.pval' output with 2 digits always
    >> >> >> > showing (like passing nsmall=2 to 'format'). That output would look like
    >> >> >> > this.
    >> >> >> >
    >> >> >> >     [1] "0.10"   "0.30"   "0.40"   "0.50"   "0.30"   "<0.01"
    >> >> >> >
    >> >> >> > That output is currently impossible because format.pval can only
    >> >> >> > produce output like this.
    >> >> >> >
    >> >> >> >     [1] "0.1"    "0.3"    "0.4"    "0.5"    "0.3"    "<0.01"
    >> >> >> >
    >> >> >> >
    >> >> >> > ---------------------------------------------------------------
    >> >> >> > a <- c(0.1, 0.3, 0.4, 0.5, 0.3, 0.0001)
    >> >> >> > format.pval(a, eps=0.01)
    >> >> >>
    >> >> >> But there's a very easy workaround:
    >> >> >>
    >> >> >> format.pval(c(0.12, a), eps=0.01)[-1]
    >> >> >>
    >> >> >> gives you what you want (because the 0.12 forces two decimal place
    >> >> >> display on all values, and then the [-1] removes it).
    >> >> >>
    >> >> >
    >> >> > Clever, but the problem would be that summary.lm, etc. call format.pval so the
    >> >> > user does not have a chance to do that.
    >> >>
    >> >> I don't see how this is relevant.  summary.lm doesn't let you pass a new
    >> >> eps value either.  Adding an "nsmall=2" argument to format.pval wouldn't
    >> >> help with the display in summary.lm.
    >> >>
    >> >> I suppose we could track down every use of format.pval in every function
    >> >> in every package and add nsmall and eps as arguments to each of them,
    >> >> but that's just ridiculous.  People should accept the fact that R
    >> >> doesn't produce publication quality text, it just provides you with ways
    >> >> to produce that yourself.
    >> >>
    >> >> Duncan Murdoch
    >> >>
    >> >
    >> > You are right in terms of my example which was not applicable but I
    >> > think in general that format.pval is used from within other routines rather than
    >> > directly by the user so the user may not have a chance to massage it
    >> > directly.
    >> 
    >> Right, but this means that it is more or less useless to change the
    >> argument list for format.pvals in the way Charles suggested, because all
    >> of the existing uses of it would ignore the new parameters.
    >> 
    >> It would not be so difficult to change the behaviour of format.pvals so
    >> that for example "digits=2" implied the equivalent of "nsmall=2", but I
    >> don't think that's a universally desirable change.
    >> 
    >> The difficulty here is that different people have different tastes for
    >> presentation-quality text.  Not everyone would agree that the version
    >> with trailing zeros is preferable to the one without.  R should be
    >> flexible enough to allow people to customize their displays, but not
    >> necessarily by having every print method flexible enough to satisfy
    >> every user:  sometimes users need to construct their own output formats.
    >> 
    >> Duncan Murdoch

    Gabor> One possibility would be to add args to format.pval whose defaults
    Gabor> can be set through options.  Not beautiful but it would give the user
    Gabor> who really needed it a way to do it.

Yes indeed, I had had the same thought (very early in this
thread).  This doesn't mean that I wouldn't agree with Duncan's
statement above anyway.

Whereas I have strong opinion on *not* allowing options() to
influence too many things [it's entirely contrary to the
principle of functional programming], 
options() have always been used to tweak print()ing; so they
could be used here as well.
As original author of format.pval(), I'm happy to accept patches
--- if they are done well and also patch 
    src/library/base/man/format.pval.Rd and ..../man/options.Rd 

Martin



[Rd] wishlist -- Fix for major format.pval limitation (PR#9574)
Martin Maechler