[Rd] wishlist -- Fix for major format.pval limitation (PR#9574)
Jeffrey Horner
jeff.horner at vanderbilt.edu
Wed Mar 21 15:09:25 CET 2007
Duncan Murdoch wrote:
> On 3/21/2007 3:39 AM, Martin Maechler wrote:
>>>>>>> "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.
>
> I think this is harder than it looks at first. The problem is knowing
> where to stop. If the value of nsmall used by format.pval() when it
> calls format() can be changed, why not other parameters? Why not allow
> the same flexibility for other users of format.default()? What about
> other defaults of format.pval and other format.XXX methods?
What about using attributes for format options? I proposed this for
difftime objects here:
http://tolstoy.newcastle.edu.au/R/e2/devel/07/02/2256.html
Jeff
>
> I'd like to see some thought put into these questions before adding an
> option, because if the option is too specific, it will make it harder to
> make other such changes in the future. On the other hand, if it's too
> general, it will be hard to document and unusable.
>
> Duncan Murdoch
>
>> 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
>
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