From murdoch at stats.uwo.ca  Tue Mar 20 19:26:26 2007
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 20 Mar 2007 14:26:26 -0400
Subject: [Rd] wishlist -- Fix for major format.pval limitation (PR#9574)
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Message-ID: <46002752.3070704@stats.uwo.ca>

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



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