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wishlist -- Fix for major format.pval limitation (PR#9574)

11 messages · Gabor Grothendieck, Duncan Murdoch, Hadley Wickham +3 more

Original
Duncan Murdoch
#
On 3/20/2007 11:19 AM, charles.dupont at vanderbilt.edu wrote:
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).

Duncan Murdoch
Gabor Grothendieck
#
On 3/20/07, murdoch at stats.uwo.ca <murdoch at stats.uwo.ca> wrote:
Clever, but the problem would be that summary.lm, etc. call format.pval so the
user does not have a chance to do that.
Duncan Murdoch
#
On 3/20/2007 12:44 PM, Gabor Grothendieck wrote:
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
Gabor Grothendieck
#
On 3/20/07, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
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.
Duncan Murdoch
#
On 3/20/2007 1:40 PM, Gabor Grothendieck wrote:
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
Hadley Wickham
#
On 3/20/07, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
It would be interesting to take a similar approach to grid - return a
table object which could then be tweaked as necessary, rather than
having to build everything up from scratch.  A very big job though!

Hadley
Gabor Grothendieck
#
On 3/20/07, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
One possibility would be to add args to format.pval whose defaults
can be set through options.  Not beautiful but it would give the user
who really needed it a way to do it.
Martin Maechler
# 

        
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

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 3/21/2007 3:39 AM, Martin Maechler wrote:

            

      
      
      
    

        
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?

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

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jeffrey Horner
    

    

      
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Duncan Murdoch wrote:

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

        

  
    
  


  


      

    

    

      
      

        


  

        

      Charles Dupont
    

    

      
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Martin Maechler wrote:

            

      
      
      
    

        
I have included a patch for 'format.pval' in which I have implemented 
what I think of as the optimal solution for the problem.  Which is to 
add a '...' arg to format.pval and pass it to the 'format' function calls.

Patch was created for the r-release branch but will successfully apply 
to the r-devel branch.

Index: src/library/base/R/format.R
===================================================================
--- src/library/base/R/format.R (revision 40867)
+++ src/library/base/R/format.R (working copy)
@@ -43,7 +43,7 @@
  }

  format.pval <- function(pv, digits = max(1, getOption("digits")-2),
-                       eps = .Machine$double.eps, na.form = "NA")
+                       eps = .Machine$double.eps, na.form = "NA", ...)
  {
      ## Format  P values; auxiliary for print.summary.[g]lm(.)

@@ -55,8 +55,8 @@
         ## be smart -- differ for fixp. and expon. display:
         expo <- floor(log10(ifelse(pv > 0, pv, 1e-50)))
         fixp <- expo >= -3 | (expo == -4 & digits>1)
-       if(any( fixp)) rr[ fixp] <- format(pv[ fixp], dig=digits)
-       if(any(!fixp)) rr[!fixp] <- format(pv[!fixp], dig=digits)
+       if(any( fixp)) rr[ fixp] <- format(pv[ fixp], dig=digits, ...)
+       if(any(!fixp)) rr[!fixp] <- format(pv[!fixp], dig=digits, ...)
         r[!is0]<- rr
      }
      if(any(is0)) {
@@ -67,7 +67,7 @@
                 digits <- max(1, nc - 7)
             sep <- if(digits==1 && nc <= 6) "" else " "
         } else sep <- if(digits==1) "" else " "
-       r[is0] <- paste("<", format(eps, digits=digits), sep = sep)
+       r[is0] <- paste("<", format(eps, digits=digits, ...), sep = sep)
      }
      if(has.na) { ## rarely
         rok <- r
Index: src/library/base/man/format.pval.Rd
===================================================================
--- src/library/base/man/format.pval.Rd (revision 40867)
+++ src/library/base/man/format.pval.Rd (working copy)
@@ -6,13 +6,14 @@
  \alias{format.pval}
  \usage{
  format.pval(pv, digits = max(1, getOption("digits") - 2),
-            eps = .Machine$double.eps, na.form = "NA")
+            eps = .Machine$double.eps, na.form = "NA", \dots)
  }
  \arguments{
    \item{pv}{a numeric vector.}
    \item{digits}{how many significant digits are to be used.}
    \item{eps}{a numerical tolerance: see Details.}
    \item{na.form}{character representation of \code{NA}s.}
+  \item{\dots}{arguments passed to the \code{\link{format}} function.}
  }
  \value{
    A character vector.