Martin Maechler wrote:
>>>>>> "Gabor" == Gabor Grothendieck <[EMAIL PROTECTED]>
>>>>>> on Tue, 20 Mar 2007 22:10:27 -0400 writes:
>
> Gabor> On 3/20/07, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> >> On 3/20/2007 1:40 PM, Gabor Grothendieck wrote:
> >> > On 3/20/07, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> >> >> On 3/20/2007 12:44 PM, Gabor Grothendieck wrote:
> >> >> > On 3/20/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> >> >> >> On 3/20/2007 11:19 AM, [EMAIL PROTECTED] 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
>
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.
--
Charles Dupont Computer System Analyst School of Medicine
Department of Biostatistics Vanderbilt University
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
