It was recently pointed out on the lists that the S-PLUS Trellis suite has a function called reorder.factor that's useful in getting useful ordering of factors for graphs. I happily went ahead and implemented it, but it turns out that R (not S-PLUS) has a generic called reorder (with a method for "dendrogram"). Naturally, this causes R to think I'm defining a method for "factor", and gives a warning during check because of mismatching argument names. Any suggestions as to what I should do? Retaining S compatibility doesn't seem to be an option. I could make a reorder method for "factor" (which sounds like a good option to me), or rename it to something like reorderFactor. Deepayan
Kjetil Brinchmann Halvorsen
2004-Aug-27 17:54 UTC
[Rd] reorder [stats] and reorder.factor [lattice]
Deepayan Sarkar wrote:>It was recently pointed out on the lists that the S-PLUS Trellis suite has >a function called reorder.factor that's useful in getting useful ordering >of factors for graphs. I happily went ahead and implemented it, but it >turns out that R (not S-PLUS) has a generic called reorder (with a method >for "dendrogram"). Naturally, this causes R to think I'm defining a >method for "factor", and gives a warning during check because of >mismatching argument names. > >Any suggestions as to what I should do? Retaining S compatibility doesn't >seem to be an option. I could make a reorder method for "factor" (which >sounds like a good option to me), or rename it to something like >reorderFactor. > > >Make a reorder method for factor, which would be usefull also outside lattice, so could be in stats Kjetil halvorsen>Deepayan > >______________________________________________ >R-devel@stat.math.ethz.ch mailing list >https://stat.ethz.ch/mailman/listinfo/r-devel > > > >
On Fri, 27 Aug 2004, Deepayan Sarkar wrote:> It was recently pointed out on the lists that the S-PLUS Trellis suite has > a function called reorder.factor that's useful in getting useful ordering > of factors for graphs. I happily went ahead and implemented it, but it > turns out that R (not S-PLUS) has a generic called reorder (with a method > for "dendrogram"). Naturally, this causes R to think I'm defining a > method for "factor", and gives a warning during check because of > mismatching argument names. > > Any suggestions as to what I should do? Retaining S compatibility doesn't > seem to be an option. I could make a reorder method for "factor" (which > sounds like a good option to me), or rename it to something like > reorderFactor.I am pretty sure you don't want to copy the Trellis call, which is function(Factor, X, Function = mean, ...) and suggests it dates from the days when S3 lookup could not distingush functions from other objects by context, hence the capitalization. Even then, it is inconsistent with tapply etc which use FUN. reorder.factor <- function(x, X, FUN=mean) looks about right. Another problem though: in Trellis reorder.factor doesn't just reorder the factor, it makes it an ordered factor. I don't really see why, especially as the modelling functions assume that ordered means equally spaced. If this is to be used more generally (as Kjetil Halvorsen suggests) then it should record the scores used to do the ordering in an attribute. -- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
I also have a reorder.factor defined in the gregmisc package. It has a
slighly different behavior.
It allows
- sorting the factor level names via 'mixedsort', which sorts mixed
numeric/character intelligently so that 'Cis 10mg' comes after
'Cis 5mg' and before 'Taxol 10mg'
- reordering by a numeric order
- reordering by named factor labels.
Combining it with the version provided by Deepayan we get:
reorder.factor <- function(x,
order,
X,
FUN,
sort=mixedsort,
make.ordered = is.ordered(x),
... )
{
constructor <- if (make.ordered) ordered else factor
if (!missing(order))
{
if (is.numeric(order))
order = levels(x)[order]
else
order = order
}
else if (!missing(FUN))
order = names(sort(tapply(X, x, FUN, ...)))
else
order = sort(levels(x))
constructor( x, levels=order)
}
Yielding:
> # Create a 4 level example factor
> trt <- factor( sample( c("PLACEBO","300 MG",
"600 MG", "1200 MG"),
+ 100, replace=TRUE ) )> summary(trt)
1200 MG 300 MG 600 MG PLACEBO
18 24 30 28 > # Note that the levels are not in a meaningful order.
>
>
> # Change the order to something useful
> # default "mixedsort" ordering
> trt2 <- reorder(trt)
> summary(trt2)
300 MG 600 MG 1200 MG PLACEBO
24 30 18 28 > # using indexes:
> trt3 <- reorder(trt, c(4,2,3,1))
> summary(trt3)
PLACEBO 300 MG 600 MG 1200 MG
28 24 30 18 > # using label names:
> trt4 <- reorder(trt, c("PLACEBO","300 MG",
"600 MG", "1200 MG") )
> summary(trt4)
PLACEBO 300 MG 600 MG 1200 MG
28 24 30 18 > # using frequency
> trt5 <- reorder(trt, X=as.numeric(trt), FUN=length)
> summary(trt5)
1200 MG 300 MG PLACEBO 600 MG
18 24 28 30 >
>
> # drop out the '300 MG' level
> trt6 <- reorder(trt, c("PLACEBO", "600 MG",
"1200 MG") )
> summary(trt6)
PLACEBO 600 MG 1200 MG NA's
28 30 18 24 >
-Greg
(the 'mixedsort' function is available in the gregmisc package, or on
request)
> -----Original Message-----
> From: r-devel-bounces@stat.math.ethz.ch
> [mailto:r-devel-bounces@stat.math.ethz.ch]On Behalf Of Deepayan Sarkar
> Sent: Friday, August 27, 2004 3:32 PM
> To: Prof Brian Ripley
> Cc: r-devel@stat.math.ethz.ch
> Subject: Re: [Rd] reorder [stats] and reorder.factor [lattice]
>
>
> On Friday 27 August 2004 11:17, Prof Brian Ripley wrote:
> > On Fri, 27 Aug 2004, Deepayan Sarkar wrote:
> > > It was recently pointed out on the lists that the S-PLUS
> Trellis suite
> > > has a function called reorder.factor that's useful in
> getting useful
> > > ordering of factors for graphs. I happily went ahead and
> implemented it,
> > > but it turns out that R (not S-PLUS) has a generic called
> reorder (with a
> > > method for "dendrogram"). Naturally, this causes R to
> think I'm defining
> > > a method for "factor", and gives a warning during check
because of
> > > mismatching argument names.
> > >
> > > Any suggestions as to what I should do? Retaining S
> compatibility doesn't
> > > seem to be an option. I could make a reorder method for
> "factor" (which
> > > sounds like a good option to me), or rename it to something like
> > > reorderFactor.
> >
> > I am pretty sure you don't want to copy the Trellis call, which is
> >
> > function(Factor, X, Function = mean, ...)
> >
> > and suggests it dates from the days when S3 lookup could
> not distingush
> > functions from other objects by context, hence the
> capitalization. Even
> > then, it is inconsistent with tapply etc which use FUN.
> >
> > reorder.factor <- function(x, X, FUN=mean)
> >
> > looks about right. Another problem though: in Trellis
> reorder.factor
> > doesn't just reorder the factor, it makes it an ordered
> factor. I don't
> > really see why, especially as the modelling functions
> assume that ordered
> > means equally spaced. If this is to be used more generally
> (as Kjetil
> > Halvorsen suggests) then it should record the scores used to do the
> > ordering in an attribute.
>
> Well, the ordered factor issue had come up before, and I
> currently define this
> as
>
>
> which is different from the S-PLUS version in 2 ways:
>
> 1. for (unordered) factors, it changes the levels, but keeps
> it a factor
>
> 2. it works for non-factors as well (which is moot if it's
> going to be
> a factor method)
>
>
> Implementation details aside, this seems to me like a good
> candidate for stats
> (although it'll probably be used very little). lattice
> functions (will) have
> an alternative way of determining panel order based on panel
> contents, which
> makes more sense to me in the plotting context.
>
> Deepayan
>
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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