reorder [stats] and reorder.factor [lattice]

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

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"DeepS" == Deepayan Sarkar <deepayan@stat.wisc.edu>
    on Mon, 13 Sep 2004 14:54:52 -0500 writes:

"DeepS" == Deepayan Sarkar <deepayan@stat.wisc.edu>
    on Mon, 13 Sep 2004 14:54:52 -0500 writes:

    DeepS> Before it's too late for R 2.0.0, do we have a final decision yet on 
    DeepS> having a reorder method for "factor" in stats?

Since the thread is quite a bit old, (and I have been in vacation back then),
could you summarize what you think about it?

When skimming through the thread I got the impression that, yes,
it was worth to "centralize" such a method in 'stats' rather
than have different slightly incompatible versions in different
other packages.
This is of tangential interest to me as I have been slightly
involved with reorder.dendrogram()

Regards,
Martin