I think that as the proponents do not agree, we need to leave this as is.
BTW, R-devel is the place to discuss patched to R, rather than R-help.
On Tue, 21 Jun 2005, Heather Turner wrote:
> Agreed my examples may be trivial and I'm sure there are more efficient ways
> to do the same thing, but I disagree that my examples are against the spirit
> of sweep (). In the first example a vector is swept out from the rows, with
> one value for odd rows and one value for even rows. In the second example an
> array of values is swept out across the third dimension. In the third example
> an array of values is swept out from the full array.
>
> The first example is a natural use of recycling. E.g.
>
> sweep(matrix(1:100, 50, 2), 1, c(1, 1000), "+", give.warning = TRUE)
>
> is a quicker way of writing
>
> sweep(matrix(1:100, 50, 2), 1, rep(c(1, 1000), 25), "+", give.warning = TRUE)
>
> but your code would give a warning in the first case, even though the intent
> and the result are exactly the same as in the second case.
>
> As you say, it is only a warning, that can be ignored. However the warning
> should at least reflect the warning condition used, i.e. warn that the length
> of STATS does not equal the extent of MARGIN, rather warning that STATS does
> not recycle exactly.
>
> Heather
>
>>>> Robin Hankin <[EMAIL PROTECTED]> 06/21/05 02:47pm >>>
> Hi
>
> On Jun 21, 2005, at 02:33 pm, Heather Turner wrote:
>
>> I think the warning condition in Robin's patch is too harsh - the
>> following examples seem reasonable to me, but all produce warnings
>>
>> sweep(array(1:24, dim = c(4,3,2)), 1, 1:2, give.warning = TRUE)
>> sweep(array(1:24, dim = c(4,3,2)), 1, 1:12, give.warning = TRUE)
>> sweep(array(1:24, dim = c(4,3,2)), 1, 1:24, give.warning = TRUE)
>>
>
>
> The examples above do give warnings (as intended) but I think all three
> cases above
> are inimical to the spirit of sweep(): nothing is being "swept" out.
>
> So a warning is appropriate, IMO.
>
> In any case, one can always suppress (or ignore!) a warning if one knows
> what one is doing. YMMV, but if I wanted to do the above operations I
> would
> replace
>
>
> sweep(array(0, dim = c(4,3,2)), c(1,3), 1:12, "+" , give.warning =
> FALSE)
>
> with
>
> aperm(array(1:12,c(4,2,3)),c(1,3,2))
>
>
> best wishes
>
> rksh
>
>
>
>
>
>
>
>> I have written an alternative (given below) which does not give
>> warnings in the above cases, but does warn in the following case
>>
>>> sweep(array(1:24, dim = c(4,3,2)), 1:2, 1:3)
>> , , 1
>>
>> [,1] [,2] [,3]
>> [1,] 0 3 6
>> [2,] 0 3 9
>> [3,] 0 6 9
>> [4,] 3 6 9
>>
>> , , 2
>>
>> [,1] [,2] [,3]
>> [1,] 12 15 18
>> [2,] 12 15 21
>> [3,] 12 18 21
>> [4,] 15 18 21
>>
>> Warning message:
>> STATS does not recycle exactly across MARGIN
>>
>> The code could be easily modified to warn in other cases, e.g. when
>> length of STATS is a divisor of the corresponding array extent (as in
>> the first example above, with length(STATS) = 2).
>>
>> The code also includes Gabor's suggestion.
>>
>> Heather
>>
>> sweep <- function (x, MARGIN, STATS, FUN = "-", warn =
>> getOption("warn"), ...)
>> {
>> FUN <- match.fun(FUN)
>> dims <- dim(x)
>> perm <- c(MARGIN, (1:length(dims))[-MARGIN])
>> if (warn >= 0) {
>> s <- length(STATS)
>> cumDim <- c(1, cumprod(dims[perm]))
>> if (s > max(cumDim))
>> warning("length of STATS greater than length of array",
>> call. = FALSE)
>> else {
>> upper <- min(ifelse(cumDim > s, cumDim, max(cumDim)))
>> lower <- max(ifelse(cumDim < s, cumDim, min(cumDim)))
>> if (any(upper %% s != 0, s %% lower != 0))
>> warning("STATS does not recycle exactly across MARGIN",
>> call. = FALSE)
>> }
>> }
>> FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...)
>> }
>>
>>>>> Gabor Grothendieck <[EMAIL PROTECTED]> 06/21/05 01:25pm >>>
>> \
>> Perhaps the signature should be:
>>
>> sweep(...other args go here..., warn=getOption("warn"))
>>
>> so that the name and value of the argument are consistent with
>> the R warn option.
>>
>> On 6/21/05, Robin Hankin <[EMAIL PROTECTED]> wrote:
>>>
>>> On Jun 20, 2005, at 04:58 pm, Prof Brian Ripley wrote:
>>>
>>>> The issue here is that the equivalent command array(1:5, c(6,6)) (to
>>>> matrix(1:5,6,6)) gives no warning, and sweep uses array().
>>>>
>>>> I am not sure either should: fractional recycling was normally
>>>> allowed
>>>> in S3 (S4 tightened up a bit).
>>>>
>>>> Perhaps someone who thinks sweep() should warn could contribute a
>>>> tested patch?
>>>>
>>>
>>>
>>> OK, modified R code and Rd file below (is this the best way to do
>>> this?)
>>>
>>>
>>>
>>>
>>> "sweep" <-
>>> function (x, MARGIN, STATS, FUN = "-", give.warning = FALSE, ...)
>>> {
>>> FUN <- match.fun(FUN)
>>> dims <- dim(x)
>>> if(give.warning & length(STATS)>1 & any(dims[MARGIN] !=
>>> dim(as.array(STATS)))){
>>> warning("array extents do not recycle exactly")
>>> }
>>> perm <- c(MARGIN, (1:length(dims))[-MARGIN])
>>> FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...)
>>> }
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> \name{sweep}
>>> \alias{sweep}
>>> \title{Sweep out Array Summaries}
>>> \description{
>>> Return an array obtained from an input array by sweeping out a
>>> summary
>>> statistic.
>>> }
>>> \usage{
>>> sweep(x, MARGIN, STATS, FUN="-", give.warning = FALSE, \dots)
>>> }
>>> \arguments{
>>> \item{x}{an array.}
>>> \item{MARGIN}{a vector of indices giving the extents of \code{x}
>>> which correspond to \code{STATS}.}
>>> \item{STATS}{the summary statistic which is to be swept out.}
>>> \item{FUN}{the function to be used to carry out the sweep. In the
>>> case of binary operators such as \code{"/"} etc., the function
>>> name
>>> must be quoted.}
>>> \item{give.warning}{Boolean, with default \code{FALSE} meaning to
>>> give no warning, even if array extents do not match. If
>>> \code{TRUE}, check for the correct dimensions and if a
>>> mismatch is detected, give a suitable warning.}
>>> \item{\dots}{optional arguments to \code{FUN}.}
>>> }
>>> \value{
>>> An array with the same shape as \code{x}, but with the summary
>>> statistics swept out.
>>> }
>>> \note{
>>> If \code{STATS} is of length 1, recycling is carried out with no
>>> warning irrespective of the value of \code{give.warning}.
>>> }
>>>
>>> \references{
>>> Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
>>> \emph{The New S Language}.
>>> Wadsworth \& Brooks/Cole.
>>> }
>>> \seealso{
>>> \code{\link{apply}} on which \code{sweep} used to be based;
>>> \code{\link{scale}} for centering and scaling.
>>> }
>>> \examples{
>>> require(stats) # for median
>>> med.att <- apply(attitude, 2, median)
>>> sweep(data.matrix(attitude), 2, med.att)# subtract the column medians
>>>
>>> a <- array(0, c(2, 3, 4))
>>> b <- matrix(1:8, c(2, 4))
>>> sweep(a, c(1, 3), b, "+", give.warning = TRUE) # no warning:
>>> all(dim(a)[c(1,3)] == dim(b))
>>> sweep(a, c(1, 2), b, "+", give.warning = TRUE) # warning given
>>>
>>> }
>>> \keyword{array}
>>> \keyword{iteration}
>>>
>>>
>>>
>>>
>>> --
>>> Robin Hankin
>>> Uncertainty Analyst
>>> National Oceanography Centre, Southampton
>>> European Way, Southampton SO14 3ZH, UK
>>> tel 023-8059-7743
>>>
>>> ______________________________________________
>>> R-help@stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide!
>>> http://www.R-project.org/posting-guide.html
>>>
>>
>>
> --
> Robin Hankin
> Uncertainty Analyst
> National Oceanography Centre, Southampton
> European Way, Southampton SO14 3ZH, UK
> tel 023-8059-7743
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
Brian D. Ripley, [EMAIL PROTECTED]
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
______________________________________________
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
