From henrik.bengtsson at gmail.com  Fri Jan 27 18:46:15 2017
From: henrik.bengtsson at gmail.com (Henrik Bengtsson)
Date: Fri, 27 Jan 2017 09:46:15 -0800
Subject: [Rd] RFC: tapply(*, ..., init.value = NA)
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On Fri, Jan 27, 2017 at 12:34 AM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
>
>     > On Jan 26, 2017 07:50, "William Dunlap via R-devel" <r-devel at r-project.org>
>     > wrote:
>
>     > It would be cool if the default for tapply's init.value could be
>     > FUN(X[0]), so it would be 0 for FUN=sum or FUN=length, TRUE for
>     > FUN=all, -Inf for FUN=max, etc.  But that would take time and would
>     > break code for which FUN did not work on length-0 objects.
>
>     > Bill Dunlap
>     > TIBCO Software
>     > wdunlap tibco.com
>
> I had the same idea (after my first post), so I agree that would
> be nice. One could argue it would take time only if the user is too lazy
> to specify the value,  and we could use
>    tryCatch(FUN(X[0]), error = NA)
> to safeguard against those functions that fail for 0 length arg.
>
> But I think the main reason for _not_ setting such a default is
> back-compatibility.  In my proposal, the new argument would not
> be any change by default and so all current uses of tapply()
> would remain unchanged.
>
>>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>
>>>>>>     on Thu, 26 Jan 2017 07:57:08 -0800 writes:
>
>     > On a related note, the storage mode should try to match ans[[1]] (or
>     > unlist:ed and) when allocating 'ansmat' to avoid coercion and hence a full
>     > copy.
>
> Yes, related indeed; and would fall "in line" with Bill's idea.
> OTOH, it could be implemented independently,
> by something like
>
>    if(missing(init.value))
>      init.value <-
>        if(length(ans)) as.vector(NA, mode=storage.mode(ans[[1]]))
>        else NA

I would probably do something like:

  ans <- unlist(ans, recursive = FALSE, use.names = FALSE)
  if (length(ans)) storage.mode(init.value) <- storage.mode(ans[[1]])
  ansmat <- array(init.value, dim = extent, dimnames = namelist)

instead.  That completely avoids having to use missing() and the value
of 'init.value' will be coerced later if not done upfront.  use.names
= FALSE speeds up unlist().

/Henrik

>
> .............
>
> A colleague proposed to use the shorter argument name 'default'
> instead of 'init.value'  which indeed maybe more natural and
> still not too often used as "non-first" argument in  FUN(.).
>
> Thank you for the constructive feedback!
> Martin
>
>     > On Thu, Jan 26, 2017 at 2:42 AM, Martin Maechler
>     > <maechler at stat.math.ethz.ch> wrote:
>     >> Last week, we've talked here about "xtabs(), factors and NAs",
>     -> https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html
>     >>
>     >> In the mean time, I've spent several hours on the issue
>     >> and also committed changes to R-devel "in two iterations".
>     >>
>     >> In the case there is a *Left* hand side part to xtabs() formula,
>     >> see the help page example using 'esoph',
>     >> it uses  tapply(...,  FUN = sum)   and
>     >> I now think there is a missing feature in tapply() there, which
>     >> I am proposing to change.
>     >>
>     >> Look at a small example:
>     >>
>     >>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]),
>     > N=3)[-c(1,5), ]; xtabs(~., D2)
>     >> , , N = 3
>     >>
>     >> L
>     >> n   A B C D E F
>     >> 1 1 2 0 0 0 0
>     >> 2 0 0 1 2 0 0
>     >> 3 0 0 0 0 2 2
>     >>
>     >>> DN <- D2; DN[1,"N"] <- NA; DN
>     >> n L  N
>     >> 2  1 A NA
>     >> 3  1 B  3
>     >> 4  1 B  3
>     >> 6  2 C  3
>     >> 7  2 D  3
>     >> 8  2 D  3
>     >> 9  3 E  3
>     >> 10 3 E  3
>     >> 11 3 F  3
>     >> 12 3 F  3
>     >>> with(DN, tapply(N, list(n,L), FUN=sum))
>     >> A  B  C  D  E  F
>     >> 1 NA  6 NA NA NA NA
>     >> 2 NA NA  3  6 NA NA
>     >> 3 NA NA NA NA  6  6
>     >>>
>     >>
>     >> and as you can see, the resulting matrix has NAs, all the same
>     >> NA_real_, but semantically of two different kinds:
>     >>
>     >> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
>     >> 2) all other NAs come from the fact that there is no such factor
>     > combination
>     >> *and* from the fact that tapply() uses
>     >>
>     >> array(dim = .., dimnames = ...)
>     >>
>     >> i.e., initializes the array with NAs  (see definition of 'array').
>     >>
>     >> My proposition is the following patch to  tapply(), adding a new
>     >> option 'init.value':
>     >>
>     >> ------------------------------------------------------------
>     > -----------------
>     >>
>     >> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
>     >> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify
>     > = TRUE)
>     >> {
>     >> FUN <- if (!is.null(FUN)) match.fun(FUN)
>     >> if (!is.list(INDEX)) INDEX <- list(INDEX)
>     >> @@ -44,7 +44,7 @@
>     >> index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
>     >> ans <- lapply(X = ans[index], FUN = FUN, ...)
>     >> if (simplify && all(lengths(ans) == 1L)) {
>     >> -       ansmat <- array(dim = extent, dimnames = namelist)
>     >> +       ansmat <- array(init.value, dim = extent, dimnames = namelist)
>     >> ans <- unlist(ans, recursive = FALSE)
>     >> } else {
>     >> ansmat <- array(vector("list", prod(extent)),
>     >>
>     >> ------------------------------------------------------------
>     > -----------------
>     >>
>     >> With that, I can set the initial value to '0' instead of array's
>     >> default of NA :
>     >>
>     >>> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
>     >> A B C D E F
>     >> 1 NA 6 0 0 0 0
>     >> 2  0 0 3 6 0 0
>     >> 3  0 0 0 0 6 6
>     >>>
>     >>
>     >> which now has 0 counts and NA  as is desirable to be used inside
>     >> xtabs().
>     >>
>     >> All fine... and would not be worth a posting to R-devel,
>     >> except for this:
>     >>
>     >> The change will not be 100% back compatible -- by necessity: any new
>     > argument for
>     >> tapply() will make that argument name not available to be
>     >> specified (via '...') for 'FUN'.  The new function would be
>     >>
>     >>> str(tapply)
>     >> function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)
>     >>
>     >> where the '...' are passed FUN(),  and with the new signature,
>     >> 'init.value' then won't be passed to FUN  "anymore" (compared to
>     >> R <= 3.3.x).
>     >>
>     >> For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
>     >> the probability the arg name is used in other functions).
>     >>
>     >>
>     >> Opinions?
>     >>
>     >> Thank you in advance,
>     >> Martin
>     >>
>     >> ______________________________________________
>     >> R-devel at r-project.org mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>
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[Rd] RFC: tapply(*, ..., init.value = NA)
Henrik Bengtsson