# [Rd] RFC: tapply(*, ..., init.value = NA)

Martin Maechler maechler at stat.math.ethz.ch
Fri Jan 27 18:01:22 CET 2017

```>>>>> Suharto Anggono Suharto Anggono via R-devel <r-devel at r-project.org>
>>>>>     on Fri, 27 Jan 2017 16:36:59 +0000 writes:

> The "no factor combination" case is distinguishable by 'tapply' with simplify=FALSE.
>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), N=3)
>> D2 <- D2[-c(1,5), ]
>> DN <- D2; DN[1,"N"] <- NA
>> with(DN, tapply(N, list(n,L), FUN=sum, simplify=FALSE))
> A    B    C    D    E    F
> 1 NA   6    NULL NULL NULL NULL
> 2 NULL NULL 3    6    NULL NULL
> 3 NULL NULL NULL NULL 6    6

Yes, I know that simplify=FALSE  behaves differently, it returns
a list with dim & dimnames, sometimes also called a "list - matrix"
... and it *can* be used instead, but to be useful needs to be
post processed and that overall is somewhat inefficient and ugly.

> There is an old related discussion starting on https://stat.ethz.ch/pipermail/r-devel/2007-November/047338.html .

Thank you, indeed, for finding that. There Andrew Robinson did
raise the same issue, but his proposed solution was not much
back compatible and I think was primarily dismissed because of that.

Martin

> ----------------------------------
> 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?