R devel - Apr 2023 - xyTable(x,y) versus table(x,y) with NAs

Le 25/04/2023 ? 10:24, Viechtbauer, Wolfgang (NP) a
?crit?:
> Hi all,
>
> Posted this many years ago
(https://stat.ethz.ch/pipermail/r-devel/2017-December/075224.html), but either
this slipped under the radar or my feeble mind is unable to understand what
xyTable() is doing here and nobody bothered to correct me. I now stumbled again
across this issue.
>
> x <- c(1, 1, 2, 2,  2, 3)
> y <- c(1, 2, 1, 3, NA, 3)
> table(x, y, useNA="always")
> xyTable(x, y)
>
> Why does xyTable() report that there are NA instances of (2,3)? I could
understand the logic that the NA could be anything, including a 3, so the
$number value for (2,3) is therefore unknown, but then the same should apply so
(2,1), but here $number is 1, so the logic is then inconsistent.
>
> I stared at the xyTable code for a while and I suspect this is coming from
order() using na.last=TRUE by default, but in any case, to me the behavior above
is surprising.
Not really. The variable 'first' in xyTable() is supposed to detect 
positions of first values in repeated pair sequences. Then it is used to 
retained only their indexes in a vector of type 1:n. Finally, by taking 
diff(), a number of repeated pairs is obtained. However, as 'first' will
contain one NA? for your example, the diff() call will produce two NAs 
by taking the difference with precedent and following number. Hence, the 
result.

Here is a slightly modified code ox xyTable to handle NA too.

xyTableNA <- function (x, y = NULL, digits)
{
 ??? x <- xy.coords(x, y, setLab = FALSE)
 ??? y <- signif(x$y, digits = digits)
 ??? x <- signif(x$x, digits = digits)
 ??? n <- length(x)
 ??? number <- if (n > 0) {
 ??????? orderxy <- order(x, y)
 ??????? x <- x[orderxy]
 ??????? y <- y[orderxy]
 ??????? first <- c(TRUE, (x[-1L] != x[-n]) | (y[-1L] != y[-n]))
 ??????? firstNA <- c(TRUE, xor(is.na(x[-1L]), is.na(x[-n])) | 
xor(is.na(y[-1L]), is.na(y[-n])))
 ??????? first[firstNA] <- TRUE
 ??????? first[is.na(first) | isFALSE(first)] <- FALSE
 ??????? x <- x[first]
 ??????? y <- y[first]
 ??????? diff(c((1L:n)[first], n + 1L))
 ??? }
 ??? else integer()
 ??? list(x = x, y = y, number = number)
}

Best,
Serguei.
>
> Best,
> Wolfgang
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

I correct myself. Obviously, the line

first[is.na(first) | isFALSE(first)] <- FALSE

should read

first[is.na(first)] <- FALSE

Serguei.

Le 25/04/2023 ? 11:30, Serguei Sokol a ?crit?:
> Le 25/04/2023 ? 10:24, Viechtbauer, Wolfgang (NP) a ?crit?:
>> Hi all,
>>
>> Posted this many years ago 
>> (https://stat.ethz.ch/pipermail/r-devel/2017-December/075224.html), 
>> but either this slipped under the radar or my feeble mind is unable 
>> to understand what xyTable() is doing here and nobody bothered to 
>> correct me. I now stumbled again across this issue.
>>
>> x <- c(1, 1, 2, 2,? 2, 3)
>> y <- c(1, 2, 1, 3, NA, 3)
>> table(x, y, useNA="always")
>> xyTable(x, y)
>>
>> Why does xyTable() report that there are NA instances of (2,3)? I 
>> could understand the logic that the NA could be anything, including a 
>> 3, so the $number value for (2,3) is therefore unknown, but then the 
>> same should apply so (2,1), but here $number is 1, so the logic is 
>> then inconsistent.
>>
>> I stared at the xyTable code for a while and I suspect this is coming 
>> from order() using na.last=TRUE by default, but in any case, to me 
>> the behavior above is surprising.
> Not really. The variable 'first' in xyTable() is supposed to detect
> positions of first values in repeated pair sequences. Then it is used 
> to retained only their indexes in a vector of type 1:n. Finally, by 
> taking diff(), a number of repeated pairs is obtained. However, as 
> 'first' will contain one NA? for your example, the diff() call will
> produce two NAs by taking the difference with precedent and following 
> number. Hence, the result.
>
> Here is a slightly modified code ox xyTable to handle NA too.
>
> xyTableNA <- function (x, y = NULL, digits)
> {
> ??? x <- xy.coords(x, y, setLab = FALSE)
> ??? y <- signif(x$y, digits = digits)
> ??? x <- signif(x$x, digits = digits)
> ??? n <- length(x)
> ??? number <- if (n > 0) {
> ??????? orderxy <- order(x, y)
> ??????? x <- x[orderxy]
> ??????? y <- y[orderxy]
> ??????? first <- c(TRUE, (x[-1L] != x[-n]) | (y[-1L] != y[-n]))
> ??????? firstNA <- c(TRUE, xor(is.na(x[-1L]), is.na(x[-n])) | 
> xor(is.na(y[-1L]), is.na(y[-n])))
> ??????? first[firstNA] <- TRUE
> ??????? first[is.na(first) | isFALSE(first)] <- FALSE
> ??????? x <- x[first]
> ??????? y <- y[first]
> ??????? diff(c((1L:n)[first], n + 1L))
> ??? }
> ??? else integer()
> ??? list(x = x, y = y, number = number)
> }
>
> Best,
> Serguei.
>
>>
>> Best,
>> Wolfgang
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Serguei Sokol
Ingenieur de recherche INRAE

Cellule Math?matiques
TBI, INSA/INRAE UMR 792, INSA/CNRS UMR 5504
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