[R] scale() and NA values

[Kaspar Pflugshaupt]

Hello,

I've a question concerning the behaviour of the "scale" function in the base
package. I'm using R 1.1.1 on Windows 95.

If I take a matrix with NA values, such as

> tm <- matrix(c(2,1,0,1,0,NA,NA,NA,0), nrow=3)
> tm
     [,1] [,2] [,3]
[1,]    2    1   NA
[2,]    1    0   NA
[3,]    0   NA    0

and scale it, the columns containing NAs come out all NA:

> scale(tm)
     [,1] [,2] [,3]
[1,]    1   NA   NA
[2,]    0   NA   NA
[3,]   -1   NA   NA

If I just center it, this does not happen:

> scale(tm, scale=F)
     [,1] [,2] [,3]
[1,]    1  0.5   NA
[2,]    0 -0.5   NA
[3,]   -1   NA    0

Is this difference in NA handling deliberate?

>From the help text and from looking at the code of "scale.default", I got
the impression that the scaling part of it would filter out NAs:

...
        if (scale) {
            f <- function(v) {
                nas <- is.na(v)
                if (any(is.na(nas)))
                  v <- v[!is.na(nas)]
                sqrt(sum(v^2)/max(1, length(v) - 1))
            }
            x <- sweep(x, 2, apply(x, 2, f), "/")
...


Is the mentioned behaviour thus a bug, or is there a reason for it?

Cheers

Kaspar Pflugshaupt

-- 

Kaspar Pflugshaupt
Geobotanisches Institut
Zuerichbergstr. 38
CH-8044 Zuerich

Tel. ++41 1 632 43 19
Fax  ++41 1 632 12 15

mailto:pflugshaupt at geobot.umnw.ethz.ch
privat:pflugshaupt at mails.ch
http://www.geobot.umnw.ethz.ch

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