On 08/07/2008 5:01 PM, Rolf Turner wrote:
On 8/07/2008, at 7:38 PM, Fiona Johnson wrote:
Hi
I have just upgraded from R2.6.0 to R2.7.1 (running on Windows) and
a part
of my code that previously ran ok now gives an error. The following
is a
simple example to demonstrate my problem.
a <- array(c(1,2,3,4,5,6,rep(NA,6)),dim=c(6,2))
apply(a,2,sd,na.rm=T)
In R2.6.0 this gives (which is what I would like)
[1] 1.870829 NA
In R2.7.1 it gives the following error
"Error in var(x, na.rm = na.rm) : no complete element pairs"
As my columns are always either all NA or all numbers, I could get
around it
by replacing the NA's with 0's but if someone could shed some light
on why
the behaviour has changed in the new version or a better work
around it
would be much appreciated. I want to keep the columns of NA's because
ultimately I am plotting the results with contour and the NA's
refer to grid
cells not on land where I don't want to have contours.
I just scanned through the release announcements (from Peter
Dalgaard) about new
versions of R (R home page --> What's new? --> Archive of important
announcements)
and found nothing about new behaviour for sd/var/cov. So I cannot
contribute
to enlightenment about ``why''.
This is the relevant but not so obvious NEWS entry:
o co[rv](use = "complete.obs") now always gives an error if there
are no complete cases: they used to give NA if
method = "pearson" but an error for the other two methods. (Note
that this is pretty arbitrary, but zero-length vectors always
give an error so it is at least consistent.)
cor(use="pair") used to give diagonal 1 even if the variable
was completely missing for the rank methods but NA for the
Pearson method: it now gives NA in all cases.
(sd calls var, which calls cov internally.)
Duncan Murdoch
>
The following function might provide
a suitable
workaround:
my.sd <- function (x, na.rm = FALSE)
{
if (is.matrix(x))
apply(x, 2, my.sd, na.rm = na.rm)
else if (is.vector(x)) {
if(na.rm) x <- x[!is.na(x)]
if(length(x) == 0) return(NA)
sqrt(var(x, na.rm = na.rm))
}
else if (is.data.frame(x))
sapply(x, my.sd, na.rm = na.rm)
else {
x <- as.vector(x)
my.sd(x,na.rm=na.rm)
}
}
It seems to work on your toy example at least. Note that my.sd
(numeric(0)) returns NA,
but my.sd(NULL) throws an error.
cheers,
Rolf Turner
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