Re: [R] Change in behaviour of sd()

From: Rolf Turner <r.turner_at_auckland.ac.nz>
Date: Wed, 09 Jul 2008 09:01:42 +1200

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''. 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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