[R] Change in behaviour of sd()

[Henrik Bengtsson]

Hi,

FYI, *the* NEWS file containing updates for all R versions is
available at http://cran.r-project.org/ - see the link 'new features
and bug fixes'.  This links to the URL (which I think is rather
stable):

  https://svn.r-project.org/R/trunk/NEWS

The NEWS file also comes with your R installation.

The error message is also there for R v2.7.0 (2008-04-22).  So, if it
would be documented in the NEWS, it should be between R v2.6.0 and R
v2.7.0.  ...and guess what, it is sitting there under "BUG FIXES" for
R v2.7.0:

"   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.)"

(It was a bit hard to search for, because neither "sd", "var", "cov"
is in that chunk of text).

/Henrik

On Tue, Jul 8, 2008 at 2:01 PM, Rolf Turner <r.turner at auckland.ac.nz> 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''.  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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