I'm resending this after a week ... I really don't want to nag, but I also would not like to see this sink below the waves.
Is there a preferred protocol for requesting comments without nagging
too much? I would add a comment to 14219 (and was curious to see
whether it was rejected) ... I went to bugzilla, and bug 14219 doesn't
seem to exist any more -- either as open or as closed -- don't know if
it got lost, or thrown away, when the bug system migrated?
cheers
Ben Bolker
[re: behavior of scale() when center=FALSE and scale=TRUE]
> Again, I agree with you that the behavior is not optimal, but it is
> very hard to make changes in R when the behavior is sub-optimal rather
> than actually wrong (by some definition). R-core is very conservative
> about changes that break backward compatibility; I would like it if they
> chose to change the function to use standard deviation rather than
> root-mean-square, but I doubt it will happen (and it would break things
> for any users who are relying on the current definition).
[snip]
> I have attached a patch
> file (and append the information below as well) that changes "standard
> deviation" back to "root mean square" and is much more explicit about
> this issue ... I hope R-core will jump in, critique it, and possibly use
> it in some form to improve (?) the documentation ...
>
> [PS: I have written that the scaling is equivalent to sd() "if and
> only if" centering was done. Technically it would also be equivalent if
> the column already had zero mean ...]
>
===================================================================
--- scale.Rd (revision 51180)
+++ scale.Rd (working copy)
@@ -41,13 +41,18 @@
equal to the number of columns of \code{x}, then each column of
\code{x} is divided by the corresponding value from \code{scale}. If
\code{scale} is \code{TRUE} then scaling is done by dividing the
- (centered) columns of \code{x} by their standard deviations, and if
+ (centered) columns of \code{x} by their root-mean-squares, and if
\code{scale} is \code{FALSE}, no scaling is done.
-
- The standard deviation for a column is obtained by computing the
- square-root of the sum-of-squares of the non-missing values in the
- column divided by the number of non-missing values minus one (whether
- or not centering was done).
+
+ The root-mean-square for a (possibly centered)
+ column is defined as
+ \eqn{\sqrt{\sum(x^2)/(n-1)}}{sqrt(sum(x^2)/(n-1))},
+ where \eqn{x} is a vector of the non-missing values
+ and \eqn{n} is the number of non-missing values.
+ If (and only if) centering was done,
+ this is equivalent to \code{sd(x,na.rm=TRUE)}.
+ (To scale by the standard deviations without centering,
+ use \code{scale(x,center=FALSE,scale=apply(x,2,sd,na.rm=TRUE))}.)
}
\references{
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
(Bump re: suggested update to scale.Rd . Is this under
consideration? I'll stop pestering if it's considered
unacceptable, just don't want it to vanish without a trace ...)
--
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bol...@ufl.edu / people.biology.ufl.edu/bolker
GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
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