Ben Bolker <bolker <at> ufl.edu> writes: [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 ...)