Thanks Simon! How irritating/wrong would it be if I opened a new bug to submit my suggested documentation patch? As detailed below, I think the documentation is somewhat confusing (it depends on a highly non-standard definition of "standard deviation" ...)
cheers
Ben Bolker
Simon Urbanek wrote:
> On Mar 12, 2010, at 1:29 PM, Ben Bolker wrote:
>
>> 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.
>>
>
> It has been closed as feature/FAQ with the note:
> "As documented on the help page!"
>
>
>> 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?
>>
>
> Hmm.. there was apparently an error when importing the feature&FAQ box.
> Unfortunately Jitterbug left some duplicate bugs in different categories so
> the import was not as easy as it should be. I'll double check the IDs to see
> if any others are missing -- I ran import for 14219 manually now.
>
> Thanks,
> Simon
>
>
>> [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
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
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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