[Rd] A bug in princomp(), perhaps?
Ravi Varadhan
ravi.varadhan at jhu.edu
Tue Jun 3 21:20:26 CEST 2014
Perhaps, adding Gavin's work around for a dataframe with missing values might also be useful to the documentation:
princomp(na.omit(x))
Thanks,
Ravi
-----Original Message-----
From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Ben Bolker
Sent: Monday, June 02, 2014 8:07 PM
To: r-devel at stat.math.ethz.ch
Subject: Re: [Rd] A bug in princomp(), perhaps?
Ben Bolker <bbolker <at> gmail.com> writes:
>
> FWIW this seems to be a FAQ:
>
> https://stat.ethz.ch/pipermail/r-devel/2003-July/027018.html
>
> http://thr3ads.net/r-devel/2013/01/
> 2171832-Re-na.omit-option-in-prcomp-formula-interface-only
>
> http://r.789695.n4.nabble.com/
> na-omit-option-in-prcomp-formula-interface-only-td4373533.html
>
> And two StackOverflow questions (the latter's a bit tangential):
>
> http://stackoverflow.com/questions/12078291/
> r-function-prcomp-fails-with-nas-values-even-though-nas-are-allowed
>
> http://stackoverflow.com/questions/23421438/
> what-was-wrong-with-running-princomp-in-r/23446938#23446938
>
> (Sorry for broken URLs and random assortment of mailing list
> aggregators.)
>
> I appreciate Gavin's points that implementing this stuff for
> princomp.default is difficult/problematic, but I second Ravi's request
> for a little more clarification in the help text; it's quite easy to
> miss the fact that 'na.action' is defined for princomp.formula but not
> for princomp.default. Perhaps just "Note that setting na.action works
> for princomp.formula, but not for princomp.default" (under the
> "na.action" argument description).
Putting my effort where my mouth is: I wonder if there is any chance that this patch against the current SVN would be accepted ... ??
Index: princomp.Rd
===================================================================
--- princomp.Rd (revision 65832)
+++ princomp.Rd (working copy)
@@ -37,7 +37,8 @@
when the data contain \code{NA}s. The default is set by
the \code{na.action} setting of \code{\link{options}}, and is
\code{\link{na.fail}} if that is unset. The \sQuote{factory-fresh}
- default is \code{\link{na.omit}}.}
+ default is \code{\link{na.omit}}. (This argument applies \emph{only}
+ to the formula method.)}
\item{x}{a numeric matrix or data frame which provides the data for the
principal components analysis.}
\item{cor}{a logical value indicating whether the calculation should
Index: prcomp.Rd
===================================================================
--- prcomp.Rd (revision 65832)
+++ prcomp.Rd (working copy)
@@ -40,7 +40,8 @@
when the data contain \code{NA}s. The default is set by
the \code{na.action} setting of \code{\link{options}}, and is
\code{\link{na.fail}} if that is unset. The \sQuote{factory-fresh}
- default is \code{\link{na.omit}}.}
+ default is \code{\link{na.omit}}. (This argument applies \emph{only}
+ to the formula method.)}
\item{\dots}{arguments passed to or from other methods. If \code{x} is
a formula one might specify \code{scale.} or \code{tol}.}
\item{x}{a numeric or complex matrix (or data frame) which provides
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