For combining imputation with PCA, transcan{Design} could be interest.
For imputation, I have been hearing about the mice program.
The documentation for princomp() suggests that a covariance matrix can be
entered via the covmat argument.
David F
r-sig-ecology-boun...@r-project.org wrote on 04/03/2009 10:34:51 AM:
> [image removed]
>
> Re: [R-sig-eco] missing data in PCA
>
> Stéphane Dray
>
> to:
>
> Jason S
>
> 04/03/2009 10:48 AM
>
> Sent by:
>
> r-sig-ecology-boun...@r-project.org
>
> Cc:
>
> r-sig-ecology
>
> ade4 has nipals() which deals with row data.
>
> Cheers.
>
> Jason S wrote:
> > Dear Jari,
> >
> > Thanks for the hints. A package such as mvnmle would be ideal, but
> it provides only the estimate of the covariance matrix, not the raw
> data. However, comments like princomp and pca require the raw data.
> >
> > Do you (or anyone else) know a command to do PCA straight from a
> covariance matrix?
> >
> > best,
> >
> > Jason
> >
> >
> >
> >
> > ________________________________
> > From: Jari Oksanen <jari.oksa...@oulu.fi>
> >
> > Cc: Jari Oksanen <jari.oksa...@oulu.fi>; r-sig-ecology@r-project.org
> > Sent: Friday, April 3, 2009 2:55:20 AM
> > Subject: Re: [R-sig-eco] missing data in PCA
> >
> >
> > On 03/04/2009, at 00:32 AM, Jason S wrote:
> >
> >
> >> Dear all,
> >>
> >> I was wondering if you have good options to deal with missing
> data on a PCA in R. I guess I could simply delete those cases, but I
> think there should be better options in terms of predicting them. Any
hints?
> >>
> >>
> > Howdy,
> >
> > There may be better ways, but they are not easy... Check paragraph
> on missing data in multivariate task view. This lists several
> alternatives of multiple imputation data. About a year ago I tried
> some of them for multivariate analysis, but that was not quite
> straightforward. The problem was summarizing multivariate results.
> Things may have been changed since then, and there may be some
> canned routines.
> >
> > Here is one link to multivariate task view (but you can use a
> mirror close to you):
> >
> > http://cran.r-project.org/web/views/Multivariate.html
> >
> > One thing you should remember: do not replace missing values with
means.
> >
> > Cheers, Jari Oksanen
> >
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-ecology mailing list
> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
> >
> >
>
> --
> Stéphane DRAY (d...@biomserv.univ-lyon1.fr )
> Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
> 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
> Tel: 33 4 72 43 27 57 Fax: 33 4 72 43 13 88
> http://pbil.univ-lyon1.fr/members/dray/
>
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