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/ > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]]
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