You can build the variance matrix you want "manually" with cov(x, use="pairwise"). You can supply a variance matrix to princomp with princomp(covmat=outputOfCov). See their manual pages for details.
Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf > Of Dimitri Liakhovitski > Sent: Wednesday, March 20, 2013 4:17 PM > To: Bert Gunter > Cc: r-help > Subject: Re: [R] Dealing with missing values in princomp (package "psych") > > Yes, Bert, you are right and I do know I might run into a non-positive > definite intercorrelation matrix. > But if I do, then I can go back to those for whom I am doing the analysis > and tell them that. Not before. > This sad truth being said - can I do it directly in the function, without > building a intercorrelation matrix manually? > Thank you! > Dimitri > > On Wed, Mar 20, 2013 at 7:04 PM, Bert Gunter <gunter.ber...@gene.com> wrote: > > > Well, you can do this, but there's no guarantee that the resulting > > correlation matrix will be positive definite. And what would principle > > components based on this mean even if it is positive definite? > > > > -- Bert > > > > On Wed, Mar 20, 2013 at 3:14 PM, Dimitri Liakhovitski < > > dimitri.liakhovit...@gmail.com> wrote: > > > >> Hello! > >> I am running principle components analysis using princomp function in > >> pacakge psych. > >> > >> mypc <- princomp(mydataforpc, cor=TRUE) > >> > >> Question: I'd like to use pairwise deletion of missing cases when > >> correlations are calculated. I.e., I'd like to have a correlation between > >> any 2 variables to be based on all cases that have valid values on both > >> variables. > >> > >> What should my na.action be in this case? > >> > >> Thank you very much! > >> -- > >> Dimitri Liakhovitski > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting- > guide.html> > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > > > > > -- > > > > Bert Gunter > > Genentech Nonclinical Biostatistics > > > > Internal Contact Info: > > Phone: 467-7374 > > Website: > > > > http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb- > biostatistics/pdb-ncb-home.htm > > > > > > > > -- > Dimitri Liakhovitski > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
