Hello! I tried on some simulated trees last night and they weren't working, but after your message I started a fresh R session and now solve() works fine for both my ultrametric tree, and my simulated trees. No idea what happened there, but thanks!
Unfortunately, I still am getting almost all negative eigenvalues for the decomposition of the distance matrix, which doesn't make sense to me. I was under the impression that the distance matrix from an ultrametric tree should be Euclidean. Further, I can confirm that the distance matrix is supposed to be euclidean by using the is.euclid() function from ade4 [is.euclid(as.dist(D)) returns "TRUE"], which means I have no idea why eigen(D) is giving me negative eigenvalues... Any thoughts? --Jon On Tue, Sep 27, 2011 at 12:23 AM, Emmanuel Paradis <emmanuel.para...@ird.fr>wrote: > Hi John, > > I tried with a couple of simulated trees (ultrametric or not) and got no > error. Have you tried using the 'tol' argument of solve()? > > Emmanuel > -----Original Message----- > From: Jonathan Mitchell <mitchel...@uchicago.edu> > Sender: r-sig-phylo-boun...@r-project.org > Date: Mon, 26 Sep 2011 17:42:49 > To: <r-sig-phylo@r-project.org> > Reply-To: jonsmit...@gmail.com > Subject: [R-sig-phylo] Negative Eigenvalues from Phylo Distance Matrix > > Hello all, > > I've run into a problem trying to find the eigen vectors for a phylogenetic > distance matrix. Namely, the transposed vector matrix crossed with the > matrix itself is singular. Also, the eigenvalues for the distance matrix > proper are almost all negative, which I don't understand whatsoever. > > #Given a tree with branch lengths (in my case, it's ultrametric) > D <- cophenetic(tree) > eD <- eigen(D, symmetric=TRUE)$vectors #note that all elements except the > first in eD$values are negative for me > inv <- solve(t(eD)%*%eD) #this is what I really want, the inverse of the > transposed matrix of vectors multiplied by itself > > Error in solve.default(t(eD) %*% eD) : > system is computationally singular: reciprocal condition number = > 2.46807e-29 > > Any help would be greatly appreciated! > > -- Jon > > _____ > > Jonathan S. Mitchell > http://home.uchicago.edu/~mitchelljs/ > > PhD Student > Committee on Evolutionary Biology > The University of Chicago > 1025 57th Str, Culver Hall 402 > Chicago, IL 60637 > > Geology Department > The Field Museum of Natural History > 1400 S. Lake Shore Dr. > Chicago, IL 60605 > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
