Hi Jesse, Can you send me the data *and* *exact* code you used so I can look into this further? I promise to delete the data once I have gotten to the bottom of the problem.
If you can, please do so *off list*. If you can't then it might help to scale the numbers a bit as range of 5 orders of magnitude may be causing some numerical issues with your data. Note this has nothing to do with vegan; cocorresp is a separate package. Re the last question; it is possible and IIRC there is some Matlab code to do some of this in the supplementary materials for the ter braak & schaffers paper. I got some way to implementing this in R but finishing it off went to the back burner and I never get back to it since. All the best, Gavin On Tue, 2013-01-15 at 19:09 -0800, Jesse_B wrote: > Question 1 - It's been a while, so I don't know who will see this, but I am > having the same issue. I have count data from two species matrices (fish > and inverts) and I am trying to run CoCA through cocorresp. Symmetric CoCA > works fine, and is the main thing that I need, but I would like to be able > to switch predictor-response species matrices in a predictive CoCA, to see > if there are differing patterns of top-down/bottom-up concordance. I have > substantial skew in the data, so I have log+1 transformed both sets of data. > I can run crossval on the raw data (not transformed, 99 samples [33 sites > over 3 seasons], 72 fish species, 226 invert species, individual numbers are > in the same ranges, between 0 and 10K for both fish and inverts), but on the > transformed data, I get the "Error in La.svd(x, nu, nv) : error code 1 from > Lapack routine 'dgesdd' " message consistently on the 5th site. I am > comfortable _using_ R and the vegan package in particular, but I am not > experienced in more deep coding, so I don't have a handle on how to turn > LINPACK on. R version 2.15.2, vegan 2.0-4, cocorresp 0.2-0 > > > crossval(fishlog,invertlog) > LOO - Site: 1 - Complete > LOO - Site: 2 - Complete > LOO - Site: 3 - Complete > LOO - Site: 4 - Complete > LOO - Site: 5Error in La.svd(x, nu, nv) : error code 1 from Lapack routine > 'dgesdd' > > Question 2 - Is it possible to run crossval on matricies for a CCA? to make > it a PLS-CCA (as in Schaffers et al. 2008) or am I misunderstanding the > process that they used? > > Thanks in advance! > > Jesse > > > > > -- > View this message in context: > http://r-sig-ecology.471788.n2.nabble.com/Error-in-La-svd-x-nu-nv-error-code-1-from-Lapack-routine-dgesdd-tp7556369p7577802.html > Sent from the r-sig-ecology mailing list archive at Nabble.com. > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology