[R-sig-eco] Error in La.svd(x, nu, nv) : error code 1 from Lapack routine 'dgesdd'

[Gavin Simpson]

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
> 
> 
> 
> 
> --
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