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

[Duarte Viana]

Hi Jesse and Gavin,

I remember that post and I think that turning the argument LINPACK of
the function "svd" on solved the problem. I did so by:

1. pasting the code of function svd (that can be found in the source code
of the base package) on the console
2. changing the argument LINPACK=FALSE to LINPACK=TRUE
3. re-assigning the function to the base package with the code:
assignInNamespace("svd", svd, "base")

However I do not know whether this is the best solution. Perhaps Gavin
can find out what the real problem is. I would appreciate if you both
could keep me informed about any progress.

Kind regards,

Duarte



On Wed, Jan 16, 2013 at 11:35 AM, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:
> 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.
>>
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