[R-sig-eco] order of explanatory variables in vegan CCA

[Gavin Simpson]

Hi Matt,

Would you mind sending me the data *off list* so I can see if I can
reproduce. The failure is within a basic part of the R stack (Lapack
matrix algebra code supplied with R) so points to something with the
data and perhaps your matrix (or a subsidiary matrix computed during the
CCA fitting) is close to being degenerate in some way and that when
re-ordered it is slightly less degenerate. [I'm using the word
degenerate loosely here).

I promise to delete the data once I've reproduced the problem.

G

On Wed, 2011-12-21 at 14:22 -0800, Gregory, Matthew wrote:
> Hi all,
> 
> We run vegan CCA as part of an automated process.  Our typical use case is to read in species and environment matrices (from CSV files) and subset the environmental matrix with a vector of field names ('vars'), e.g. 
> 
>   spp <- read.csv(spp_file, row.names = id_field)
>   env <- read.csv(env_file, row.names = id_field)
>   env <- env[,vars]
>   cca_obj <- cca(spp, env)
> 
> Today, for the first time, we received the following error:
> 
>   Error in La.svd(x, nu, nv) : error code 1 from Lapack routine 'dgesdd'
> 
> which from googling implies that the SVD did not converge.  If I reorder the 'vars' list and rerun, I can have it run to completion.  I am completely naïve with ordination modeling, but is there any reason why the order of environmental variables would matter to CCA?  I would have thought this wouldn't matter.
> 
> Thanks for any pointers.
> 
> matt
> 
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