cross validation in CoCA and CCA

Besides, one can use (I hope) GNU Octave (free, libre, opensource) to do
it with the original MatLab code, as Octave is compatible with MatLab.
HTH.
Martin

 Gavin Simpson p??e v P? 28. 03. 2014 v 20:44 -0600:

In short, no. I haven't ported the rough code for LOO CV of CCA or
CCA-PLS models. I think I ported the mean centring and crossval
functions from the Matlab sources, but not the code in the
`example_crossvalCCA.m` file from the supplementary materials on the
CoCA paper in Ecology.

I could take a look and see how easy i will be to add this, but it
doesn't sit well with cocorresp or vegan as the former was designed
really for CoCA and the latter doesn't have the other functionality
needed (which exists in cocorresp) and we've not really implemented CV
for ordination methods.

That said, this is R and it is relatively trivial to write your own
LOO or k-fold CV loop, and you can predict from a CCA model using the
`predict()` method for cca objects available in vegan.

Part of the reason, at least as far as I see things, for not having CV
in the common ordination software (closed or open source) is that
these methods tend not to be seen as purely predictive models, which
is what CV is designed to evaluate.

Don't hold your breath for me getting this in cocorresp, but if you
want to follow up I might be persuaded to take a look and see if what
is already in cocorresp will enable you to follow the code in the
`example_crosvalCCA.m` file to write your own LOO code.

HTH

G

On 28 March 2014 14:57, Jesse Becker <jcbecker42 at gmail.com> wrote:

Hello list,
I am doing a concordance study between riverine environmental conditions,
invertebrate, and fish assemblages.  I am doing a predictive CoCA as part
of the analysis with the cocorresp package.  My question is whether there
is an implementation of the cross-validation procedure in the cocorresp
package that would work on the results of a CCA or RDA, without having to
use MATLAB (which I don't have access to)?  My understanding is that by
doing the cross validation on the CCA (and hopefully RDA, although I've
never seen it done) it allows for a more consistent evaluation of
differences between the two methods.  I haven't seen this as a function in
vegan.

Jari?  Gavin?

Thanks,
Jesse


Jesse C. Becker, Ph.D.
765.285.8889765.285.8889 office
512.587.4428512.587.4428 cell
jcbecker at bsu.edu
jcbecker42 at gmail.com

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