[R-sig-eco] cross validation in CoCA and CCA

[Martin Weiser]

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 píše v Pá 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
> >
> > Call
> > Send SMS
> > Add to Skype
> > You'll need Skype CreditFree via SkypeI am
> >
> >         [[alternative HTML version deleted]]
> >
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> 
> 
> 




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