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 <jcbecke...@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 > jcbec...@bsu.edu > jcbecke...@gmail.com > > Call > Send SMS > Add to Skype > You'll need Skype CreditFree via SkypeI am > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
