Hi Jesse,
I have most if not all the code from the ter Braak Schaffers paper ported
to R ins some state or other. Steve Juggins sent me the CCA-PLS port IIRC
but I've been distracted with other things and this method is not in
cocorresp (yet! but I've been saying that for years :-( ). We don't have
anything in Vegan that will do CV for you.
It wouldn't be the most efficient of codes but it would be relatively
simple to do CV by hand with Vegan. IIRC the CV for CoCA is leave-one-out,
so you just need to loop over the rows, fit the cca to all the data minus
the ith row and then predict for the ith row and compare with the observed.
I've just gotten back from a few weeks out of the office so I'm going to be
tied up for a wee while clearing the backlog but if you can't get this
working get back in touch and I'll see if I can flesh these ideas out a bit
more in code for you.
All the best
G
On 14 August 2015 at 16:13, Jesse Becker jcbecke...@gmail.com wrote:
A couple of years ago I was doing some Co-Correspondence analysis and asked
if the cross validation method in ter Braak and Shaffers (2004) which is
available in the cocoresp package had been implemented to work on a CCA
output from vegan? I ended up not needing it for that project, but I'm
using the method for another paper. In an effort to put CoCA and CCA on
the same footing in terms of evaluating fit, I'd like to use the cross
validation on CCA. I don't have access to MATLAB, I do have access to R
(and am a user, not a programmer)
So has anyone adapted the MATLAB code to R? Gavin?
Thanks in advance!
Jesse C. Becker, Ph.D.
765.285.8889 office
512.587.4428 cell
jcbecker at bsu.edu
jcbecker42 at gmail.com
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Gavin Simpson, PhD
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