Hi Jari,

Thank you very much for your quick answer. I was aware of that difference
already though, so I did scale the environmental variables before using
them, and used the square root on the species counts as described in the
paper of ter Braak. I believe I have the correct transformation, as the
coefficients and correlation on the first axis are pretty much comparable.

Cheers
Joris

On Thu, Jun 14, 2012 at 9:09 PM, Jari Oksanen <jari.oksanen@oulu.fi> wrote:

> Joris,
> On 14/06/2012, at 17:39 PM, Joris Meys wrote:
>
> > Hi all,
> >
> >
> > I get results that differ from the table given by ter Braak. I can
> explain
> > the differences in sign (that's normal, as the solution of cca is defined
> > up to the sign), and I can believe there would be small differences as
> > we're talking different ways of estimation, but the canonical
> coefficients
> > for the second axis differ substantially.
> >
> > My question :
> >
> > - Did I use the correct methods to extract what ter Braak calls
> "canonical
> > coefficients" and "correlation coefficients"?
> > - is there a logical explanation for the big difference in some results ?
> >
> I haven't checked that paper, and can't do that for several days. However,
> one essential difference in "canonical" coefficients between Canoco and
> vegan::cca is that Canoco standardizes all constraining variables to unit
> variance whereas vegan uses unstandardized variables. Does it help if you
> use
>
> Model <- cca(hs.spec ~ ., data = scale(hs.ev))
>
> ?
>
> Cheers, Jari Oksanen
> --
> Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
> jari.oksanen@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
>
>
>
>


-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
Joris.Meys@Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

	[[alternative HTML version deleted]]

