[R-sig-eco] Retrieving canonical coefficients and correlation coefficients according to ter Braak using vegan package cca() function

[Jari Oksanen]

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 at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa