[R-sig-eco] Vegan DCCA axis length

[Jari Oksanen]

On 13/01/2009, at 15:30 PM, David Giordano Armanini wrote:

> Hi everyone,
> happy new year.
> I am new to the list so apologise for uncorrect use.
> I am using the Vegan package version 1.16.9 and I am encountering
> problems on obtaining the length of axis of a DCCA/pCCA,
> I have read previous threads in which Gavin Simpson and Jari Oksanen
> states that are not available routines in vegan to retrieve this
> information.
> I am interested in the length of the DCCA/pCCA axis as I would like to
> perform a similar analyses to the one Lancaster et al. 1996 performed
> to measure community persistence in acified stream (Freshwater Biology
> 1996 36, 179–201) and to the similar one performed as well by Woodward
> (Freshwater biology 2002 47 1419-1435).
> Thus, my question is how can I retrieve the standard deviations of
> species turnover in a DCCA/pCCA? I can not use a simple DCA as I need
> to use both conditions (Site) and Constrains (years),
> thanks in advance,
>
I have been involved in this discussion earlier, but here some points:
1. You cannot perform DCCA in vegan, and this is not easily changed.  
As far as I know, there are no other packages to perform this. This is  
due to a deliberate design decisions in the Fortran code for  
decorana(), and a re-design is needed.
2. You can perform pCCA in vegan, and there you have the so-called  
"Hill scaling" that should approximate the "sd scaling". See docs for  
scores.cca for the scaling.
3. I don't think that the determination of the "length of the axes"  
makes much sense.

Best wishes, Jari Oksanen