[R-sig-eco] vegan package: goodness.cca function? (citations needed)

[Jari Oksanen]

On 25/11/2009 16:56, "L Quinn" <lquinn at hotmail.com> wrote:

> 
> Hello,
> 
> I posted this R-help and Ecolog-L before I knew about R-sig-ecology.
> I hope you will forgive the cross-posting, if you subscribe to those lists
> too.
> 
> I deleted a number of species
> from a canonical correspondence analysis (CCA) model after using the
> function goodness.cca in vegan.  In his explanation of the diagnostic
> tools for CCA
> (http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/goodness.cca.html),
> Jari Oksanen states that "It is a common practise to use goodness
> statistics to remove
> species from ordination plots". However, I have not been able to find
> references on this "common practice" in the literature. I may be using
> inappropriate search terms?? However, if anybody can point me towards
> some cite-able references/rules of thumb on this, I would very much
> appreciate it.
> 
Hello,

CanoDraw does so as default (or did when I last used several years ago), and
since people commonly use CanoDraw, they commonly omit "badly fitting"
species. This doesn't mean that they are aware of doing so. I don't know how
well this is documented, but check CanoDraw manual and books about CANOCO.

Cheers, Jari Oksanen

> And yes, I am also aware that Jari goes on to say that deleting species isn't
> always a good idea.
> 
> Thank you!
> 
> Lauren Quinn          
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