[R-sig-eco] passive projection of species richness

[Gavin Simpson]

On Fri, 2011-04-29 at 11:06 +0200, Zoltan Botta-Dukat wrote:
> Dear All,
> 
> Can I passively project species richness (or any variables not included 
> in the analysis)  into RDA plot made in vegan? I know that there is such 
> option in CanoDraw, but I couldn't find it in R.
> 
> Thanks
> 
> Zoltan

Zoltan,

I wouldn't really call this passively projecting, if only for the reason
that in Canoco (prior to the Windows version) used the term "passive" to
mean species or sites added in to the ordination but which didn't
influence it.

What you appear to want to be doing is easily handled by the functions
Jari mentioned - I suspect ordisurf(...., bubble = TRUE) may be more
what you want than ordisurf() itself or envfit() - i.e. scale the
species point by N2 or scale a site point by richness or N2.

If you are interested in passively placing samples into ordinations,
then I have a function timetrack() in my analogue package - it should be
in the R-forge version of the package but not the CRAN version.

There are also things you can do with the predict() methods for cca
objects and the calibrate() function in vegan, but it does all depend
what you want to project in to the ordination.

HTH

G

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