[R-sig-eco] species scores for ordination in vegan

[Gavin Simpson]

On Sun, 2013-02-24 at 11:22 +0400, Stas Malavin wrote:
> Dear list readers,
> 
> Please forgive me for asking trivial questions, but I've failed to find the
> exact answer by myself. I'm interested in how the species scores are
> calculated for ordination configuration in vegan package. It's written they
> are weighted averages (of sites scores?): vegan/html/metaMDS.html,
> vegan/html/wascores.html.
> 
> My questions are:
> (1) Are all sites used for calculation of the average, or just those where
> the species presents?

As the weight for an absent species is 0 the contributions of those
absent species at any given site are zero. So in one sense, they are not
used, but the computations themselves certainly use them; their effect
is just zero. Which way you want to think of this depends on what you
mean by "calculated".

> (2) What's used as weights: site totals, or the abundances of particular
> species which score is calculated?

The species abundances. The fitted species score for species i is the
weighted average of the site scores for all sites k with weights given
by the abundance of species i on those sites k.

HTH

G

> Thank you in advance,
> Stas
> 
> --------------------------------------------
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> Hydrobiology Lab
> Institute of Limnology
> Russian Academy of Sciences
> 
> Sevastyanova 9
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