[R-sig-eco] Fwd: how to calculate "axis variance" in metaMDS, pakage vegan?

[Gavin Simpson]

On Tue, 2009-12-08 at 20:27 +0100, Gian Maria Niccolò Benucci wrote:
> Jari, Gavin, Chris, Gabriel and Carsten...
<snip />
> ...So, I would explain a little about my datasets:
> 
> - the species matrix is done by roots samples in which were counted the
> ectomycorrhizal fungal species present (cells entities are different tips
> individuals);
> - sample where taken into four "Area" (A,B,C,D). The ares are about 30
> meters far away one to each other;
> - areas A and B are both form Corylus roots while areas C and D are both
> from Ostrya roots.
> 
> To be more clear that is the enviromental matix used:

Are you interested scientifically in the 4 communities or can we
consider this a nuisance factor? If not interested, then you should
control for the fact that your data come from 4 discrete sections of
land, but only focus on testing 'host'.

We don't have the full kind of flexibility you get within something like
Canoco in vegan just yet (but it is coming - if I ever get rid of this
cold...) but you can condition the permutations on 'Community' when
testing 'Host'. By doing this you are restricting the permutations to
only allow free permutation within the levels of 'Community'. This
reflects a Null hypothesis where your samples aren't freely permutable
(they from from the 4 discrete parcels of land), but are freely permuted
within the levels of 'Community'.

To alter your envfit call accordingly, set the 'strata' argument to
env.table$Community. Then adjust the formula to be sqrtABCD ~ Host. You
can do the same thing in adonis, too.

HTH

G

> 
> > env.table
>     Community    Host
> A1          A Corylus
> A2          A Corylus
> A3          A Corylus
> A4          A Corylus
> A5          A Corylus
> A6          A Corylus
> A7          A Corylus
> A8          A Corylus
> A9          A Corylus
> A10         A Corylus
> B1          B Corylus
> B2          B Corylus
> B3          B Corylus
> B4          B Corylus
> B5          B Corylus
> B6          B Corylus
> B7          B Corylus
> B8          B Corylus
> B9          B Corylus
> B10         B Corylus
> C1          C  Ostrya
> C2          C  Ostrya
> C3          C  Ostrya
> C4          C  Ostrya
> C5          C  Ostrya
> C6          C  Ostrya
> C7          C  Ostrya
> C8          C  Ostrya
> C9          C  Ostrya
> C10         C  Ostrya
> D1          D  Ostrya
> D2          D  Ostrya
> D3          D  Ostrya
> D4          D  Ostrya
> D5          D  Ostrya
> D6          D  Ostrya
> D7          D  Ostrya
> D8          D  Ostrya
> D9          D  Ostrya
> D10         D  Ostrya
> >
> 
> ...maybe could be helpfull to say that I calculated diversity indices
> (richness, shannon, simpson and evenness) for my 4 areas and I use ANOVA to
> see if them are diffent one from each other.
> The results show me that area A and B are always different form areas C and
> D but no differences are between them, so clearly Corylus fungal community
> is alwasy different from Ostrya one.
> 
> ...So, I think that "Host" effect is  clear while the effect of "Community"
> couldn't be the same in reason to that areas are similar 2 by 2, ...is it
> right?
> 
> When I plot the MNS.2 and I watch to the Graph I clearly see that sample
> points of A,B areas or Corylus are positioned on the left side while areas C
> and D of Ostrya are more sparse and are positioned into the low right
> side...
> 
> So, what else to say... I'll leave you space for any comments :))))
> 
> Tank you all,
> 
> Gian
> 
> 	[[alternative HTML version deleted]]
> 
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