[R-sig-eco] Question on block effect significance in 'adonis' PERMANOVA

[Gavin Simpson]

On Fri, 2012-07-27 at 09:45 +0100, Gavin Simpson wrote:
> On Mon, 2012-07-23 at 10:31 -0200, Alexandre Fadigas de Souza wrote:
> > Dear friends,
> > 
> >    In performing a PERMANOVA in VEGAN's 'adonis' function, we can use strata
> > to indicate a blocking variable. Contrary to standard statistical packages,
> > however, adonis' output does not include the block variable explicitly among
> > its Sources of Variation.

Sorry but the first line of my reply contains a critical typo:

> That is what is intended for `strata`.

That should have read "That is *not* what is intended for `strata`."
Hopefully that was obvious given the following sentence, but I hope I
didn't lead to any confusion.

G

>  It is a conditioning variable for
> the permutation test *only*, so it never enters into the computations
> other than to force the permutations to be freely exchangeable within
> each hill but not exchangeable between hills.
> 
> If you want to include the effect of hill it needs to be included as a
> variable in the formula.
> 
> I'm not fully familiar with adonis() but if you include hill in the
> fixed effects formula then I don't think you can't test significance of
> hill if you also use `strata = hill` (because each permutation will
> essentially have the same samples allocated at the hill level.
> 
> HTH
> 
> G
> 
> >    Sometimes, as is my present situation, the blocking variable is
> > interpretable and we want to know whether it varied significantly.
> > 
> >    I could not find this discussion in the log files of this list.
> > 
> >    Our response variable is the abundances of tree species in 18 square plots
> > in southern Brazil, our explanatory variables are distance to a power dam
> > (near x far, binary) and altitude. Our strata/blocking variable is hill, since
> > treatments near or far from the power dam were replicated on the slopes of
> > three different hills.
> > 
> >    It would be important to know if there were compositional differences
> > between hills but this result does not appear in the output. We tried to force
> > its appearance using the following formula, but I do not know if this distorts
> > the analysis:
> > 
> > > adonis (species ~ hill + dam + altitude + declivity, method="Chao", strata 
> > = environment$hill, perm=4999)
> > 
> >   Thanks in advance for your attention,
> > 
> >   Alexandre
> > 
> > _______________________________________________
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> > R-sig-ecology at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> > 
> 

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