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

[Gavin Simpson]

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.

That is what is intended for `strata`. 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
> 
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> 

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%