Dear list,

We are working with a dataset of bird community composition across four
regions, each of which contain three land use treatments.  We are
interesting in understanding if the community dissimilarity within regions
and between regions differs according to land use treatment.  I understand
that multivariate analysis of variance (as implemented in adonis{vegan}) can
partition sums of squares between main effects and residuals, which I
understand would, for example, test the ratio (F-statistic) of between
versus within region dissimilarity.

What we'd like to know is effectively if this partitioning of sums of
squares within (residual) and between (main effects) regions changes
significantly under the different land use treatments.  So would the
following model to the trick?

adonis(bird.com~region*land.
use,data=site.data)

where...
bird.com is a sites by species matrix, and
site.data is a data.frame containing columns that indicate to which region
(column 'region') and land use (column 'land.use') each site belongs.

I appoligize for this simple question (and probably wrong model) I'm very
naive about these multivariate analyses.  We assumed that this approach was
probably wrong and so we are also working on a bootstrap method, which I
could post for your consideration if this use of adonis is incorrect, or if
no perMANOVA-based method would answer our question.

Thanks in advance for your help--
Andy Rominger

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