Dear Laura,

You may want to compare distances to centroid instead of individual pairwise
distances (note that the latter also implies some non-independence; the
issue is described in Anderson 2006 Biometrics). This can be done via

?betadisper

in vegan. The following refs from Marti Anderson are very helpful,
especially the 2010 one for a more general treatment of beta diversity
analyses:

Anderson, M. J. 2006. Distance-based tests for homogeneity of multivariate
dispersions. Biometrics 62:245-253.

Anderson, M. J., T. O. Crist, J. M. Chase, M. Vellend, B. D. Inouye, A. L.
Freestone, N. J. Sanders, H. V. Cornell, L. S. Comita, K. F. Davies, S. P.
Harrison, N. J. B. Kraft, J. C. Stegen, and N. G. Swenson. 2010. Navigating
the multiple meanings of ā diversity: a roadmap for the practicing
ecologist. Ecology Letters:in press.

Anderson, M. J., K. E. Ellingsen, and B. H. McArdle. 2006. Multivariate
dispersion as a measure of beta diversity. Ecology Letters 9:683-693.

Hope that helps,

Etienne

2011/1/17 Laura S <leslaura@gmail.com>

> Dear all:
>
> I have box plots at the moment of beta-diversity pairwise comparisons
> grouped by a categorical variable.  Not all the pair-wise comparisons are
> independent.
>
> Given the violation of independence of some pairwise comparisons, I was
> wondering the best R package to use in order to compare among groups.
>
> Please let me know if you have any suggestions.
>
> Thank you for your time and consideration,
> Laura
>
> --
> " Genius is the summed production of the many with the names of the few
> attached for easy recall, unfairly so to other scientists"
>
> - E. O. Wilson (The Diversity of Life)
>
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