Vegan-Adonis-NMDS-SIMPER

Gavin and Brandon,

Yes, I am aware that betadisper() does not actually give you a test of
differences between centroids, but the fact that it does calculate
centroids is quite valuable for interpretation, in my opinion, especially
when using non-euclidean distance matrices (e.g., Bray-Curtis) and also if
you would prefer NOT to do additional pairwise tests between levels, but
still would like to have some idea as to which pairwise differences
between levels might be most responsible for the effect. When using
bray-curtis distances, you can't get centroids by calculating averages of
abundances among the observations of interest. If you just want to use a
NMDS ordination with levels symbol-coded to make them distinct, that's
fine. Sometimes folks calculate the average axis score per group or level
of group and plot that. That's fine, too. The nice thing about obtaining
centroids calculated using betadisper() is that they are based on a
principal coordinates analysis that uses ALL the axes, not just the first
two or three axes in the ordination. It is likely that if the first two or
three axes of the NMDS explain most of the important variation, the
average scores per level for those three axes will probably tell the same
information as the centroids will.

Even though it wasn't intended for this purpose, Sharon Graham and I,
together, figured out that you could use the centroids calculated by
betadisper() to analyze split-plot and repeated-measures designs using
adonis. So, its value extends beyond what it was intended for.

Steve

J. Stephen Brewer 
Professor 
Department of Biology
PO Box 1848
 University of Mississippi
University, Mississippi 38677-1848
 Brewer web page - http://home.olemiss.edu/~jbrewer/
FAX - 662-915-5144
Phone - 662-915-1077

Vegan-Adonis-NMDS-SIMPER

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