[R-sig-eco] pairwise comparisons in community structure

[Penelope_Pooler at nps.gov]

Thanks for all of your great comments and questions.  I think I got what I
needed.  Two people (Elgin Perry and Jarrett Byrnes) recommended a paper
about controlling the FDR (False Discovery rate) by Benjamini and Hochberg
(1995) and Jarrett also mentioned newer paper by the same authors that
updates their work with another procedure called an adaptive FDR.  These
procedures will be ideal for what I am doing.

To answer some of your questions, I am using adonis(), because it is
analogous to what has been used in the past (anosim()) for this project,
but I feel it is better algorithm and has the added benefit of outputing
the results in a format similar to a univariate ANOVA table.  Gavin
mentioned the possibility of also checking out betadisper() in the same
vegan package and I will.

Unfortunately, for this particular research I can't use NMDS because I am
presenting the results to park managers and other non scientists so the
methods as well as the results and how I explain them have to be very
straightforward.  Otherwise, I think that would be a great solution.  As
for why I am doing pairwise comparisons, I agree that they are not always
the best approach, but in this particular case the park managers want
simple straightforwad answers as to whether or not site a differs from site
b differs from site c, etc and what species, characteristics contribute to
those differences.

Thank you again for your help and useful suggestions and comments.

-Penelope

==============================
Penelope S. Pooler
Quantitative Ecologist
National Park Service I&M
Northeast Coastal and Barrier Network

URI Coastal Institute in Kingston
#1 Greenhouse Rd., Rm 205
Kingston, RI 02881

Penelope_Pooler at nps.gov
Ph.: (401) 874-7060