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

Penelope_Pooler at nps.gov Penelope_Pooler at nps.gov
Mon Aug 10 22:43:27 CEST 2009

I have a question that I'm not sure has a right answer, but I would
appreciate any and all opinions, especially if you know of any citations to
back them up.

In the past, when dealing with univariate data, I have always been a
proponent of using Fisher's Protected LSD for pairwise comparisons because
it is the most powerful procedure, and the accuracy of its experimentwise
error rate is based on a sound argument that was subsequently proven to be
true with simulations in Carmer and Swanson (1973 ).  I included the full
reference below.

At the moment, I'm working with community structure data (multivariate
nonparametric) at multiple sites and there is an need to determine which
sites are different from which other sites.  My colleague has used a
Bonferroni correction  for this type of question the past, but I tend to
think that is most likely too conservative.  I'm interested to know if any
of you have dealt with a similar problem and/or if you know if anyone has
done any work on comparing pariwise comparisons procedures for multivariate
nonparametric data.

I've done a preliminary literature search with no success, but am still

Thanks for your help.


Carmer, S. G. and M. R. Swanson (1973). "An evaluation of ten pairwise
multiple comparison procedures by Monte Carlo methods." Journal of the
American Statistical Association 68 (341): 66-74.

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

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