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

[Jari Oksanen]

Penelope,

Check ?p.adjust for the adjustment methods for multiple comparisons. It is
in standard R (stats) so that it is immediately available for use. There are
several methods available, and in my installation those include both FDR and
Hochberg among others:

> p.adjust.methods
[1] "holm"       "hochberg"   "hommel"     "bonferroni" "BH"
[6] "BY"         "fdr"        "none"

Cheers, Jari Oksanen


On 11/08/09 21:03 PM, "Penelope_Pooler at nps.gov" <Penelope_Pooler at nps.gov>
wrote:

> 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
> 
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