[R-sig-eco] pairwise comparisons in community structure
jari.oksanen at oulu.fi
Tue Aug 11 21:06:18 CEST 2009
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:
 "holm" "hochberg" "hommel" "bonferroni" "BH"
 "BY" "fdr" "none"
Cheers, Jari Oksanen
On 11/08/09 21:03 PM, "Penelope_Pooler at nps.gov" <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 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
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
More information about the R-sig-ecology