Non-metric Multidimensional Scaling (NMS or NMDS) is one procedure used to
analyze differences in sites regarding vegetation structure. It uses a
dissimilarity matrix to orient sites in species space. It is available as a
base package in R as isoMDS, or in the package Vegan as metaMDS. It is not a
pairwise analysis, as you are requesting, but it is useful for showing
community differences among multiple sites.
Jonathan White
UofL Biology
Louisville, KY

On Tue, Aug 11, 2009 at 6:00 AM, <r-sig-ecology-request@r-project.org>wrote:

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>   1. pairwise comparisons in community structure analysis      data
>      (Penelope_Pooler@nps.gov)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 10 Aug 2009 16:43:27 -0400
> From: Penelope_Pooler@nps.gov
> Subject: [R-sig-eco] pairwise comparisons in community structure
>        analysis        data
> To: r-sig-ecology@r-project.org
> Message-ID:
>        <OF398A6A96.05C56518-ON8525760E.006FCEBB-8525760E.0071D564@nps.gov>
> Content-Type: text/plain; charset=US-ASCII
>
>
> 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
> looking.
>
> Thanks for your help.
>
> -Penelope
>
>
>
>
> 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@nps.gov
> Ph.: (401) 874-7060
>
>
>
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