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

[Chris Stallings]

Penelope,

Following up on Rodney's email, it may be useful to ask whether pairwise 
comparisons are necessary.  Depending on your question and what you want 
to gain from the research, pairwise comparisons may not be the best 
approach.  If you are interested in the general patterns and potential 
processes across your study system, NMS would be a useful approach to 
determine how sites differ and what measured "environmental" variables 
are correlated with those differences.  You may wish to also use 
Multi-response Permutation Procedures (MRPP), either independently of, 
or in connection with, the results from the NMS to test for group 
differences. 

Good luck,
Chris

Christopher D. Stallings, Ph.D.
Postdoctoral Associate
Florida State University Coastal & Marine Lab
St. Teresa, FL 32358, USA

phone: 850.697.4103
fax: 850.697.3822
web: http://www.marinelab.fsu.edu/faculty/stallings.aspx



Rodney White wrote:
> 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 at r-project.org>wrote:
>
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>>   1. pairwise comparisons in community structure analysis      data
>>      (Penelope_Pooler at nps.gov)
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>> ----------------------------------------------------------------------
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>> Message: 1
>> Date: Mon, 10 Aug 2009 16:43:27 -0400
>> From: Penelope_Pooler at nps.gov
>> Subject: [R-sig-eco] pairwise comparisons in community structure
>>        analysis        data
>> To: r-sig-ecology at r-project.org
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>>        <OF398A6A96.05C56518-ON8525760E.006FCEBB-8525760E.0071D564 at nps.gov>
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>>
>> 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 at nps.gov
>> Ph.: (401) 874-7060
>>
>>
>>
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