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

[Gavin Simpson]

On Mon, 2009-08-10 at 16:43 -0400, Penelope_Pooler at nps.gov wrote:
> 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.

You don't say how you are comparing sites, i.e. to what is the
Bonferroni correction applied? The p-value from ...?

You are also a bit vague about the data structures/layout. If your data
represent a set of sites with multiple samples taken at each of these
sites, then you might want to look at adonis() and betadisper(), both
functions in the vegan package.

adonis() partitions the dissimilarities between sites on the basis of
certain factors - so it is like ANOVA but with multivariate responses
using any dissimilarity and you can think of this analysis as looking at
whether the distances between points within a group (factor, site etc)
are greater than the between groups distances or distances to other
groups.

If adonis() shows a significant difference between sites, this
difference may be due to differences in the spread or variance of the
respective groups, just like in standard ANOVA. betadisper() can be used
to test for this.

Unfortunately, adonis doesn't do pairwise comparisons, but with the
right amount of force could be changed to do so. betadisper does do
pairwise comparisons and even has a TukeyHSD method for it (for the
multiple comparisons), but a user has recently pointed out that both the
parametric p-value and the permutation-derived p-value of the main
betadisper analysis don't have the right Type I error rates - Ho is
accepted too many times when given random groups. This seems to be a
problem with the general method and not with the implementation in
vegan, and is something that I (as the author of betadisper) and Jari
Oksanen are currently looking into (slowly on my part, I'm afraid...).

If the above and Rodney's reply don't address your real problem per se,
perhaps you could elaborate on what tests you are using and wish to
correct for multiple comparisons?

All the best,

G


> 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
> 
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
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