[R-sig-eco] Mixed effects and nested designs in ADONIS

[Steve Brewer]

Adrian,

Others have asked similar questions, for example, how to get adonis to
handle repeated-measures designs. The issue in both cases is how to get
adonis to use more than one error term in testing effects in a
hierarchical design. I'll be interested to see the responses, because as
far as I know, no one has ever responded to this query with a solution.
This suggests to me that no one has developed code to get adonis to use
more than one error term to test effects. I could be (and hope) that I am
wrong.

Good luck,
Steve


J. Stephen Brewer 
Professor 
Department of Biology
PO Box 1848
 University of Mississippi
University, Mississippi 38677-1848
 Brewer web page - http://home.olemiss.edu/~jbrewer/
FAX - 662-915-5144
Phone - 662-915-1077




On 1/28/13 5:14 AM, "Adrian Rasmussen" <adrasmu at gmail.com> wrote:

>Dear members.
>
>I have a relatively simple question about how to create a formula in
>adonis, when I have observations that are spatially clustered, and a block
>design.
>
>Here is a simple description of my study design:
>I have three forest management categories.
>In each management category I have several clusters of logs.
>In each cluster, I have selected 5 logs randomly, and mounted an insect
>trap on each selected log.
>In addition, for one of the 5 logs, I have mounted a smaller, but similar,
>type of insect trap.
>
>My question is if there is a significant difference in species composition
>between forest management categories. And I would like to include both
>types of traps in the same test.
>
>Here is the test I have used so far:
>
>adonis(Species ~ Category, permutations=4999, strata=TrapType)
>Species = Species matrix with traps in rows, and species in columns. This
>matrix includes both types of traps.
>Category = A vector which specifies which forest management category the
>trap is located in.
>TrapType = A vector which specifies the trap type.
>
>Thus, I consider the two different traps as different blocks, as they do
>not sample from the insect community in the same way, and are thus not
>directly comparable, only similar.
>
>As you can tell, this model ignores the nested design, and assumes that
>all
>the traps are equally independent.
>
>How can I formulate the model so that it takes into consideration the
>cluster the trap is located in? I have searched around for some time now,
>but I cannot find any solution to this problem.
>
>Any hints would be greatly appreciated!
>
>Additionally: As far as I understand, my use of strata on trap type, is
>analogous to how they have specified the block design in the adonis help
>page, in the vegan package help document. However, if you feel that I have
>used the strata-function wrong, I would like to hear your opinion.
>
>Regards,
>Adrian Rasmussen
>
>Master student in general ecology,
>University of Life Sciences,
>Ås, Norway
>
>	[[alternative HTML version deleted]]
>
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