[R-sig-eco] adonis and temporal changes

[Steve Brewer]

Valerie,

Adonis does not define fixed or random effects, and you therefore cannot
define multiple error terms. However, if your model statement looks
something like this - isolation*year + site, strata = site - then you will
get the correct test for the isolation x year interaction and the correct
test for the year effect. The test for isolation will be wrong, because
the residual error is used to test all effects, when it is only
appropriate for testing the year effect and the year * isolation
interaction. The isolation between-subjects effect should be tested with
the site effect but is not.

The key point is here to make strata = site and to NOT specify the site-
interactions with isolation or year. In this way, site will be treated as
a block for the within-subjects effects and thus could be considered a
random effect.

Hope this helps.

 
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 2/18/13 8:19 AM, "v_coudrain at voila.fr" <v_coudrain at voila.fr> wrote:

>Thank you for these explanations. If I put strata=site, this means that
>for each site my dissimilarity matrix of year 1 and year 2 will be
>permuted and the observed
>changes compared to these random permutation? Adding site as a fixed
>factor then ensure that I am testing changes in time site by site. Am I
>correct?
>
>To my design:
>I have 30 permanent sites, 10 of each category of isolation (Isolation =
>factor with 3 levels: 3x10 sites = 30 sites). I conducted the samples in
>three years in each
>site. I have thus 1 sampling (species composition) pro site pro year. I
>would like to know how the sampled communities change with time, either
>on a site basis, 
>or at the level of isolation (I may compare multi-site dissimilarity
>among isolation levels between years).
>I am not really interested in knowing what proportion of differences in
>species community is due to space vs time, but I would like to really
>focus on the temporal
>changes. That's why I think putting site as a fixed effect should be
>appropriate. But if you have any suggestion or think this is not correct,
>I would be pleased to
>have your opinion.
>Cheers,
>
>Valerie
>
>
>
>
>
>On 18/02/2013, at 14:04 PM, Pierre THIRIET wrote:
>
>> Dear Valérie,
>> 
>> If I remember well, your design includes:
>> Isolation categories: 3 levels
>> Sites: nested within Isolation categories (10 levels, a total of 30
>>sites)
>> How many replicates per site and time?
>> Time:? how many years you have? Only one sampling per year? Within
>>sites and years, samples were random or it is always exactly the same
>>area you 
>sample (e.g. permanent quadrats)?
>> 
>> for adonis, consider that strata is for constraining permutations,
>>which is different than terms in the formulae.
>> 
>Exactly. The 'strata' only influence the permutations and have no effect
>in formula nor effect defined in the formula.
>
>Currently the 'strata' are the only way to constrain the permutations.
>However, in the R-Forge version of vegan and in vegan 2.2-0 (to be
>released in April) you
>can give a permutation matrix as an input to adonis. You can generate the
>permutation matrix with, say, shuffleSet function of the permute package.
>This allows 
>generation of restricted permutations for instance for time series. Vegan
>command vegandocs("permutations") will open up the vignette of the
>permute package 
>for your inspection, and this will give some examples of defining
>restricted permutations. At some timeframe we are completely moving to
>the permute package,
>but you can already use its permutation matrices as input with these new
>and upcoming versions of vegan from R-Forge.
>
>Cheers, Jari
>--
>Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
>___________________________________________________________
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>___________________________________________________________
>C'est l'année du Serpent ! Connaissez-vous votre signe astral chinois ?
>Découvrez-le ici 
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