[R-sig-eco] adonis and temporal changes

[v_coudrain at voila.fr]

Dear Steve,

Thank you very much. I do not exactly understand why the test for isolation will be wrong, would you have some some explanation? 
In a linear regression, you cannot assess the effect of single variable if the interaction (in which your variable is part) is significant. So if I get a significant result 
for the isolation*year effect I should conclude that there is an interaction between isolation and year. If the interaction is not significant, should I drop it to get the 
correct estimate for the year effect?
I would have an additional question: I have also an environemental gradient (continuous, one value pro site, constant over the years). Is it possible to include it?

Best wishes
Valerie


> Message du 18/02/13 à 15h41
> De : "Steve Brewer" 
> A : v_coudrain at voila.fr, r-sig-ecology at r-project.org
> Copie à : 
> Objet : Re: [R-sig-eco] adonis and temporal changes
> 
> 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"  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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> 
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