[R-sig-eco] adonis and temporal changes

[v_coudrain at voila.fr]

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
___________________________________________________________
C'est l'année du Serpent ! Connaissez-vous votre signe astral chinois ? Découvrez-le ici http://astrocenter.voila.fr/voila/Presentation.aspx?
product=StEdCH2K2&Af=-3000
___________________________________________________________
C'est l'année du Serpent ! Connaissez-vous votre signe astral chinois ? Découvrez-le ici http://astrocenter.voila.fr/voila/Presentation.aspx?product=StEdCH2K2&Af=-3000