[R-sig-eco] adonis and temporal changes

[Jari Oksanen]

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