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_coudr...@voila.fr, r-sig-ecology@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_coudr...@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 > >___________________________________________________________ > >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 > > > >_______________________________________________ > >R-sig-ecology mailing list > >R-sig-ecology@r-project.org > >https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > ___________________________________________________________ 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 _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology