Apologies, I seem to have deleted the important part of a sentence below: On Wed, 2009-05-13 at 09:37 +0100, Gavin Simpson wrote: <snip /> > > adonis(a~site, data=b, strata=b[,"date"] ,Permutations=999) > > I don't think the permutations will be stratified correctly - you want > them to represent a time series yes? 'strata' is meant to define in > vegan.
Should have said: 'strata' is meant to define groups of samples, or blocks, in vegan. G > Samples within the strata are permuted. So if you only have two > samples per unique time point (1 for up and 1 for dn), the effect of > setting strata to the date variable will be to permute only pairs of > samples. > > Work has begun (and stalled for a little while - my fault) on providing > a wider range of restricted permutation tests. The function > permuted.index2 in vegan can generate permutations for time series (or > other ordered observations), but you'd have to a) edit adonis in place > to use permuted.index2 and work out how to set up the call to this > function correctly so that it returns the permutation structure adonis > wants. Then check it does what it says it does - there is at least one > bug that I know of but I'm not fixing it as the development version on > my local machine has completely changed the way the permutation schemes > are specified. Contact me off-list if you would like some help with > this, though as I'm teaching for two weeks, I won't be able to look at > it until later. > > For now, perhaps you could just ignore the time-series aspects and run > the analysis without strata, but require a far lower p-value than you > might normally use to reflect the fact that the permutations do not take > into account correlations between time points. > > HTH > > > > > Is this the correct way of testing the null hypothesis that : > > > > There is no difference in community structure between treatments. > > > > Thank you very much in advance, and anything that you need to make > > this easier please don't hessitate to ask. > > > > regards, > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
