On Sat, 2011-07-09 at 09:35 -0700, VG wrote: > Hi, > > I was wondering if someone can tell me what is the difference between > "strata" argument (function "adonis" in "vegan" package) and > using random effects in PERMANOVA+ add-on package to PRIMER6 when doing > permutational MANOVA-s? Is the way permutations are done the same? > > Thank you very much in advance, > Vesna
By the looks of the Primer page on this new add-on, there are substantial differences between adonis() and PERMANOVA+. The current way that adonis() permutes data is either to shuffle the data totally at random, or at random *within* the levels of `strata`. This conditions the permutations on the clusterings of samples, and reflects a null hypothesis where samples are not fully freely exchangeable (independent), but exchangeable only within the groups/clusters of samples. It appears PERMANOVA+ has facilities for more complex permutations that this. I have implemented some of these restricted permutations in my package `permute` - on r.forge within the vegan stable of packages - that will hopefully be used within vegan for all it's permutations, perhaps by as soon as the end of the summer break. As PERMANOVA+ is closed source and I have not seen any works from Marti Anderson describing the newer features of her software, which are included in the new PRIMER add-on, I would suggest you enquire with the PRIMER people as to the similarities/differences between adonis() and PERMANOVA+ and report back your findings? HTH G > -- > View this message in context: > http://r.789695.n4.nabble.com/PERMANOVA-and-adonis-in-vegan-package-tp3656397p3656397.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org 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.
