On Thu, 2010-03-04 at 01:30 -0800, Kay Cichini wrote: > ....inclusion of repeated measures of course should gain power, but here I > guess one would have to restrict permutations and that's what may reduce > power drastically if sample size is small, at least that's how I understood > it. > I have also dug out a thread where someone asked for random factors in > adonis() and that's quite the same topic, I think. Gavin answered that > function permuted.Index2() would serve - but still I don't know how to do it > practically..
You can't - without ripping these particular guts out of vegan, inserting the code from package 'permute', and then hacking adonis to use the new code. That's quite a lot of user-intervention. Not to mention that 'permute' is pre-alpha at the moment and full of bugs... > There is one of my postings in the r forge vegan forum that handles the same > problem with sampling design for beta.disper() and if it turns out that in > both cases the key is permuted.Index2() this thread may be redundant. For the moment, there isn't really a permutation-based solution that works for your problem within vegan and adonis. We are planning on a major update to vegan over the summer to interface vegan's ordination functions with the permutation code in 'permute'. Of course, that is conditional upon me getting 'permute' working well first. G > > Greetings, > Kay -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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.
