On Tue, 2010-01-19 at 11:39 +0100, Kay Cecil Cichini wrote: > Hallo List, > > I'm trying to implemement a restricted permutation scheme in > permutest(). More > precisely I have dependence in my data that should be allowed for in > the > permutation - I simulated the problem in the example of the vegan > documentation > p.24: <snip /> > > ##the unrestricted Permutation test for F is > permutest(mod, pairwise = TRUE) > > > ..I wasn't able to find out the right syntax for implementation of > blocks, I > tried with argument strata, which would be blocks, in permutest(mod, > pairwise = > TRUE, blocks) but this doesn't work. By the way, what is 'pairwise = > TRUE' for?
This looks like you haven't really read or understood the help for permutest.betadisper? If you had, you'd have noticed that this method doesn't (currently) support the 'strata' argument and because you didn't name the argument you supplied 'blocks' to, this would have gone to argument 'control' and that should have resulted in an error. You can't implement a restricted permutation for any model in vegan at the moment, unless you fancy hacking the code. Work is in progress to implement for vegan the type of dependence structures available in Canoco. I produced a new package 'permute' that is available on r-forge: http://r-forge.r-project.org/R/?group_id=68 (within the vegan stable) to do those kinds of restricted permutations, but this is very much at alpha status at the moment as some aspects of the code just don't work. There is enough there to generate a restricted permutation of a dataset, but not the extra checking code. If you can explain what kind of dependence structure you have in your data perhaps I can help with a bespoke version of permutest.betadisper until permute is ready for release, but if you do so, please move this to a thread on the r-forge vegan help forum: http://r-forge.r-project.org/forum/forum.php?forum_id=194 'pairwise = TRUE' indicates that you also want pairwise comparisons of group variances. I.e. if you have 3 groups, pairwise = FALSE would only give an overall analysis (one p-value) for differences in variances across all groups, where as pairwise = TRUE conducts tests of the difference between group 1 and 2, between group 1 and 3, and between 2 and 3, as well as the overall analysis. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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.