Kay, using strata (restricting permutations within time points, and not within locations) in adonis makes some sense, given that permutation tests assume independence. But that does not solve the problem of dependence, but it is a good starter. If you have a before-after control-treatment design, you might want to use the absolute difference between observations and do the adonis on the matrix of differences (the dissimilarity then will represent distance in terms of absolute deviation between time points). However, this won't show the sign of the change, which might be of interest. If you have larger number of repeated observations, the MARSS package is just appeared on CRAN to fit multivariate autoregressive state-space models using a Kalman-filter approach.
Cheers, Peter Péter Sólymos Alberta Biodiversity Monitoring Institute and Boreal Avian Modelling project Department of Biological Sciences CW 405, Biological Sciences Bldg University of Alberta Edmonton, Alberta, T6G 2E9, Canada Phone: 780.492.8534 Fax: 780.492.7635 email <- paste("solymos", "ualberta.ca", sep = "@") http://www.abmi.ca http://sites.google.com/site/psolymos On Fri, Jul 23, 2010 at 1:02 PM, Kay Cichini <kay.cich...@uibk.ac.at> wrote: > > dear list, > > i searched though the archives and the question of repeated measure analysis > with species data was often brought up but, as far as i found, never clearly > worked out. > > if i have, say two time points at wich i sampled replicated plots and thus > had replicated paired mutivariate obervations, how to deal with them > properly. > > if i used adonis, to restrict permutations on the pairs of plots (as this > would be done in an univariate permutation test for paired observations) > does not make sense to me but i'm also dubious about neglecting the > dependence of the pairing. > > any ideas would be highly appreciated, > kay > > ----- > ------------------------ > Kay Cichini > Postgraduate student > Institute of Botany > Univ. of Innsbruck > ------------------------ > > -- > View this message in context: > http://r-sig-ecology.471788.n2.nabble.com/repeated-measures-with-multivariate-data-tp5330819p5330819.html > Sent from the r-sig-ecology mailing list archive at Nabble.com. > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology