[R] Two-Way PERMANOVA with Repeated Measurements

Kallin Tea kallin.tea at gmail.com
Thu Feb 2 19:19:44 CET 2012


I want to perform a permanova where the first factor called Treatment
has four levels. The second factor involves sampling the same research
plots for four consecutive years, hence the repeated measurements.

I have been able to use the adonis function from the package vegan to
run this analysis.

code below:
TC.perMANOVA.adonis<-adonis(TC.PerMANOVA ~ Treatment*Year,
data=TC.PerMANOVA.ENV, permutations=99, method="bray", strata = NULL)

However, my concern is that this does not take into account that Year
is a repeated measurement on the same research plots.

Any suggestions would be appreciated.

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