I have run the two analysis. The only differences are the p-values that appear in the anova tables. Other values (Df, SumsOfSqs, MeanSqs, F.Model) are not modified because they are calculated on the "original" (not permuted) data.
The p-value is calculated by comparing the value of F obtained with the original data to the distribution obtained by permutations. If i understand well, the strata argument is used to constrain the permutations of the original data within the groups specified in the strata argument. The distribution of the F-statistic that is generated by permutations is not the same according to whether the strata argument is specified or not. This is why the p-values are modified when the strata argument is specified. However, I'm not sure that strata=Site_Hydro correctly specify the nested structure of my data. -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/split-split-plot-design-and-adonis-tp7332029p7342690.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
