[R-sig-eco] split-split-plot design and adonis

[Arnaud Foulquier]

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. 





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