Question on block effect significance in 'adonis' PERMANOVA
On Mon, 2012-07-23 at 10:31 -0200, Alexandre Fadigas de Souza wrote:
Dear friends, In performing a PERMANOVA in VEGAN's 'adonis' function, we can use strata to indicate a blocking variable. Contrary to standard statistical packages, however, adonis' output does not include the block variable explicitly among its Sources of Variation.
That is what is intended for `strata`. It is a conditioning variable for the permutation test *only*, so it never enters into the computations other than to force the permutations to be freely exchangeable within each hill but not exchangeable between hills. If you want to include the effect of hill it needs to be included as a variable in the formula. I'm not fully familiar with adonis() but if you include hill in the fixed effects formula then I don't think you can't test significance of hill if you also use `strata = hill` (because each permutation will essentially have the same samples allocated at the hill level. HTH G
Sometimes, as is my present situation, the blocking variable is interpretable and we want to know whether it varied significantly. I could not find this discussion in the log files of this list. Our response variable is the abundances of tree species in 18 square plots in southern Brazil, our explanatory variables are distance to a power dam (near x far, binary) and altitude. Our strata/blocking variable is hill, since treatments near or far from the power dam were replicated on the slopes of three different hills. It would be important to know if there were compositional differences between hills but this result does not appear in the output. We tried to force its appearance using the following formula, but I do not know if this distorts the analysis:
adonis (species ~ hill + dam + altitude + declivity, method="Chao", strata
= environment$hill, perm=4999) Thanks in advance for your attention, Alexandre
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