Question on block effect significance in 'adonis' PERMANOVA

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.

   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

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