How to obtain P value from Monte Carlo sampling for adonis (permanova)?

Dear all,

I have recently decided to switch from Permanova/Primer to R, because the
latter is freeware (and I don't know for how long I will still have a
license). However, if I cannot seem to resolve my problem (see below), I
might have to go back to using Primer/Permanova.

If I run pairwise permanova/adonis tests on my data, the number of unique
permutations is small (I have two groups, each group has 3 observations)
and the minimum P value I can get is larger than the alpha value I (and
most people) that I use to determine statistical significance (i.e. 0.05).
In the manual of the PERMANOVA+ add-on in Primer by Anderson et al. (2008)
 it is mentioned (page 28 and onwards) that when the number of unique
permutations is small (<100) than one should preferably interpret the
Monte-Carlo p value.

Does anyone know how to do this in R?


In my internet search I stumbled upon this page:
http://r.789695.n4.nabble.com/monte-carlo-simulations-in-permanova-in-vegan-package-td4714034.html.
"JAri Oksanen answered here: 2. If you want to do so, you can generate your
resampling matrices by hand and use that matrix as the argument of
permutations=. See the documentations (?adonis) which tells how to do so.
", but I don't understand how to this..

Thank you very much!

Ellen

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