[R] PERMANOVA+ and adonis in vegan package

Gavin Simpson gavin.simpson at ucl.ac.uk
Tue Jul 12 08:43:17 CEST 2011

On Sat, 2011-07-09 at 09:35 -0700, VG wrote:
> Hi,
> I was wondering if someone can tell me what is the difference between
> "strata" argument (function "adonis" in "vegan" package) and
> using random effects in PERMANOVA+ add-on package to PRIMER6 when doing
> permutational MANOVA-s? Is the way permutations are done the same?
> Thank you very much in advance,
> Vesna 

By the looks of the Primer page on this new add-on, there are
substantial differences between adonis() and PERMANOVA+. The current way
that adonis() permutes data is either to shuffle the data totally at
random, or at random *within* the levels of `strata`. This conditions
the permutations on the clusterings of samples, and reflects a null
hypothesis where samples are not fully freely exchangeable
(independent), but exchangeable only within the groups/clusters of

It appears PERMANOVA+ has facilities for more complex permutations that
this. I have implemented some of these restricted permutations in my
package `permute` - on r.forge within the vegan stable of packages -
that will hopefully be used within vegan for all it's permutations,
perhaps by as soon as the end of the summer break.

As PERMANOVA+ is closed source and I have not seen any works from Marti
Anderson describing the newer features of her software, which are
included in the new PRIMER add-on, I would suggest you enquire with the
PRIMER people as to the similarities/differences between adonis() and
PERMANOVA+ and report back your findings?



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 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
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