[R] adonis(), design

Gavin Simpson gavin.simpson at ucl.ac.uk
Fri Mar 5 10:35:02 CET 2010

On Thu, 2010-03-04 at 01:30 -0800, Kay Cichini wrote:
> ....inclusion of repeated measures of course should gain power, but here I
> guess one would have to restrict permutations and that's what may reduce
> power drastically if sample size is small, at least that's how I understood
> it.
> I have also dug out a thread where someone asked for random factors in
> adonis() and that's quite the same topic, I think. Gavin answered that
> function permuted.Index2() would serve - but still I don't know how to do it
> practically..

You can't - without ripping these particular guts out of vegan,
inserting the code from package 'permute', and then hacking adonis to
use the new code. That's quite a lot of user-intervention. Not to
mention that 'permute' is pre-alpha at the moment and full of bugs...

> There is one of my postings in the r forge vegan forum that handles the same
> problem with sampling design for beta.disper() and if it turns out that in
> both cases the key is permuted.Index2() this thread may be redundant.

For the moment, there isn't really a permutation-based solution that
works for your problem within vegan and adonis. We are planning on a
major update to vegan over the summer to interface vegan's ordination
functions with the permutation code in 'permute'. Of course, that is
conditional upon me getting 'permute' working well first.


> Greetings,
> Kay
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
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