[R] adonis help - (non-parametric (permutational) manova)

Gavin Simpson gavin.simpson at ucl.ac.uk
Wed May 13 10:49:49 CEST 2009

Apologies, I seem to have deleted the important part of a sentence

On Wed, 2009-05-13 at 09:37 +0100, Gavin Simpson wrote:
<snip /> 
> > adonis(a~site, data=b, strata=b[,"date"] ,Permutations=999)
> I don't think the permutations will be stratified correctly - you want
> them to represent a time series yes? 'strata' is meant to define in
> vegan. 

Should have said:

'strata' is meant to define groups of samples, or blocks, in vegan.


> Samples within the strata are permuted. So if you only have two
> samples per unique time point (1 for up and 1 for dn), the effect of
> setting strata to the date variable will be to permute only pairs of
> samples.
> Work has begun (and stalled for a little while - my fault) on providing
> a wider range of restricted permutation tests. The function
> permuted.index2 in vegan can generate permutations for time series (or
> other ordered observations), but you'd have to a) edit adonis in place
> to use permuted.index2 and work out how to set up the call to this
> function correctly so that it returns the permutation structure adonis
> wants. Then check it does what it says it does - there is at least one
> bug that I know of but I'm not fixing it as the development version on
> my local machine has completely changed the way the permutation schemes
> are specified. Contact me off-list if you would like some help with
> this, though as I'm teaching for two weeks, I won't be able to look at
> it until later.
> For now, perhaps you could just ignore the time-series aspects and run
> the analysis without strata, but require a far lower p-value than you
> might normally use to reflect the fact that the permutations do not take
> into account correlations between time points.
> > 
> > Is this the correct way of testing the null hypothesis that :
> > 
> > There is no difference in community structure between treatments.
> > 
> > Thank you very much in advance, and anything that you need to make
> > this easier please don't hessitate to ask.
> > 
> > regards,
> > 
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
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 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk

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