[R-sig-eco] adonis/vegan

[Gavin Simpson]

On Wed, 2008-07-02 at 10:37 +0100, Diego Fontaneto wrote:
> Why does order matter in specifying a model in adonis?

Because they are sequential sums of squares. See the Value section
of ?adonis.

<snip />
        
> 
> ----------------------------------------------------------------
> 
> Another question in adonis: is there a way to specify an error term, like
> adding "random=~1|locality" to the previous models?

No, not with the current implementation.

Do you want to do this to take account of group structure in your data?
If so, the permutation test can be altered so that it doesn't permute
freely but permutes within levels of 'locality' for example.

I have added code to vegan to generate these restricted permutations
(and for spatial grids and time series/transects, amongst others), in
function permuted.index2. However the code is not quite finished and the
API is still bedding down whilst I make the last few additions to the
code. Once this is done, we vegan developers can begin moving functions
that use permuted.index internally to use the new permutation code from
permuted.index2. This isn't a minor job however so may take a little bit
of time. 

> Thanks,
> Diego

All the best,

G

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