Hi Jari and others,


*...At least you must think very carefully what you do, and be able to
justify that
both to yourself and other people (like the referees)...
*
Does a better explanation of what adonis() do already exist?
So briefly and to summerize... What are, at the end, the differences about
these different following functions?

adonis(ABCDsqrt ~ Host, env.table)

adonis(ABCDsqrt ~ Host/Community, env.table)

adonis(ABCDsqrt ~ Host*Community, env.table)

adonis(ABCDsqrt ~ Host, strata = env.table$Community, env.table)

Thank you,

Gian



2009/12/11 Jari Oksanen <jari.oksanen@oulu.fi>

> On 11/12/09 00:26 AM, "Jari Oksanen" <jari.oksanen@oulu.fi> wrote:
>
> > On 10/12/09 23:03 PM, "gabriel singer" <gabriel.singer@univie.ac.at>
> wrote:
> >
> >> A difference between two communities within a host could still exist and
> >> could make perfect sense, too, when you regard "community" as a random
> >> factor. Then "community" may introduce some extra variation (compared to
> >> the within-community variation), experimentally seen interesting and
> >> important, because the replication of communities makes sure you are not
> >> pseudoreplicating. I am not sure however, how to declare the correct df
> >> for the random factor in adonis in this case... anybody knows better
> than I?
> >
> > There is no way.
> >
> > Random factors can be only mimicked by stratified permutation, but they
> > cannot be defined in adonis. It is only for fixed effect models.
> >
> Howdy,
>
> Just to make clearer what I mean: adonis() uses standard formula
> interpretation, and you can have nested factors in adonis(). So the
> following work, and both define the same model:
>
>  adonis(dune ~ A1/Management, dune.env)
>  adonis(dune ~ A1 + A1 %in% Management, dune.env)
>
> You can also have full crossed interactions
>
>  adonis(dune ~ A1*Management, dune.env)
>
> However, you should not combine nesting within a factor and stratification
> with the same factor. The stratification is supposed to mimic the same
> effects that you may want to show by nesting, but in more "random" way. At
> least you must think very carefully what you do, and be able to justify
> that
> both to yourself and other people (like the referees). Further, you must
> remember that adonis() uses sequential tests and the effect of nesting is
> not shown in terms before nesting, like the main effects. This may not be
> what you wanted to do. Most importantly, there is no real way of having
> *random* effects in adonis(), which was intended as the main message of my
> previous posting on this issue. They are all fixed effects.
>
> Cheers, Jari Oksanen
>
>


-- 
Dr. Gian Maria Niccolò Benucci
Department of Applied Biology - University of Perugia
Borgo XX Giugno, 74
I-06121 - Perugia, ITALY
Email: gian.benucci@gmail.com
Tel: +39.075.5856433

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