Kim Milferstedt <milferst <at> uiuc.edu> writes:
>
> Hello,
>
> I am trying to run some AMOVA analyses with the amova function in the
> package ade4.
>
> When running the example dataset provided in ade4, I noticed a
> difference between the published results from the same data (Excoffier
> et al. 1992) and what ade4 calculates.
>
A generic answer to this type of question is that you should contact
the package maintainers (see help(package="ade4") for their
e-mail addresses) -- especially for
these kinds of specialized questions (most R-helpers are not population
geneticists and wouldn't know an AMOVA if it bit them) ...
On the other hand, running example(randtest.amova) [which is
what I assume you did, although you don't say] I do confirm
your results, and furthermore the plot that is produced looks
like the p-value *should* be very low -- and the std. obs.
is large (which I think is a *good* thing from the point of
view of rejecting null hypothesis -- seems like this is the
analogue of a t- or z-score), but negative. Perhaps the package
authors did an upper 1-tailed test by mistake? (I would follow
through with this but it looks like the important stuff goes
through into C code and I can't take the time to dig that
deep right now.)
Bottom line: looks like a mistake, take it up with
the package maintainers.
good luck,
Ben Bolker
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