[R] AMOVA results from ade4 different than in the reference publication

[Ben Bolker]

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