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

From: Ben Bolker <bolker_at_ufl.edu>
Date: Thu, 22 May 2008 17:18:19 +0000 (UTC)

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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