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

From: Stéphane Dray <>
Date: Thu, 22 May 2008 22:46:15 +0200


Ben is correct. The alternative hypothesis is not good for this test (within pop). I will modify it and submit a new version of the package on CRAN (probably next week).

BTW, for question about ade4 please send your email to adelist (


Ben Bolker wrote:
> Kim Milferstedt <milferst <at>> 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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Stéphane DRAY ( )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
Tel: 33 4 72 43 27 57       Fax: 33 4 72 43 13 88

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Received on Thu 22 May 2008 - 21:01:27 GMT

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