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

[Stéphane Dray]

Hi,

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 
(http://listes.univ-lyon1.fr/wws/info/adelist)

Cheers.

Ben Bolker wrote:
> 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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>   

-- 
Stéphane DRAY (dray at biomserv.univ-lyon1.fr )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
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