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

[Kim Milferstedt]

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.

Below are the data for "within sample/population" from ade4 and from the 
haplotypic distance matrix in the paper:

source	name	Variance	% total variance	p-value	phi
ade4	within samples	0.478	75.390	1.000	0.246
paper	within populations	0.478	75.390	0.000	0.246

In the R output, it seems that the Std.Obs for "within samples" in ade4 
is very high and may be the reason why the difference is not 
significant. Std.Obs is not given in the publication.

Is the high p-value an error in ade4 or am I missing something?

Thanks already for your help!

Kim
-- 
___________________________________________
Kim Milferstedt, PhD
Postdoctoral Researcher
University of Illinois at Urbana-Champaign
Department of Microbiology
C207 CLSL
601 S. Goodwin Avenue
Urbana, IL 61801

phone: 001-217-244-0721
email: milferst at uiuc.edu