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: [EMAIL PROTECTED]
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