[adegenet-forum] Fstat vs pairwise.fst for 2 populations

[Thibaut Jombart]

Hi Manuel

I think this has been discussed already on the hierfstat issues. Best
check and report this there. It may be a bug, or different estimators
being used (inc. different group weightings), but I don't have time to
check this now.

Best
Thibaut

--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
sites.google.com/site/thibautjombart/
Twitter: @TeebzR
+44(0)20 7594 3658


On 10 November 2017 at 16:20, Manuel A. Morales <mmorales at williams.edu> wrote:
> I may have a fundamental misunderstanding of what's happening but it
> seems to me that the functions Fst() and pairwise.fst() should give the
> same value for the case of two populations, which they do not.
>
> A reproducible example:
> data(nancycats)
> obj1 <- seppop(nancycats)$P01
> obj2 <- seppop(nancycats)$P02
> obj3 <- repool(obj1, obj2)
> fstat(obj3)
> pairwise.fst(obj3)
>
> And output:
>> fstat(obj3)
>             pop       Ind
> Total 0.1307741 0.2804306
> pop   0.0000000 0.1721722
>> pairwise.fst(obj3)
>          1
> 2 0.080185
>
> Any help would be very much appreciated.
>
> Best,
> Manuel
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum