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

[Manuel A. Morales]

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