Fst {Biodem} | R Documentation |
Calculates the Fst from a conditional kinship matrix.
Fst(rval, N)
rval |
is a conditional kinship matrix, normally obtained by the functions 'R' and 'rel.cond' in the Biodem library. |
N |
the vector of effective populations size, nominally obtained by dividing the total population size by three. Starting form surname data, effective population size coincides with the number of marriages |
The use of the Fst function follows Harpending and Jenkins 1974, and Jorde 1982. It gives an estimate of Wright's Fst, which is a measure of between-subdivision genetic heterogeneity.
Fst returns one numeric value.
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Federico C. F. Calboli f.calboli@gmail.com
Harpending, H. C. and T. jenkins. 1974. !Kung population structure. In: J. F. Crow and C. F. Denniston (eds.), Genetic distance, pp 137-161. Plenum Press, NY.
Jorde, L. B. 1982. The genetic structure of the Utah mormons: migration analysis. Human Biology 54(3): 583-597.
# Swedlund data again... data(P); data(S); data(N) # starting with how many cycles to equilibrium x<-mal.eq(S,P,N) # calculation of phi phi<-mal.phi(S,P,N,x) # calculation of the conditional kinship matrix cond<-mal.cond(phi,N) # finally! we get the Fst value fst<-Fst(cond,N) fst # starting from a raw marriage records dataset: data(valley) tot <- sur.freq(valley,valley$PAR,valley$SURM,valley$SURF) tot # a frequency table calculated above all the surnames iso.matrix <- uri(tot) iso.matrix # an unbiased random isonymy matrix reg <- rri(tot) reg # a coefficient of unbiased Regional Random Isonymy kin.cond <- rel.cond(iso.matrix,reg) kin.cond # a conditional kinship matrix N <- colSums(tot) # effective population size fst<-Fst(kin.cond,N) fst