Biodem (version 0.5)

Fst: Calculates the Fst from the conditional kinship matrix

Description

Calculates the Fst from a conditional kinship matrix.

Usage

Fst(rval, N)

Arguments

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

Value

Fst returns one numeric value.

Details

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.

References

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.

Examples

# NOT RUN {
# 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
# }