Usage Arguments Value Examples
View source: R/fst.pairwise.monoecious.R
1 2 | fst.pairwise.monoecious(N,i,j,xi,xj,ti,tj)
fst.pairwise.monoecious(folder.name,i,j,xi,xj,ti,tj)
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N |
A 4-D array (ex: |
folder.name |
Character string giving the name of the folder where the results of |
i, xi, ti |
Identifiers of the first group of individuals: it specifies the individuals of deme |
i, xi, ti |
Identifiers of the second group of individuals: as above. |
Pairwise genetic differentiation index Fst calculated as ratio of heterozygosities: (Ht - Hs) / Ht
. Ht
is the expected heterozygosity over the population formed by the two groups. Hs
is the average expected heterozygosity over the two groups. The average is weighted by the number of individuals in each group: Hs = (n_i * H_S_i + n_j * H_S_j)/(n_i + n_j)
where n_i
and n_j
are the number of individuals in the first and second group, respectively, and H_s_i
and H_s_j
are the expected heterozygosities in the first and second group, respectively.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | # Load the example data and simulates metapopulation genetics
data(FourPopMonoecious)
N <- sim.metapopgen.monoecious(input.type="array",N1=N1, sigma=sigma, phi_F=phi_F, phi_M=phi_M, mu=mu, delta=delta, settler.surv=settler.surv)
# Calculates fst between various pairs of groups of individuals
fst.pairwise.monoecious(N,1,2,1,1,50,50) # Between one-year old individuals of deme 1 and 2 at time 50
fst.pairwise.monoecious(N,1,1,1,1,1,50) # Between one-year old individuals of deme 1 at time 50 and at time 1 (temporal fst)
# Temporal evolution of fst
fst <- array(NA,dim=c(3,50))
for (t in 1 : 50) {
for (deme in 1 : 3){
fst[deme,t] <- fst.pairwise.monoecious(N,1,(deme+1),1,1,t,t)
}
}
plot(c(1:50),fst[1,],type="l",col="blue",xlab="Year",ylab="Fst")
matplot(c(1:50),fst[2,],type="l",col="darkgreen",add=T)
matplot(c(1:50),fst[3,],type="l",col="red",add=T)
legend(30,1,c("1 vs 2","1 vs 3","1 vs 4"),col=c("blue","darkgreen","red"),lty=1)
# Example with results from sim.metapopgen.monoecious saved on disk
# Let us assume that results are stored in a folder named "2013-nov-13-12.04"
fst.pairwise.monoecious("2013-nov-13-12.04",1,1,1,1,1,50) # Between one-year old individuals of deme 1 at time 50 and at time 1 (temporal fst)
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