strataG (version 2.4.905)

popGenEqns: Population Genetics Equations

Description

Collection of classical population genetics equations.

Usage

wrightFst(Ne, dispersal, gen.time, ploidy)
numGensEq(fst, Ne, gen.time)
fstToNm(fst, ploidy)
expectedNumAlleles(n, theta, ploidy)

Arguments

Ne

Effective population size.

dispersal

Migration rate in terms of probability of an individual migrating in a generation.

gen.time

Number of generations since ancestral population.

ploidy

Ploidy of the locus.

fst

value of Fst at equilibrium.

n

Sample size.

theta

Product of effective population size (Ne) and mutation rate (mu).

Value

wrightFst

numGensEq

fstToNm

expectedNumAlleles

a two element vector with the expected number of alleles (num.alleles) and variance (var.num.alleles).

Details

wrightFst

Calculate Wright's Fst from Ne, dispersal, and generation time.

numGensEq

Calculate the number of generations to equilibrium based on a an ideal Wright model.

fstToNm

Calculate Nm (number of migrants per generation) for a given value of Fst.

expectedNumAlleles

Calculate the expected number of alleles in a sample of a given size and value of theta.

References

Ewens, W. 1972. The sampling theory of selectively neutral alleles. Theoretical Population Biology 3:87-112. Eqns. 11 and 24.

Examples

# NOT RUN {
dispersal <- seq(0.05, 0.8, by = 0.05)
fst <- wrightFst(100, dispersal, 20, 2)
plot(dispersal, fst, type = "l")

numGensEq(0.15, 100, 20)
numGensEq(0.3, 100, 20)
numGensEq(0.15, 50, 20)

fst <- seq(0.001, 0.2, length.out = 100)
Nm <- fstToNm(fst, 2)
plot(fst, Nm, type = "l")

expectedNumAlleles(20, 1, 2)
# double the samples
expectedNumAlleles(40, 1, 2)
# for a haploid locus
expectedNumAlleles(40, 1, 1)
# double theta
expectedNumAlleles(40, 2, 1)

# }