popGenEqns: Population Genetics Equations

In strataG: Summaries and Population Structure Analyses of Genetic Data

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).

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.

Value

wrightFst

numGensEq

fstToNm

expectedNumAlleles

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

Author(s)

Eric Archer [e-mail]

References

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

Examples

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)

strataG documentation built on Feb. 28, 2020, 9:07 a.m.