pop_Ne: Effective population size

In purgeR: Inbreeding-Purging Estimation in Pedigreed Populations

Effective population size

Description

Estimate the effective population size (Ne). This is computed from the increase in individual inbreeding, following the method described by Gutiérrez et al (2008, 2009).

Usage

pop_Ne(ped, Fcol, tcol)

Arguments

ped	A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.
Fcol	Name of column with inbreeding coefficient values.
tcol	Name of column with generation numbers.

Value

A list with the effective population size (Ne) and its standard error (se_Ne).

References

• Gutiérrez JP, Cervantes I, Molina A, Valera M, Goyache F. 2008. Individual increase in inbreeding allows estimating effective sizes from pedigrees. Genet. Sel. Evol. 40: 359-378.

• Gutiérrez JP, Cervantes I, Goyache F. 2009. Improving the estimation of realized effective population sizes in farm animals. J. Anim. Breed. Genet. 126: 327-332.

See Also

ip_F, pop_t

Examples

data(atlas)
atlas <- ip_F(atlas) # compute inbreeding, appending column "F"
atlas <- pop_t(atlas) # compute generations, appending column "t"
pop_Ne(atlas, Fcol = "Fi", tcol = "t")

purgeR documentation built on Aug. 16, 2023, 9:07 a.m.