calcA: Count each individual's rare alleles per simulation

In nprcgenekeepr: Genetic Tools for Colony Management

Count each individual's rare alleles per simulation

Description

Part of Genetic Value Analysis

Usage

calcA(alleles, threshold = 1L, byID = FALSE)

Arguments

alleles	a matrix with {V1 ... Vn, id, parent} providing the alleles an animal received during each simulation. The first n columns provide the alleles; the final two columns provide the animal ID and the parent the allele came from.
threshold	an integer indicating the maximum number of copies of an allele that can be present in the population for it to be considered rare. Default is 1.
byID	logical variable of length 1 that is passed through to eventually be used by alleleFreq(), which calculates the count of each allele in the provided vector. If byID is TRUE and ids are provided, the function will only count the unique alleles for an individual (homozygous alleles will be counted as 1).

Value

A matrix with named rows indicating the number of unique alleles an animal had during each round of simulation (indicated in columns).

References

Ballou JD, Lacy RC. 1995. Identifying genetically important individuals for management of genetic variation in pedigreed populations, p 77-111. In: Ballou JD, Gilpin M, Foose TJ, editors. Population management for survival and recovery. New York (NY): Columbia University Press.

MacCluer JW, et al. 1986. Pedigree analysis by computer simulation. Zoo Biology 5:147-160.

See Also

Other genetic value analysis: calcFE(), calcFEFG(), calcFG(), calcFGSE(), calcGU(), calcGUSE(), calcGeneDiversity(), calcNeSexRatio(), calcNeVariance(), calcRetention()

Examples

library(nprcgenekeepr)
rare <- calcA(nprcgenekeepr::ped1Alleles, threshold = 3, byID = FALSE)

nprcgenekeepr documentation built on July 26, 2026, 5:06 p.m.