neMarker: Effective population size based on marker matrix

In enhancer: Mixed-Effects Models Enhancing Functions

Effective population size based on marker matrix

Description

'neMarker' uses a marker matrix to approximate the effective population size (Ne) by discovering how many individuals are needed to sample all possible alleles in a population.

Usage

  neMarker(M, neExplore=NULL, maxMarker=1000, nSamples=5)

Arguments

M	marker matrix coded in a numerical faashion (any allele dosage is fine).
neExplore	a vector of numbers with the effective population sizes to be explored.
maxMarker	maximum number of markers to use for the analysis.
nSamples	number of individuals to sample for the Ne calculation.

Value

$S3

A vector with allele coverage based on different number of individuals

Author(s)

Giovanny Covarrubias-Pazaran

References

Not based on any theory published yet but in a solid intuition on what is really important for a breeding program when we ask what is the effective population size

Examples

  
nInds=300
nMarks=1000

#random population of nInds lines with nMarks markers
M <- matrix(rep(0,nInds*nMarks),nInds,nMarks)
for (i in 1:nInds) {
  M[i,] <- ifelse(runif(nMarks)<0.5,-1,1)
}

# run the function
ne <- neMarker(M, neExplore = seq(2,300,100), nSamples = 5)
# plot(ne$Ne)

enhancer documentation built on April 12, 2026, 9:07 a.m.