gl.sim.ind: Simulates individuals based on the allele frequencies...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Simulates individuals based on the allele frequencies provided via a genlight object.

Description

This function simulates individuals based on the allele frequencies of a genlight object. The output is a genlight object with the same number of loci as the input genlight object.

Usage

gl.sim.ind(x, n = 50, popname = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
n	Number of individuals that should be simulated [default 50].
popname	A population name for the simulated individuals [default NULL].

Details

The function can be used to simulate populations for sampling designs or for power analysis. Check the example below where the effect of drift is explored, by simply simulating several generation a genlight object and putting in the allele frequencies of the previous generation. The beauty of the function is, that it is lightning fast. Be aware this is a simulation and to avoid lengthy error checking the function crashes if there are loci that have just NAs. If such a case can occur during your simulation, those loci need to be removed, before the function is called.

Value

A genlight object with n individuals.

Author(s)

Bernd Gruber ([e-mail])

Examples

glsim <- gl.sim.ind(testset.gl, n=10, popname='sims')
glsim
###Simulate drift over 10 generation
# assuming a bottleneck of only 10 individuals
# [ignoring effect of mating and mutation]
# Simulate 20 individuals with no structure and 50 SNP loci
founder <- glSim(n.ind = 20, n.snp.nonstruc = 50, ploidy=2)
#number of fixed loci in the first generation

res <- sum(colMeans(as.matrix(founder), na.rm=TRUE) %%2 ==0)
simgl <- founder
#49 generations of only 10 individuals
for (i in 2:50)
{
   simgl <- gl.sim.ind(simgl, n=10, popname='sims')
   res[i]<- sum(colMeans(as.matrix(simgl), na.rm=TRUE) %%2 ==0)
}
plot(1:50, res, type='b', xlab='generation', ylab='# fixed loci')

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.