popgen.sim: Simulate genetic data for populations with different allele...
In spflanagan/gwscaR: Genome-wide Selection Components Analysis in R

Simulate genetic data for populations with different allele frequencies

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popgen.sim(npops = 8, inds = 10, nloc = 10000, p = rep(0.01, 8),
  outname = "simulated.ped", analyze = TRUE, ns = c(12, 24, 36, 48,
  96))

`npops`	The number of populations to simulate
`inds`	The number of individuals per population to simulate
`nloc`	The number of loci to simulate
`p`	A vector of average minor allele frequencies per locus to simulate
`outname`	The output name for the file
`analyze`	A logical value for whether or not to run the analysis (defaults to TRUE)
`ns`	A vector of numbers of individuals to simulate