pedigrees_all_populate_haplotypes: Populate haplotypes in pedigrees (0-founder/unbounded).
In malan: MAle Lineage ANalysis

Description Usage Arguments Details See Also Examples

Populate haplotypes from founder and down in all pedigrees. Note, that haplotypes are unbounded and that all founders get haplotype rep(0L, loci).

pedigrees_all_populate_haplotypes(
  pedigrees,
  loci,
  mutation_rates,
  prob_two_step = 0,
  prob_genealogical_error = 0,
  progress = TRUE
)

`pedigrees`	Pedigree list in which to populate haplotypes
`loci`	Number of loci
`mutation_rates`	Vector with mutation rates, length `loci`
`prob_two_step`	Given a mutation happens, this is the probability that the mutation is a two-step mutation
`prob_genealogical_error`	Probability that a genealogical error happens: if so, give individual haplotype `rep(0L, loci)` instead of father's
`progress`	Show progress

Note, that pedigrees must first have been inferred by build_pedigrees().

pedigrees_all_populate_haplotypes_custom_founders() and pedigrees_all_populate_haplotypes_ladder_bounded().

sim <- sample_geneology(100, 10)
peds <- build_pedigrees(sim$population)
pedigrees_all_populate_haplotypes(peds, 2, c(1, 1))
get_haplotype(sim$end_generation_individuals[[1]])