Populate haplotypes from founder and down in all pedigrees. Note, that haplotypes are unbounded. All founders get a haplotype from calling the user provided function get_founder_haplotype().

pedigrees_all_populate_haplotypes_custom_founders(
pedigrees,
mutation_rates,
get_founder_haplotype = NULL,
prob_two_step = 0,
prob_genealogical_error = 0,
progress = TRUE
)

## Arguments

pedigrees Pedigree list in which to populate haplotypes Vector with mutation rates Function taking no arguments returning a haplotype of length(mutation_rates) Given a mutation happens, this is the probability that the mutation is a two-step mutation Probability that a genealogical error happens: if so, give individual haplotype get_founder_haplotype() instead of father's Show progress

## Details

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

pedigrees_all_populate_haplotypes() and pedigrees_all_populate_haplotypes_ladder_bounded().
sim <- sample_geneology(100, 10)
peds <- build_pedigrees(sim$population) pedigrees_all_populate_haplotypes_custom_founders( peds, c(1, 1), function(x) c(10, 10)) get_haplotype(sim$end_generation_individuals[[1]])#> [1] 11  5