R/RcppExports.R
pedigrees_all_populate_haplotypes_custom_founders.Rd
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 )
pedigrees | Pedigree list in which to populate haplotypes |
---|---|
mutation_rates | Vector with mutation rates |
get_founder_haplotype | Function taking no arguments returning a haplotype of |
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 |
progress | Show progress |
Note, that pedigrees must first have been inferred by build_pedigrees()
.
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