[[.malan_pedigreelist   Get pedigree from pedigree list
[[.malan_population     Get individual from population by pid
analyse_mixture_result
                        Analyse mixture results
analyse_mixture_results
                        Analyse mixture results in a vectorised fashion
as_tbl_graph.malan_pedigreelist
                        Get tidy graph object
brothers_matching       Number of brothers with matching haplotype
build_haplotype_hashmap
                        Build hashmap of haplotype to individuals
build_pedigrees         Build pedigrees from (individuals in) a
                        population.
calc_autosomal_genotype_conditional_cumdist
                        Calculate conditional genotype cumulative
                        probabilities with theta
calc_autosomal_genotype_probs
                        Calculate genotype probabilities with theta
construct_M             Construct M matrix
count_brothers          Number of brothers
count_haplotype_near_matches_individuals
                        Count near haplotype matches in list of
                        individuals
count_haplotype_occurrences_individuals
                        Count haplotypes occurrences in list of
                        individuals
count_haplotype_occurrences_pedigree
                        Count haplotypes occurrences in pedigree
count_uncles            Number of uncles
delete_haplotypeids_hashmap
                        Delete haplotype hashmap
estimate_autotheta_1subpop_genotypes
                        Estimate autosomal theta from genotypes
estimate_autotheta_1subpop_individuals
                        Estimate autosomal theta from individuals
estimate_autotheta_subpops_genotypes
                        Estimate autosomal F, theta, and f from
                        subpopulations of genotypes
estimate_autotheta_subpops_individuals
                        Estimate autosomal F, theta, and f from
                        subpopulations of individuals
estimate_autotheta_subpops_pids
                        Estimate autosomal F, theta, and f from
                        subpopulations of individual ids
estimate_autotheta_subpops_unweighted_genotypes
                        Unweighted estimate of autosomal theta from
                        subpopulations of genotypes
estimate_autotheta_subpops_unweighted_pids
                        Unweighted estimate of autosomal theta from
                        subpopulations of individual ids
father_matches          Father matches
from_igraph             Convert igraph to population
from_igraph_rcpp        Generate paternal brothers population
generate_get_founder_haplotype_db
                        Generate a function to simulate pedigree
                        founder haplotype based on a haplotype
                        databasep
generate_get_founder_haplotype_ladder
                        Generate a function to simulate pedigree
                        founder haplotype based on ladder information
get_allele_counts_genotypes
                        Get autosomal allele counts from subpopulations
                        of genotypes
get_allele_counts_pids
                        Get autosomal allele counts from subpopulations
                        given by pids
get_brothers            Get brothers
get_children            Get children
get_cousins             Get cousins
get_family_info         Get individual's family information
get_father              Get father
get_generation          Get individual's generation number
get_haplotype           Get haplotype from an individual
get_haplotypes_in_pedigree
                        Get haplotypes in pedigree
get_haplotypes_individuals
                        Get haplotype matrix from list of individuals
get_haplotypes_pids     Get haplotypes from a vector of pids.
get_individual          Get individual by pid
get_individuals         Get all individuals in population
get_matching_pids_from_hashmap
                        Get individuals with a certain haplotype id by
                        hashmap lookup
get_nodes_edges         Get nodes and edges
get_pedigree_as_graph   Get pedigree information as graph (mainly
                        intended for plotting)
get_pedigree_from_individual
                        Get pedigree from individual
get_pedigree_id         Get pedigree id
get_pedigree_id_from_pid
                        Get pedigree ids from pids
get_pedigrees_tidy      Get pedigrees information in tidy format
get_pid                 Get pid from individual
get_pids_in_pedigree    Get pids in pedigree
get_uncles              Get uncles
get_zero_haplotype_generator
                        Generate a function to generate the zero
                        haplotype
grandfather_matches     Grandfather matches
haplotype_matches_individuals
                        Get individuals matching from list of
                        individuals
haplotype_partially_matches_individuals
                        Get individuals partially matching from list of
                        individuals
haplotypes_to_hashes    Convert haplotypes to hashes (integers)
infer_generation        Infer individual's generation number
infer_generations       Infer generation numbers from pedigrees
load_haplotypes         Load haplotypes to individuals
load_individuals        Construct a population from data
malan-package           MAle Lineage ANalysis
meioses_generation_distribution
                        Meiotic distribution
meiotic_dist            Meiotic distance between two individuals
meiotic_dist_threshold
                        Meiotic distance between two individuals (with
                        threshold)
meiotic_radius          Meiotic radius
mixture_info_by_individuals_2pers
                        Mixture information about 2 persons' mixture of
                        donor1 and donor2.
mixture_info_by_individuals_3pers
                        Mixture information about 3 persons' mixture of
                        donor1, donor2 and donor3.
mixture_info_by_individuals_4pers
                        Mixture information about 4 persons' mixture of
                        donor1, donor2, donor3 and donor4.
mixture_info_by_individuals_5pers
                        Mixture information about 5 persons' mixture of
                        donor1, donor2, donor3, donor4 and donor5.
pedigree_as_igraph      Convert pedigree to igraph
pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists
                        Information about matching individuals
pedigree_haplotype_near_matches_meiosis
                        Information about almost matching individuals
pedigree_size           Get pedigree size
pedigree_size_generation
                        Size of pedigree
pedigrees_all_populate_autosomal
                        Populate 1-locus autosomal DNA profile in
                        pedigrees with single-step mutation model.
pedigrees_all_populate_haplotypes
                        Populate haplotypes in pedigrees
                        (0-founder/unbounded).
pedigrees_all_populate_haplotypes_custom_founders
                        Populate haplotypes in pedigrees (custom
                        founder/unbounded).
pedigrees_all_populate_haplotypes_ladder_bounded
                        Populate haplotypes in pedigrees (custom
                        founder/bounded).
pedigrees_count         Get number of pedigrees
pedigrees_table         Get distribution of pedigree sizes
plot.malan_pedigree     Plot pedigree
plot.malan_pedigreelist
                        Plot pedigree list
population_populate_autosomal_infinite_alleles
                        Populate 1-locus autosomal DNA profile in
                        pedigrees with infinite alleles mutation model.
population_size_generation
                        Size of population
print.malan_pedigree    Print pedigree
print.malan_pedigreelist
                        Print pedigree list
print.malan_population
                        Print population
print.malan_population_abort
                        Print 'malan_population_abort'
print_individual        Print individual
relationship_allele_diff_dist
                        Calculate distribution of allele difference
relationship_allele_diff_dist_sym
                        Calculate distribution of allele difference for
                        symmetric mutation rates
sample_autosomal_genotype
                        Sample genotype with theta
sample_geneology        Simulate a geneology with constant population
                        size.
sample_geneology_varying_size
                        Simulate a geneology with varying population
                        size.
set_generation          Set individual's generation number
split_by_haplotypes     Split pids by haplotype
test_create_population
                        Generate test population
ystr_kits               Kit information about Y-STR markers
ystr_markers            Mutational information about Y-STR markers
