All functions

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_generations()

Infer generation numbers from pedigrees

load_individuals()

Construct a population from data

malan-package

MAle Lineage ANalysis

meioses_generation_distribution()

Meiotic distribution

meiotic_dist()

Meiotic distance between two individuals

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.

split_by_haplotypes()

Split pids by haplotype

`[[`(<malan_pedigreelist>)

Get pedigree from pedigree list

`[[`(<malan_population>)

Get individual from population by pid

test_create_population()

Generate test population

ystr_kits

Kit information about Y-STR markers

ystr_markers

Mutational information about Y-STR markers