Function reference • malan

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_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` `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
`[[`(<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

Reference

All functions