# MAle Lineage ANalysis

## Documentation for package ‘malan’ version 1.0.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M P R S T Y misc

malan-package | MAle Lineage ANalysis

## -- A --

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

## -- B --

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.

## -- C --

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

## -- D --

delete_haplotypeids_hashmap | Delete haplotype hashmap

## -- E --

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

## -- F --

father_matches | Father matches
from_igraph | Convert igraph to population
from_igraph_rcpp | Generate paternal brothers population

## -- G --

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_individuals | Get haplotype matrix from list of individuals
get_haplotypes_in_pedigree | Get haplotypes in pedigree
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_pedigrees_tidy | Get pedigrees information in tidy format
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_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

## -- H --

haplotypes_to_hashes | Convert haplotypes to hashes (integers)
haplotype_matches_individuals | Get individuals matching from list of individuals
haplotype_partially_matches_individuals | Get individuals partially matching from list of individuals

## -- I --

infer_generation | Infer individual's generation number
infer_generations | Infer generation numbers from pedigrees

## -- L --

load_haplotypes | Load haplotypes to individuals
load_individuals | Construct a population from data

## -- M --

malan | 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.

## -- P --

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
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
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

## -- R --

relationship_allele_diff_dist | Calculate distribution of allele difference
relationship_allele_diff_dist_sym | Calculate distribution of allele difference for symmetric mutation rates

## -- S --

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

## -- T --

test_create_population | Generate test population

## -- Y --

ystr_kits | Kit information about Y-STR markers
ystr_markers | Mutational information about Y-STR markers

## -- misc --

[[.malan_pedigreelist | Get pedigree from pedigree list
[[.malan_population | Get individual from population by pid