Man pages for malan
MAle Lineage ANalysis
| 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... |
| 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... |
| estimate_autotheta_subpops_individuals | Estimate autosomal F, theta, and f from subpopulations of... |
| estimate_autotheta_subpops_pids | Estimate autosomal F, theta, and f from subpopulations of... |
| estimate_autotheta_subpops_unweighted_genotypes | Unweighted estimate of autosomal theta from subpopulations of... |
| estimate_autotheta_subpops_unweighted_pids | Unweighted estimate of autosomal theta from subpopulations of... |
| 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... |
| generate_get_founder_haplotype_ladder | Generate a function to simulate pedigree founder haplotype... |
| 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_pedigree_as_graph | Get pedigree information as graph (mainly intended for... |
| 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... |
| mixture_info_by_individuals_3pers | Mixture information about 3 persons' mixture of donor1,... |
| mixture_info_by_individuals_4pers | Mixture information about 4 persons' mixture of donor1,... |
| mixture_info_by_individuals_5pers | Mixture information about 5 persons' mixture of donor1,... |
| 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 |
| pedigrees_all_populate_autosomal | Populate 1-locus autosomal DNA profile in pedigrees with... |
| 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 |
| pedigree_size | Get pedigree size |
| pedigree_size_generation | Size of pedigree |
| 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... |
| population_size_generation | Size of population |
| print_individual | Print individual |
| print.malan_pedigree | Print pedigree |
| print.malan_pedigreelist | Print pedigree list |
| print.malan_population | Print population |
| print.malan_population_abort | Print 'malan_population_abort' |
| relationship_allele_diff_dist | Calculate distribution of allele difference |
| relationship_allele_diff_dist_sym | Calculate distribution of allele difference for symmetric... |
| 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 |
| sub-sub-.malan_pedigreelist | Get pedigree from pedigree list |
| sub-sub-.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 |
