All functions
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build_haplotypeids_hashmap()
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Build hashmap of haplotype ids to individuals |
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build_pedigrees()
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Build pedigrees from (individuals in) a population. |
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count_haplotype_occurrences_individuals()
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Count haplotypes occurrences in list of individuals |
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count_haplotype_occurrences_pedigree()
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Count haplotypes occurrences in pedigree |
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delete_haplotypeids_hashmap()
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Delete haplotype id hashmap |
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get_generations_from_final()
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Get individual's generations from final generation |
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get_haplotype()
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Get haplotype from an individual |
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get_haplotype_id_individual()
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Get haplotype id from individual |
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get_haplotype_ids_individuals()
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Get haplotype ids from list of individuals |
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get_haplotype_matching_individuals()
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Get individuals matching from list of individuals |
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get_haplotype_no_variants()
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Get number of variants in haplotype |
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get_haplotypeid_matching_individuals_from_hashmap()
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Get individuals with a certain haplotype id by hashmap lookup |
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get_haplotypes_in_pedigree()
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Get haplotypes in pedigree |
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get_haplotypes_individuals()
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Get haplotype matrix from list of individuals |
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get_haplotypes_pids()
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Get haplotypes from a vector of pids. |
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get_individual()
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Get individual by pid |
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get_individual_is_female()
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Is individual female (or male) |
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get_individuals()
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Get all individuals in population |
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get_individuals_is_female()
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Is individuals females (or males) |
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get_is_female_in_pedigree()
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Get sexes of individuals in pedigree |
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get_matches_info()
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Information about matching individuals |
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get_nodes_edges()
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Get nodes and edges |
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get_pedigree_as_graph()
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Get pedigree information as graph (mainly intended for plotting) |
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get_pedigree_from_individual()
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Get pedigree from individual |
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get_pedigree_id()
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Get pedigree id |
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get_pedigree_id_from_pid()
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Get pedigree ids from pids |
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get_pedigrees_tidy()
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Get pedigrees information in tidy format |
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get_pid()
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Get pid from individual |
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get_pids_in_pedigree()
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Get pids in pedigree |
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haplotypes_to_hashes()
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Convert haplotypes to hashes (integers) |
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infer_haplotype_ids()
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Infer haplotype ids |
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meioses_generation_distribution()
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Meiotic distribution |
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meiotic_dist()
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Meiotic distance between two individuals |
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mitolina-package
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MITOchondrial LINeage Analysis |
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mtdna_mut_Oversti
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Mitogenome mutation rates according to Översti et al. (2017) |
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mtdna_mut_Rieux
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Mitogenome mutation rates according to Rieux et al. (2014) |
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mtdna_partitions
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Mitogenome annotated |
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mtdna_vars_Just
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588 forensic-quality haplotypes representing three U.S. populations |
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pedigree_as_igraph()
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Convert pedigree to igraph |
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pedigree_size()
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Get pedigree size |
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pedigree_size_generation()
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Size of pedigree |
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pedigrees_all_populate_haplotypes()
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Populate haplotypes in pedigrees (founder types same for all). |
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pedigrees_all_populate_haplotypes_custom_founders()
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Populate haplotypes in pedigrees (custom founder types). |
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pedigrees_count()
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Get number of pedigrees |
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pedigrees_table()
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Get distribution of pedigree sizes |
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population_size_generation()
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Size of population |
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print_individual()
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Print individual |
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sample_mtdna_geneology_varying_size()
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Simulate a geneology with varying population size. |
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test_create_population()
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Generate test population |