{ "_id": "6a1edb23b401979e7340f777", "Package": "malan", "Type": "Package", "Title": "MAle Lineage ANalysis", "Version": "1.0.4", "Authors@R": "c(\nperson(given = \"Mikkel Meyer\", family = \"Andersen\",\nemail = \"mikl@math.aau.dk\", role = c(\"aut\", \"cre\"))\n)", "Author": "Mikkel Meyer Andersen [aut, cre]", "Maintainer": "Mikkel Meyer Andersen ", "Description": "MAle Lineage ANalysis by simulating genealogies backwards\nand imposing short tandem repeats (STR) mutations forwards.\nIntended for forensic Y chromosomal STR (Y-STR) haplotype\nanalyses. Numerous analyses are possible, e.g. number of\nmatches and meiotic distance to matches. Refer to papers\nmentioned in citation(\"malan\") (DOI's:\n, \nand ).", "License": "GPL-2 | file LICENSE", "BugReports": "https://github.com/mikldk/malan/issues", "URL": "https://mikldk.github.io/malan/", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE, roclets = c(\"rd\", \"collate\",\n\"namespace\"))", "RoxygenNote": "7.3.1", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev", "Repository": "https://mikldk.r-universe.dev", "Date/Publication": "2025-08-19 21:17:53 UTC", "RemoteUrl": "https://github.com/mikldk/malan", "RemoteRef": "HEAD", "RemoteSha": "7c58e462af18e21bd093fc79c6eca803ebec2692", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-20 08:56:44 UTC", "User": "root" }, "MD5sum": "e159412ddcf50508c3be28d1bfd39009", "_user": "mikldk", "_type": "src", "_file": "malan_1.0.4.tar.gz", "_fileid": "4ec5a3ab0f19951de3ac5568cae4fef32166a1981f1a08583bbb44a58f300186", "_filesize": 3076707, "_sha256": 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"analyse_mixture_result" ] }, { "page": "analyse_mixture_results", "title": "Analyse mixture results in a vectorised fashion", "topics": [ "analyse_mixture_results" ] }, { "page": "as_tbl_graph.malan_pedigreelist", "title": "Get tidy graph object", "topics": [ "as_tbl_graph.malan_pedigreelist" ] }, { "page": "brothers_matching", "title": "Number of brothers with matching haplotype", "topics": [ "brothers_matching" ] }, { "page": "build_haplotype_hashmap", "title": "Build hashmap of haplotype to individuals", "topics": [ "build_haplotype_hashmap" ] }, { "page": "build_pedigrees", "title": "Build pedigrees from (individuals in) a population.", "topics": [ "build_pedigrees" ] }, { "page": "calc_autosomal_genotype_conditional_cumdist", "title": "Calculate conditional genotype cumulative probabilities with theta", "topics": [ "calc_autosomal_genotype_conditional_cumdist" ] }, { "page": "calc_autosomal_genotype_probs", "title": "Calculate genotype probabilities with theta", "topics": [ "calc_autosomal_genotype_probs" ] }, { "page": "construct_M", "title": "Construct M matrix", "topics": [ "construct_M" ] }, { "page": "count_brothers", "title": "Number of brothers", "topics": [ "count_brothers" ] }, { "page": "count_haplotype_near_matches_individuals", "title": "Count near haplotype matches in list of individuals", "topics": [ "count_haplotype_near_matches_individuals" ] }, { "page": "count_haplotype_occurrences_individuals", "title": "Count haplotypes occurrences in list of individuals", "topics": [ "count_haplotype_occurrences_individuals" ] }, { "page": "count_haplotype_occurrences_pedigree", "title": "Count haplotypes occurrences in pedigree", "topics": [ "count_haplotype_occurrences_pedigree" ] }, { "page": "count_uncles", "title": "Number of uncles", "topics": [ "count_uncles" ] }, { "page": "delete_haplotypeids_hashmap", "title": "Delete haplotype hashmap", "topics": [ "delete_haplotypeids_hashmap" ] }, { "page": "estimate_autotheta_1subpop_genotypes", "title": "Estimate autosomal theta from genotypes", "topics": [ "estimate_autotheta_1subpop_genotypes" ] }, { "page": "estimate_autotheta_1subpop_individuals", "title": "Estimate autosomal theta from individuals", "topics": [ "estimate_autotheta_1subpop_individuals" ] }, { "page": "estimate_autotheta_subpops_genotypes", "title": "Estimate autosomal F, theta, and f from subpopulations of genotypes", "topics": [ "estimate_autotheta_subpops_genotypes" ] }, { "page": "estimate_autotheta_subpops_individuals", "title": "Estimate autosomal F, theta, and f from subpopulations of individuals", "topics": [ "estimate_autotheta_subpops_individuals" ] }, { "page": "estimate_autotheta_subpops_pids", "title": "Estimate autosomal F, theta, and f from subpopulations of individual ids", "topics": [ "estimate_autotheta_subpops_pids" ] }, { "page": "estimate_autotheta_subpops_unweighted_genotypes", "title": "Unweighted estimate of autosomal theta from subpopulations of genotypes", "topics": [ "estimate_autotheta_subpops_unweighted_genotypes" ] }, { "page": "estimate_autotheta_subpops_unweighted_pids", "title": "Unweighted estimate of autosomal theta from subpopulations of individual ids", "topics": [ "estimate_autotheta_subpops_unweighted_pids" ] }, { "page": "father_matches", "title": "Father matches", "topics": [ "father_matches" ] }, { "page": "from_igraph", "title": "Convert igraph to population", "topics": [ "from_igraph" ] }, { "page": "from_igraph_rcpp", "title": "Generate paternal brothers population", "topics": [ "from_igraph_rcpp" ] }, { "page": "generate_get_founder_haplotype_db", "title": "Generate a function to simulate pedigree founder haplotype based on a haplotype databasep", "topics": [ "generate_get_founder_haplotype_db" ] }, { "page": "generate_get_founder_haplotype_ladder", "title": "Generate a function to simulate pedigree founder haplotype based on ladder information", "topics": [ "generate_get_founder_haplotype_ladder" ] }, { "page": "get_allele_counts_genotypes", "title": "Get autosomal allele counts from subpopulations of genotypes", "topics": [ "get_allele_counts_genotypes" ] }, { "page": "get_allele_counts_pids", "title": "Get autosomal allele counts from subpopulations given by pids", "topics": [ "get_allele_counts_pids" ] }, { "page": "get_brothers", "title": "Get brothers", "topics": [ "get_brothers" ] }, { "page": "get_children", "title": "Get children", "topics": [ "get_children" ] }, { "page": "get_cousins", "title": "Get cousins", "topics": [ "get_cousins" ] }, { "page": "get_family_info", "title": "Get individual's family information", "topics": [ "get_family_info" ] }, { "page": "get_father", "title": "Get father", "topics": [ "get_father" ] }, { "page": "get_generation", "title": "Get individual's generation number", "topics": [ "get_generation" ] }, { "page": "get_haplotype", "title": "Get haplotype from an individual", "topics": [ "get_haplotype" ] }, { "page": "get_haplotypes_in_pedigree", "title": "Get haplotypes in pedigree", "topics": [ "get_haplotypes_in_pedigree" ] }, { "page": "get_haplotypes_individuals", "title": "Get haplotype matrix from list of individuals", "topics": [ "get_haplotypes_individuals" ] }, { "page": "get_haplotypes_pids", "title": "Get haplotypes from a vector of pids.", "topics": [ "get_haplotypes_pids" ] }, { "page": "get_individual", "title": "Get individual by pid", "topics": [ "get_individual" ] }, { "page": "get_individuals", "title": "Get all individuals in population", "topics": [ "get_individuals" ] }, { "page": "get_matching_pids_from_hashmap", "title": "Get individuals with a certain haplotype id by hashmap lookup", "topics": [ "get_matching_pids_from_hashmap" ] }, { "page": "get_nodes_edges", "title": "Get nodes and edges", "topics": [ "get_nodes_edges" ] }, { "page": "get_pedigree_as_graph", "title": "Get pedigree information as graph (mainly intended for plotting)", "topics": [ "get_pedigree_as_graph" ] }, { "page": "get_pedigree_from_individual", "title": "Get pedigree from individual", "topics": [ "get_pedigree_from_individual" ] }, { "page": "get_pedigree_id", "title": "Get pedigree id", "topics": [ "get_pedigree_id" ] }, { "page": "get_pedigree_id_from_pid", "title": "Get pedigree ids from pids", "topics": [ "get_pedigree_id_from_pid" ] }, { "page": "get_pedigrees_tidy", "title": "Get pedigrees information in tidy format", "topics": [ "get_pedigrees_tidy" ] }, { "page": "get_pid", "title": "Get pid from individual", "topics": [ "get_pid" ] }, { "page": "get_pids_in_pedigree", "title": "Get pids in pedigree", "topics": [ "get_pids_in_pedigree" ] }, { "page": "get_uncles", "title": "Get uncles", "topics": [ "get_uncles" ] }, { "page": "get_zero_haplotype_generator", "title": "Generate a function to generate the zero haplotype", "topics": [ "get_zero_haplotype_generator" ] }, { "page": "grandfather_matches", "title": "Grandfather matches", "topics": [ "grandfather_matches" ] }, { "page": "haplotype_matches_individuals", "title": "Get individuals matching from list of individuals", "topics": [ "haplotype_matches_individuals" ] }, { "page": "haplotype_partially_matches_individuals", "title": "Get individuals partially matching from list of individuals", "topics": [ "haplotype_partially_matches_individuals" ] }, { "page": "haplotypes_to_hashes", "title": "Convert haplotypes to hashes (integers)", "topics": [ "haplotypes_to_hashes" ] }, { "page": "infer_generation", "title": "Infer individual's generation number", "topics": [ "infer_generation" ] }, { "page": "infer_generations", "title": "Infer generation numbers from pedigrees", "topics": [ "infer_generations" ] }, { "page": "load_haplotypes", "title": "Load haplotypes to individuals", "topics": [ "load_haplotypes" ] }, { "page": "load_individuals", "title": "Construct a population from data", "topics": [ "load_individuals" ] }, { "page": "meioses_generation_distribution", "title": "Meiotic distribution", "topics": [ "meioses_generation_distribution" ] }, { "page": "meiotic_dist", "title": "Meiotic distance between two individuals", "topics": [ "meiotic_dist" ] }, { "page": "meiotic_dist_threshold", "title": "Meiotic distance between two individuals (with threshold)", "topics": [ "meiotic_dist_threshold" ] }, { "page": "meiotic_radius", "title": "Meiotic radius", "topics": [ "meiotic_radius" ] }, { "page": "mixture_info_by_individuals_2pers", "title": "Mixture information about 2 persons' mixture of donor1 and donor2.", "topics": [ "mixture_info_by_individuals_2pers" ] }, { "page": "mixture_info_by_individuals_3pers", "title": "Mixture information about 3 persons' mixture of donor1, donor2 and donor3.", "topics": [ "mixture_info_by_individuals_3pers" ] }, { "page": "mixture_info_by_individuals_4pers", "title": "Mixture information about 4 persons' mixture of donor1, donor2, donor3 and donor4.", "topics": [ "mixture_info_by_individuals_4pers" ] }, { "page": "mixture_info_by_individuals_5pers", "title": "Mixture information about 5 persons' mixture of donor1, donor2, donor3, donor4 and donor5.", "topics": [ "mixture_info_by_individuals_5pers" ] }, { "page": "pedigree_as_igraph", "title": "Convert pedigree to igraph", "topics": [ "pedigree_as_igraph" ] }, { "page": "pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists", "title": "Information about matching individuals", "topics": [ "pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists" ] }, { "page": "pedigree_haplotype_near_matches_meiosis", "title": "Information about almost matching individuals", "topics": [ "pedigree_haplotype_near_matches_meiosis" ] }, { "page": "pedigree_size", "title": "Get pedigree size", "topics": [ "pedigree_size" ] }, { "page": "pedigree_size_generation", "title": "Size of pedigree", "topics": [ "pedigree_size_generation" ] }, { "page": "pedigrees_all_populate_autosomal", "title": "Populate 1-locus autosomal DNA profile in pedigrees with single-step mutation model.", "topics": [ "pedigrees_all_populate_autosomal" ] }, { "page": "pedigrees_all_populate_haplotypes", "title": "Populate haplotypes in pedigrees (0-founder/unbounded).", "topics": [ "pedigrees_all_populate_haplotypes" ] }, { "page": "pedigrees_all_populate_haplotypes_custom_founders", "title": "Populate haplotypes in pedigrees (custom founder/unbounded).", "topics": [ "pedigrees_all_populate_haplotypes_custom_founders" ] }, { "page": "pedigrees_all_populate_haplotypes_ladder_bounded", "title": "Populate haplotypes in pedigrees (custom founder/bounded).", "topics": [ "pedigrees_all_populate_haplotypes_ladder_bounded" ] }, { "page": "pedigrees_count", "title": "Get number of pedigrees", "topics": [ "pedigrees_count" ] }, { "page": "pedigrees_table", "title": "Get distribution of pedigree sizes", "topics": [ "pedigrees_table" ] }, { "page": "plot.malan_pedigree", "title": "Plot pedigree", "topics": [ "plot.malan_pedigree" ] }, { "page": "plot.malan_pedigreelist", "title": "Plot pedigree list", "topics": [ "plot.malan_pedigreelist" ] }, { "page": "population_populate_autosomal_infinite_alleles", "title": "Populate 1-locus autosomal DNA profile in pedigrees with infinite alleles mutation model.", "topics": [ "population_populate_autosomal_infinite_alleles" ] }, { "page": "population_size_generation", "title": "Size of population", "topics": [ "population_size_generation" ] }, { "page": "print_individual", "title": "Print individual", "topics": [ "print_individual" ] }, { "page": "print.malan_pedigree", "title": "Print pedigree", "topics": [ "print.malan_pedigree" ] }, { "page": "print.malan_pedigreelist", "title": "Print pedigree list", "topics": [ "print.malan_pedigreelist" ] }, { "page": "print.malan_population", "title": "Print population", "topics": [ "print.malan_population" ] }, { "page": "print.malan_population_abort", "title": "Print 'malan_population_abort'", "topics": [ "print.malan_population_abort" ] }, { "page": "relationship_allele_diff_dist", "title": "Calculate 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