Package: malan 1.0.3
malan: MAle Lineage ANalysis
MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches. Refer to papers mentioned in citation("malan") (DOI's: <doi:10.1371/journal.pgen.1007028>, <doi:10.21105/joss.00684> and <doi:10.1016/j.fsigen.2018.10.004>).
Authors:
malan_1.0.3.tar.gz
malan_1.0.3.tar.gz(r-4.5-noble)malan_1.0.3.tar.gz(r-4.4-noble)
malan_1.0.3.tgz(r-4.4-emscripten)malan_1.0.3.tgz(r-4.3-emscripten)
malan.pdf |malan.html✨
malan/json (API)
NEWS
# Install 'malan' in R: |
install.packages('malan', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mikldk/malan/issues
- ystr_kits - Kit information about Y-STR markers
- ystr_markers - Mutational information about Y-STR markers
Last updated 1 years agofrom:e30c4cb481. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 23 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 23 2024 |
Exports:brothers_matchingbuild_haplotype_hashmapbuild_pedigreescalc_autosomal_genotype_conditional_cumdistcalc_autosomal_genotype_probsconstruct_Mcount_brotherscount_haplotype_near_matches_individualscount_haplotype_occurrences_individualscount_haplotype_occurrences_pedigreecount_unclesdelete_haplotypeids_hashmapestimate_autotheta_1subpop_genotypesestimate_autotheta_1subpop_individualsestimate_autotheta_subpops_genotypesestimate_autotheta_subpops_individualsestimate_autotheta_subpops_pidsestimate_autotheta_subpops_unweighted_genotypesestimate_autotheta_subpops_unweighted_pidsfather_matchesfrom_igraphgenerate_get_founder_haplotype_dbgenerate_get_founder_haplotype_ladderget_allele_counts_genotypesget_allele_counts_pidsget_brothersget_childrenget_cousinsget_family_infoget_fatherget_generationget_haplotypeget_haplotypes_in_pedigreeget_haplotypes_individualsget_haplotypes_pidsget_individualget_individualsget_matching_pids_from_hashmapget_nodes_edgesget_pedigree_as_graphget_pedigree_from_individualget_pedigree_idget_pedigree_id_from_pidget_pidget_pids_in_pedigreeget_unclesget_zero_haplotype_generatorgrandfather_matcheshaplotype_matches_individualshaplotype_partially_matches_individualshaplotypes_to_hashesinfer_generationinfer_generationsload_haplotypesload_individualsmeioses_generation_distributionmeiotic_distmeiotic_dist_thresholdmeiotic_radiusmixture_info_by_individuals_2persmixture_info_by_individuals_3persmixture_info_by_individuals_4persmixture_info_by_individuals_5perspedigree_as_igraphpedigree_haplotype_matches_in_pedigree_meiosis_L1_distspedigree_haplotype_near_matches_meiosispedigree_sizepedigree_size_generationpedigrees_all_populate_autosomalpedigrees_all_populate_haplotypespedigrees_all_populate_haplotypes_custom_founderspedigrees_all_populate_haplotypes_ladder_boundedpedigrees_countpedigrees_tablepopulation_populate_autosomal_infinite_allelespopulation_size_generationprint_individualrelationship_allele_diff_distrelationship_allele_diff_dist_symsample_autosomal_genotypesample_geneologysample_geneology_varying_sizeset_generationsplit_by_haplotypes
Dependencies:clicpp11dplyrfansigenericsglueigraphlatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RcppRcppArmadilloRcppProgressrlangstringistringrtibbletidygraphtidyrtidyselectutf8vctrswithr