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:Mikkel Meyer Andersen [aut, cre]

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NEWS

# Install 'malan' in R:
install.packages('malan', repos = c('https://mikldk.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mikldk/malan/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

5.08 score 6 scripts 189 downloads 3 mentions 84 exports 28 dependencies

Last updated 10 months agofrom:dbc17ed841. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-win-x86_64NOTENov 11 2024
R-4.5-linux-x86_64NOTENov 11 2024
R-4.4-win-x86_64OKNov 11 2024
R-4.4-mac-x86_64OKNov 11 2024
R-4.4-mac-aarch64OKNov 11 2024
R-4.3-win-x86_64OKNov 11 2024
R-4.3-mac-x86_64OKNov 11 2024
R-4.3-mac-aarch64OKNov 11 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

Case study: Partial profiles

Mikkel Meyer Andersen

Rendered fromcase-study-partial.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2020-06-25
Started: 2018-03-19

Introduction

Mikkel Meyer Andersen

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2019-03-05
Started: 2017-01-27

Readme and manuals

Help Manual

Help pageTopics
MAle Lineage ANalysismalan-package malan
Get pedigree from pedigree list[[.malan_pedigreelist
Get individual from population by pid[[.malan_population
Analyse mixture resultsanalyse_mixture_result
Analyse mixture results in a vectorised fashionanalyse_mixture_results
Get tidy graph objectas_tbl_graph.malan_pedigreelist
Number of brothers with matching haplotypebrothers_matching
Build hashmap of haplotype to individualsbuild_haplotype_hashmap
Build pedigrees from (individuals in) a population.build_pedigrees
Calculate conditional genotype cumulative probabilities with thetacalc_autosomal_genotype_conditional_cumdist
Calculate genotype probabilities with thetacalc_autosomal_genotype_probs
Construct M matrixconstruct_M
Number of brotherscount_brothers
Count near haplotype matches in list of individualscount_haplotype_near_matches_individuals
Count haplotypes occurrences in list of individualscount_haplotype_occurrences_individuals
Count haplotypes occurrences in pedigreecount_haplotype_occurrences_pedigree
Number of unclescount_uncles
Delete haplotype hashmapdelete_haplotypeids_hashmap
Estimate autosomal theta from genotypesestimate_autotheta_1subpop_genotypes
Estimate autosomal theta from individualsestimate_autotheta_1subpop_individuals
Estimate autosomal F, theta, and f from subpopulations of genotypesestimate_autotheta_subpops_genotypes
Estimate autosomal F, theta, and f from subpopulations of individualsestimate_autotheta_subpops_individuals
Estimate autosomal F, theta, and f from subpopulations of individual idsestimate_autotheta_subpops_pids
Unweighted estimate of autosomal theta from subpopulations of genotypesestimate_autotheta_subpops_unweighted_genotypes
Unweighted estimate of autosomal theta from subpopulations of individual idsestimate_autotheta_subpops_unweighted_pids
Father matchesfather_matches
Convert igraph to populationfrom_igraph
Generate paternal brothers populationfrom_igraph_rcpp
Generate a function to simulate pedigree founder haplotype based on a haplotype databasepgenerate_get_founder_haplotype_db
Generate a function to simulate pedigree founder haplotype based on ladder informationgenerate_get_founder_haplotype_ladder
Get autosomal allele counts from subpopulations of genotypesget_allele_counts_genotypes
Get autosomal allele counts from subpopulations given by pidsget_allele_counts_pids
Get brothersget_brothers
Get childrenget_children
Get cousinsget_cousins
Get individual's family informationget_family_info
Get fatherget_father
Get individual's generation numberget_generation
Get haplotype from an individualget_haplotype
Get haplotypes in pedigreeget_haplotypes_in_pedigree
Get haplotype matrix from list of individualsget_haplotypes_individuals
Get haplotypes from a vector of pids.get_haplotypes_pids
Get individual by pidget_individual
Get all individuals in populationget_individuals
Get individuals with a certain haplotype id by hashmap lookupget_matching_pids_from_hashmap
Get nodes and edgesget_nodes_edges
Get pedigree information as graph (mainly intended for plotting)get_pedigree_as_graph
Get pedigree from individualget_pedigree_from_individual
Get pedigree idget_pedigree_id
Get pedigree ids from pidsget_pedigree_id_from_pid
Get pedigrees information in tidy formatget_pedigrees_tidy
Get pid from individualget_pid
Get pids in pedigreeget_pids_in_pedigree
Get unclesget_uncles
Generate a function to generate the zero haplotypeget_zero_haplotype_generator
Grandfather matchesgrandfather_matches
Get individuals matching from list of individualshaplotype_matches_individuals
Get individuals partially matching from list of individualshaplotype_partially_matches_individuals
Convert haplotypes to hashes (integers)haplotypes_to_hashes
Infer individual's generation numberinfer_generation
Infer generation numbers from pedigreesinfer_generations
Load haplotypes to individualsload_haplotypes
Construct a population from dataload_individuals
Meiotic distributionmeioses_generation_distribution
Meiotic distance between two individualsmeiotic_dist
Meiotic distance between two individuals (with threshold)meiotic_dist_threshold
Meiotic radiusmeiotic_radius
Mixture information about 2 persons' mixture of donor1 and donor2.mixture_info_by_individuals_2pers
Mixture information about 3 persons' mixture of donor1, donor2 and donor3.mixture_info_by_individuals_3pers
Mixture information about 4 persons' mixture of donor1, donor2, donor3 and donor4.mixture_info_by_individuals_4pers
Mixture information about 5 persons' mixture of donor1, donor2, donor3, donor4 and donor5.mixture_info_by_individuals_5pers
Convert pedigree to igraphpedigree_as_igraph
Information about matching individualspedigree_haplotype_matches_in_pedigree_meiosis_L1_dists
Information about almost matching individualspedigree_haplotype_near_matches_meiosis
Get pedigree sizepedigree_size
Size of pedigreepedigree_size_generation
Populate 1-locus autosomal DNA profile in pedigrees with single-step mutation model.pedigrees_all_populate_autosomal
Populate haplotypes in pedigrees (0-founder/unbounded).pedigrees_all_populate_haplotypes
Populate haplotypes in pedigrees (custom founder/unbounded).pedigrees_all_populate_haplotypes_custom_founders
Populate haplotypes in pedigrees (custom founder/bounded).pedigrees_all_populate_haplotypes_ladder_bounded
Get number of pedigreespedigrees_count
Get distribution of pedigree sizespedigrees_table
Plot pedigreeplot.malan_pedigree
Plot pedigree listplot.malan_pedigreelist
Populate 1-locus autosomal DNA profile in pedigrees with infinite alleles mutation model.population_populate_autosomal_infinite_alleles
Size of populationpopulation_size_generation
Print individualprint_individual
Print pedigreeprint.malan_pedigree
Print pedigree listprint.malan_pedigreelist
Print populationprint.malan_population
Print 'malan_population_abort'print.malan_population_abort
Calculate distribution of allele differencerelationship_allele_diff_dist
Calculate distribution of allele difference for symmetric mutation ratesrelationship_allele_diff_dist_sym
Sample genotype with thetasample_autosomal_genotype
Simulate a geneology with constant population size.sample_geneology
Simulate a geneology with varying population size.sample_geneology_varying_size
Set individual's generation numberset_generation
Split pids by haplotypesplit_by_haplotypes
Generate test populationtest_create_population
Kit information about Y-STR markersystr_kits
Mutational information about Y-STR markersystr_markers