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malan-1.0.0.zip

mikldk-malan-5931866
- .Rbuildignore 136 Bytes
- .gitignore 570 Bytes
- .travis.yml 1.5 kB
- DESCRIPTION 1.2 kB
- LICENSE 18.0 kB
- NAMESPACE 2.7 kB
- R
  - RcppExports.R 34.7 kB
  - data.R 1.1 kB
  - haplotypes.R 1.0 kB
  - malan-package.R 25 Bytes
  - malan.R 873 Bytes
  - meta.R 76 Bytes
  - print.R 9.4 kB
- README.md 3.1 kB
- codemeta.json 1.0 kB
- data
  - ystr_kits.RData 410 Bytes
  - ystr_markers.RData 1.8 kB
- docs
  - LICENSE-text.html 21.9 kB
  - articles
    - case-study-partial.html 27.2 kB
    - case-study-partial_files
      - figure-html
        
        unnamed-chunk-10-1.png 49.3 kB
        
        unnamed-chunk-11-1.png 49.3 kB
        
        unnamed-chunk-18-1.png 129.9 kB
        
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        unnamed-chunk-4-1.png 18.0 kB
        
        unnamed-chunk-5-1.png 18.0 kB
        
        unnamed-chunk-9-1.png 57.2 kB
    - index.html 4.1 kB
    - introduction.html 45.6 kB
    - introduction_files
      - figure-html
        
        unnamed-chunk-13-1.png 54.6 kB
        
        unnamed-chunk-14-1.png 49.9 kB
        
        unnamed-chunk-15-1.png 127.8 kB
        
        unnamed-chunk-16-1.png 128.2 kB
        
        unnamed-chunk-17-1.png 145.4 kB
        
        unnamed-chunk-18-1.png 150.1 kB
        
        unnamed-chunk-22-1.png 167.8 kB
        
        unnamed-chunk-33-1.png 15.0 kB
        
        unnamed-chunk-44-1.png 120.0 kB
        
        unnamed-chunk-49-1.png 108.0 kB
        
        unnamed-chunk-6-1.png 141.2 kB
        
        unnamed-chunk-7-1.png 51.1 kB
        
        unnamed-chunk-8-1.png 17.1 kB
  - authors.html 4.7 kB
  - index.html 11.1 kB
  - jquery.sticky-kit.min.js 2.8 kB
  - link.svg 810 Bytes
  - pkgdown.css 3.9 kB
  - pkgdown.js 2.8 kB
  - pkgdown.yml 180 Bytes
  - reference
    - as_tbl_graph.malan_pedigreelist.html 5.3 kB
    - brothers_matching.html 5.2 kB
    - build_pedigrees.html 6.4 kB
    - calc_autosomal_genotype_conditional_cumdist.html 5.5 kB
    - calc_autosomal_genotype_probs.html 5.1 kB
    - count_brothers.html 5.2 kB
    - count_haplotype_occurrences_individuals.html 5.8 kB
    - count_haplotype_occurrences_pedigree.html 6.1 kB
    - count_uncles.html 5.2 kB
    - estimate_theta_1subpop_genotypes.html 5.9 kB
    - estimate_theta_1subpop_individuals.html 5.9 kB
    - estimate_theta_1subpop_sample.html 5.9 kB
    - estimate_theta_subpops_genotypes.html 5.7 kB
    - estimate_theta_subpops_individuals.html 5.7 kB
    - estimate_theta_subpops_pids.html 5.8 kB
    - father_matches.html 5.0 kB
    - generate_get_founder_haplotype_db.html 5.2 kB
    - generate_get_founder_haplotype_ladder.html 5.4 kB
    - get_brothers.html 5.3 kB
    - get_children.html 5.3 kB
    - get_cousins.html 5.3 kB
    - get_family_info.html 5.0 kB
    - get_generation.html 5.1 kB
    - get_haplotype.html 5.9 kB
    - get_haplotypes_in_pedigree.html 5.0 kB
    - get_haplotypes_individuals.html 6.0 kB
    - get_haplotypes_pids.html 6.1 kB
    - get_individual.html 5.0 kB
    - get_individuals.html 4.8 kB
    - get_nodes_edges.html 5.2 kB
    - get_pedigree_as_graph.html 5.0 kB
    - get_pedigree_from_individual.html 5.0 kB
    - get_pedigree_id.html 4.7 kB
    - get_pedigree_id_from_pid.html 5.1 kB
    - get_pedigrees_tidy.html 4.9 kB
    - get_pid.html 4.9 kB
    - get_pids_in_pedigree.html 4.8 kB
    - get_uncles.html 5.2 kB
    - grandfather_matches.html 5.1 kB
    - haplotype_matches_individuals.html 5.7 kB
    - haplotypes_to_hashes.html 5.7 kB
    - index.html 20.5 kB
    - malan-package.html 6.0 kB
    - meioses_generation_distribution.html 5.5 kB
    - meiotic_dist.html 5.4 kB
    - mixture_info_by_individuals.html 5.9 kB
    - mixture_info_by_individuals_3pers.html 6.1 kB
    - pedigree_as_igraph.html 5.1 kB
    - pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists.html 7.1 kB
    - pedigree_size.html 4.7 kB
    - pedigree_size_generation.html 5.3 kB
    - pedigrees_all_populate_autosomal.html 6.6 kB
    - pedigrees_all_populate_haplotypes.html 6.4 kB
    - pedigrees_all_populate_haplotypes_custom_founders.html 6.7 kB
    - pedigrees_all_populate_haplotypes_ladder_bounded.html 7.2 kB
    - pedigrees_count.html 4.8 kB
    - pedigrees_table.html 4.8 kB
    - plot.malan_pedigree.html 6.2 kB
    - plot.malan_pedigreelist.html 5.0 kB
    - population_size_generation.html 5.3 kB
    - print.malan_pedigree.html 4.9 kB
    - print.malan_pedigreelist.html 5.1 kB
    - print.malan_population.html 5.2 kB
    - print.malan_population_abort.html 5.0 kB
    - print_individual.html 4.7 kB
    - sample_autosomal_genotype.html 5.0 kB
    - sample_geneology.html 10.2 kB
    - sample_geneology_varying_size.html 9.7 kB
    - split_by_haplotypes.html 5.4 kB
    - sub-sub-.malan_pedigreelist.html 5.2 kB
    - sub-sub-.malan_population.html 5.0 kB
    - test_create_population.html 4.6 kB
    - ystr_kits.html 5.1 kB
    - ystr_markers.html 5.8 kB
- inst
  - CITATION 495 Bytes
  - doc
    - case-study-partial.R 5.2 kB
    - case-study-partial.Rmd 6.3 kB
    - case-study-partial.html 132.6 kB
    - introduction.R 11.1 kB
    - introduction.Rmd 12.7 kB
    - introduction.html 509.1 kB
- malan.Rproj 343 Bytes
- man
  - as_tbl_graph.malan_pedigreelist.Rd 495 Bytes
  - brothers_matching.Rd 445 Bytes
  - build_pedigrees.Rd 1.1 kB
  - calc_autosomal_genotype_conditional_cumdist.Rd 667 Bytes
  - calc_autosomal_genotype_probs.Rd 492 Bytes
  - count_brothers.Rd 382 Bytes
  - count_haplotype_occurrences_individuals.Rd 773 Bytes
  - count_haplotype_occurrences_pedigree.Rd 1.0 kB
  - count_uncles.Rd 366 Bytes
  - estimate_theta_1subpop_genotypes.Rd 1.0 kB
  - estimate_theta_1subpop_individuals.Rd 991 Bytes
  - estimate_theta_subpops_genotypes.Rd 684 Bytes
  - estimate_theta_subpops_individuals.Rd 694 Bytes
  - estimate_theta_subpops_pids.Rd 725 Bytes
  - father_matches.Rd 391 Bytes
  - generate_get_founder_haplotype_db.Rd 533 Bytes
  - generate_get_founder_haplotype_ladder.Rd 667 Bytes
  - get_brothers.Rd 444 Bytes
  - get_children.Rd 444 Bytes
  - get_cousins.Rd 440 Bytes
  - get_family_info.Rd 356 Bytes
  - get_generation.Rd 380 Bytes
  - get_haplotype.Rd 867 Bytes
  - get_haplotypes_in_pedigree.Rd 347 Bytes
  - get_haplotypes_individuals.Rd 910 Bytes
  - get_haplotypes_pids.Rd 927 Bytes
  - get_individual.Rd 329 Bytes
  - get_individuals.Rd 313 Bytes
  - get_nodes_edges.Rd 461 Bytes
  - get_pedigree_as_graph.Rd 377 Bytes
  - get_pedigree_from_individual.Rd 361 Bytes
  - get_pedigree_id.Rd 261 Bytes
  - get_pedigree_id_from_pid.Rd 386 Bytes
  - get_pedigrees_tidy.Rd 333 Bytes
  - get_pid.Rd 297 Bytes
  - get_pids_in_pedigree.Rd 286 Bytes
  - get_uncles.Rd 436 Bytes
  - grandfather_matches.Rd 421 Bytes
  - haplotype_matches_individuals.Rd 743 Bytes
  - haplotypes_to_hashes.Rd 694 Bytes
  - malan-package.Rd 1.2 kB
  - meioses_generation_distribution.Rd 714 Bytes
  - meiotic_dist.Rd 563 Bytes
  - mixture_info_by_individuals.Rd 765 Bytes
  - mixture_info_by_individuals_3pers.Rd 838 Bytes
  - pedigree_as_igraph.Rd 341 Bytes
  - pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists.Rd 1.7 kB
  - pedigree_size.Rd 259 Bytes
  - pedigree_size_generation.Rd 602 Bytes
  - pedigrees_all_populate_autosomal.Rd 1.2 kB
  - pedigrees_all_populate_haplotypes.Rd 1.1 kB
  - pedigrees_all_populate_haplotypes_custom_founders.Rd 1.2 kB
  - pedigrees_all_populate_haplotypes_ladder_bounded.Rd 1.5 kB
  - pedigrees_count.Rd 290 Bytes
  - pedigrees_table.Rd 312 Bytes
  - plot.malan_pedigree.Rd 738 Bytes
  - plot.malan_pedigreelist.Rd 400 Bytes
  - population_size_generation.Rd 618 Bytes
  - print.malan_pedigree.Rd 302 Bytes
  - print.malan_pedigreelist.Rd 429 Bytes
  - print.malan_population.Rd 500 Bytes
  - print.malan_population_abort.Rd 389 Bytes
  - print_individual.Rd 282 Bytes
  - sample_autosomal_genotype.Rd 446 Bytes
  - sample_geneology.Rd 4.0 kB
  - sample_geneology_varying_size.Rd 3.6 kB
  - split_by_haplotypes.Rd 604 Bytes
  - sub-sub-.malan_pedigreelist.Rd 436 Bytes
  - sub-sub-.malan_population.Rd 361 Bytes
  - test_create_population.Rd 311 Bytes
  - ystr_kits.Rd 528 Bytes
  - ystr_markers.Rd 912 Bytes
- paper-fig-simulation.png 164.7 kB
- paper.bib 1.5 kB
- paper.md 3.9 kB
- src
  - Makevars 64 Bytes
  - Makevars.win 64 Bytes
  - PROTO.cpp 7.0 kB
  - RcppExports.cpp 41.9 kB
  - api_build_pedigrees.cpp 3.1 kB
  - api_simulate.cpp 14.6 kB
  - api_simulate.h 1.0 kB
  - api_simulate_helper.cpp 2.5 kB
  - api_simulate_varying_size.cpp 10.1 kB
  - api_utility_autosomal.cpp 32.8 kB
  - api_utility_haplotypes.cpp 21.5 kB
  - api_utility_individual.cpp 12.2 kB
  - api_utility_individual.h 1.2 kB
  - api_utility_misc.cpp 4.4 kB
  - api_utility_mixtures.cpp 7.4 kB
  - api_utility_pedigree.cpp 5.8 kB
  - class_Individual.cpp 13.9 kB
  - class_Individual.h 2.5 kB
  - class_Pedigree.cpp 5.4 kB
  - class_Pedigree.h 1.4 kB
  - class_Population.cpp 1.5 kB
  - class_Population.h 526 Bytes
  - class_SimulateChooseFather.cpp 2.7 kB
  - class_SimulateChooseFather.h 1.1 kB
  - helper_Individual.cpp 1.7 kB
  - helper_Individual.h 499 Bytes
  - helper_hash.h 833 Bytes
  - malan_types.h 1.2 kB
  - test_misc.cpp 2.1 kB
- tests
  - testthat
    - test-autosomal.R 26.3 kB
    - test-create-population.R 8.3 kB
    - test-family.R 2.5 kB
    - test-graph.R 1.6 kB
    - test-mixtures.R 2.9 kB
    - test-simulate-population.R 1.6 kB
  - testthat.R 54 Bytes
- tic.R 167 Bytes
- vignettes
  - case-study-partial.Rmd 6.3 kB
  - introduction.Rmd 12.7 kB