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  "Package": "GenomeAdmixR",
  "Title": "Simulate Admixture of Genomes",
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  "Description": "Individual-based simulations forward in time, simulating\nhow patterns in ancestry along the genome change after\nadmixture. Full description can be found in Janzen (2021)\n<doi:10.1111/2041-210X.13612>.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/thijsjanzen/GenomeAdmixR",
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  "Repository": "https://thijsjanzen.r-universe.dev",
  "Date/Publication": "2026-05-14 09:05:31 UTC",
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  "Author": "Thijs Janzen [aut, cre],\nFernando Diaz G. [ctb],\nRichèl J.C. Bilderbeek [ctb]",
  "Maintainer": "Thijs Janzen <thijsjanzen@gmail.com>",
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  "_realowner": "thijsjanzen",
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      "date": "2021-01-21"
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      "date": "2021-01-25"
    },
    {
      "version": "2.0.2",
      "date": "2021-02-26"
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  "_exports": [
    "ancestry_module",
    "calculate_allele_frequencies",
    "calculate_average_ld",
    "calculate_dist_junctions",
    "calculate_fst",
    "calculate_heterozygosity",
    "calculate_ld",
    "calculate_marker_frequency",
    "combine_input_data",
    "create_artificial_genomeadmixr_data",
    "create_iso_female",
    "default_params_doc",
    "iso_female_ancestry",
    "iso_female_sequence",
    "load_population",
    "migration_settings",
    "plink_to_genomeadmixr_data",
    "plot_chromosome",
    "plot_difference_frequencies",
    "plot_dist_junctions",
    "plot_frequencies",
    "plot_joyplot_frequencies",
    "plot_over_time",
    "plot_start_end",
    "read_input_data",
    "save_population",
    "sequence_module",
    "simulate_admixture",
    "simulate_ancestry_migration",
    "simulate_sequence_migration",
    "simulation_data_to_genomeadmixr_data",
    "vcfR_to_genomeadmixr_data",
    "write_as_plink"
  ],
  "_datasets": [
    {
      "name": "dgrp2.3R.5k.data",
      "title": "A subset of sequencing data from the Drosophila Genetics Reference Panel",
      "object": "dgrp2.3R.5k.data",
      "file": "dgrp2.3R.5k.data.rda",
      "class": [
        "genomeadmixr_data"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "GenomeAdmixR-package",
      "title": "Simulate Admixture of Genomes",
      "topics": [
        "GenomeAdmixR-package",
        "GenomeAdmixR"
      ]
    },
    {
      "page": "ancestry_module",
      "title": "Creates a module to start simulations tracking local ancestry",
      "topics": [
        "ancestry_module"
      ]
    },
    {
      "page": "calculate_allele_frequencies",
      "title": "Calculate allele frequencies",
      "topics": [
        "calculate_allele_frequencies"
      ]
    },
    {
      "page": "calculate_average_ld",
      "title": "Calculates the ld between two alleles",
      "topics": [
        "calculate_average_ld"
      ]
    },
    {
      "page": "calculate_dist_junctions",
      "title": "collect the full distribution of junctions in the population",
      "topics": [
        "calculate_dist_junctions"
      ]
    },
    {
      "page": "calculate_fst",
      "title": "Calculate FST",
      "topics": [
        "calculate_fst"
      ]
    },
    {
      "page": "calculate_heterozygosity",
      "title": "Calculate heterozygosity",
      "topics": [
        "calculate_heterozygosity"
      ]
    },
    {
      "page": "calculate_ld",
      "title": "Calculate linkage disequilibrium statistics This function calculates two matrices, once containing all pairwise linkage disequilibrium (ld) values, and one matrix containing all pairwise r statistics",
      "topics": [
        "calculate_ld"
      ]
    },
    {
      "page": "calculate_marker_frequency",
      "title": "Calculate allele frequencies at a specific marker location",
      "topics": [
        "calculate_marker_frequency"
      ]
    },
    {
      "page": "combine_input_data",
      "title": "combine sequence data that was previously read from file into a population",
      "topics": [
        "combine_input_data"
      ]
    },
    {
      "page": "create_artificial_genomeadmixr_data",
      "title": "function to generate artificial genomeadmixr_data",
      "topics": [
        "create_artificial_genomeadmixr_data"
      ]
    },
    {
      "page": "create_iso_female",
      "title": "function to simulate creation of an isofemale line",
      "topics": [
        "create_iso_female"
      ]
    },
    {
      "page": "dgrp2.3R.5k.data",
      "title": "A subset of sequencing data from the Drosophila Genetics Reference Panel",
      "topics": [
        "dgrp2.3R.5k.data"
      ]
    },
    {
      "page": "iso_female_ancestry",
      "title": "Create isofemale",
      "topics": [
        "iso_female_ancestry"
      ]
    },
    {
      "page": "iso_female_sequence",
      "title": "Create isofemale",
      "topics": [
        "iso_female_sequence"
      ]
    },
    {
      "page": "load_population",
      "title": "Load a population from file",
      "topics": [
        "load_population"
      ]
    },
    {
      "page": "migration_settings",
      "title": "Function to manage settings associated with migration",
      "topics": [
        "migration_settings"
      ]
    },
    {
      "page": "plink_to_genomeadmixr_data",
      "title": "function to convert plink style (ped/map) data to genome_admixr_data",
      "topics": [
        "plink_to_genomeadmixr_data"
      ]
    },
    {
      "page": "plot_chromosome",
      "title": "plots a chromosome",
      "topics": [
        "plot_chromosome"
      ]
    },
    {
      "page": "plot_difference_frequencies",
      "title": "Plot the change in frequency between the start and end of a simulation",
      "topics": [
        "plot_difference_frequencies"
      ]
    },
    {
      "page": "plot_dist_junctions",
      "title": "plot the distribution of junctions",
      "topics": [
        "plot_dist_junctions"
      ]
    },
    {
      "page": "plot_frequencies",
      "title": "Plot the frequencies of all ancestors along the genome.",
      "topics": [
        "plot_frequencies"
      ]
    },
    {
      "page": "plot_joyplot_frequencies",
      "title": "make a joy plot of the distribution of allele frequencies within a region",
      "topics": [
        "plot_joyplot_frequencies"
      ]
    },
    {
      "page": "plot_over_time",
      "title": "Plot the frequencies of all ancestors over time",
      "topics": [
        "plot_over_time"
      ]
    },
    {
      "page": "plot_start_end",
      "title": "Plot both the starting frequencies and the final frequencies in one plot",
      "topics": [
        "plot_start_end"
      ]
    },
    {
      "page": "plot.individual",
      "title": "plot the genome of an individual",
      "topics": [
        "plot.individual"
      ]
    },
    {
      "page": "print.genomeadmixr_data",
      "title": "print an individual to the console",
      "topics": [
        "print.genomeadmixr_data"
      ]
    },
    {
      "page": "print.individual",
      "title": "print an individual to the console",
      "topics": [
        "print.individual"
      ]
    },
    {
      "page": "print.population",
      "title": "print a population object",
      "topics": [
        "print.population"
      ]
    },
    {
      "page": "read_input_data",
      "title": "read sequence data from file to be used in simulation",
      "topics": [
        "read_input_data"
      ]
    },
    {
      "page": "save_population",
      "title": "Save a population to file",
      "topics": [
        "save_population"
      ]
    },
    {
      "page": "sequence_module",
      "title": "create sequence module",
      "topics": [
        "sequence_module"
      ]
    },
    {
      "page": "simulate_admixture",
      "title": "Individual based simulation of the breakdown of contiguous ancestry blocks.",
      "topics": [
        "simulate_admixture"
      ]
    },
    {
      "page": "simulate_ancestry",
      "title": "Individual based simulation of the breakdown of contiguous ancestry blocks.",
      "topics": [
        "simulate_ancestry"
      ]
    },
    {
      "page": "simulate_ancestry_migration",
      "title": "Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migration",
      "topics": [
        "simulate_ancestry_migration"
      ]
    },
    {
      "page": "simulate_sequence",
      "title": "Individual based simulation of the breakdown of contiguous ancestry blocks.",
      "topics": [
        "simulate_sequence"
      ]
    },
    {
      "page": "simulate_sequence_migration",
      "title": "Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migration",
      "topics": [
        "simulate_sequence_migration"
      ]
    },
    {
      "page": "simulation_data_to_genomeadmixr_data",
      "title": "function to convert ped/map data to genome_admixr_data",
      "topics": [
        "simulation_data_to_genomeadmixr_data"
      ]
    },
    {
      "page": "vcfR_to_genomeadmixr_data",
      "title": "function to convert a vcfR object to genome_admixr_data",
      "topics": [
        "vcfR_to_genomeadmixr_data"
      ]
    },
    {
      "page": "write_as_plink",
      "title": "function to write simulation output as PLINK style data",
      "topics": [
        "write_as_plink"
      ]
    }
  ],
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