{
  "_id": "6a2bcfd9ba420f1ac0cbc51e",
  "Package": "polySimIBD",
  "Type": "Package",
  "Title": "Structured Wright Fisher Simulator for Malaria Genetics",
  "Version": "1.1.0",
  "Authors@R": "as.person(c(\n\"Nick Brazeau <nbrazeau@med.unc.edu> [aut, cre]\",\n\"Bob Verity <r.verity@imperial.ac.uk> [aut]\"\n))",
  "Description": "Unique features of the malaria life-cycle and transmission\ndynamics requires extensions of typical population genetic\nsimulators. Using a spatial discrete-loci, discrete-time\nstructured Wright Fisher framework, we simulate malaria\npopulation genetics forwards in time. Users are then able to\ncapture the full Ancestral Recombination Graph.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/nickbrazeau/polySimIBD",
  "BugReports": "https://github.com/nickbrazeau/polySimIBD/issues",
  "Remotes": [
    "nickbrazeau/goodegg",
    ""
  ],
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "SystemRequirements": "C++11",
  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2025-11-14 03:19:55 UTC",
  "RemoteUrl": "https://github.com/nickbrazeau/polySimIBD",
  "RemoteRef": "HEAD",
  "RemoteSha": "9046b62014229d14220b457176658875965c7fc3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-12 09:09:07 UTC",
    "User": "root"
  },
  "Author": "Nick Brazeau [aut, cre],\nBob Verity [aut]",
  "Maintainer": "Nick Brazeau <nbrazeau@med.unc.edu>",
  "MD5sum": "ef21f47f299b68239bf4831186d8c813",
  "_user": "plasmogenepi",
  "_type": "src",
  "_file": "polySimIBD_1.1.0.tar.gz",
  "_fileid": "3dc5f7d0338dd5626b9c3474371bcff47cd12748b6f35dbae0ffac9c91c57e6c",
  "_filesize": 1094372,
  "_sha256": "3dc5f7d0338dd5626b9c3474371bcff47cd12748b6f35dbae0ffac9c91c57e6c",
  "_created": "2026-06-12T09:09:07.000Z",
  "_published": "2026-06-12T09:22:33.064Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80995989144,
      "time": 445,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7587718840"
    },
    {
      "job": 80995988980,
      "time": 385,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7587698869"
    },
    {
      "job": 80995989001,
      "time": 426,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7587711890"
    },
    {
      "job": 80995988965,
      "time": 312,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7587673690"
    },
    {
      "job": 80995989009,
      "time": 345,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7587684818"
    },
    {
      "job": 80995988998,
      "time": 752,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7587824428"
    },
    {
      "job": 80995988990,
      "time": 464,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7587724675"
    },
    {
      "job": 80995989012,
      "time": 660,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7587791577"
    },
    {
      "job": 80995360743,
      "time": 233,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7587567611"
    },
    {
      "job": 80995988924,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7587616461"
    },
    {
      "job": 80995988984,
      "time": 382,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7587698163"
    },
    {
      "job": 80995988966,
      "time": 328,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7587679933"
    },
    {
      "job": 80995988985,
      "time": 345,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7587685759"
    }
  ],
  "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/nickbrazeau/polySimIBD",
  "_commit": {
    "id": "9046b62014229d14220b457176658875965c7fc3",
    "author": "Nicholas Brazeau <nbrazeau1@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #24 from nickbrazeau/nickbrazeau-patch-1\n\nUpdate README.md",
    "time": 1763090395
  },
  "_maintainer": {
    "name": "Nick Brazeau",
    "email": "nbrazeau@med.unc.edu"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "goodegg",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    },
    {
      "package": "stats",
      "role": "Suggests"
    },
    {
      "package": "tidygraph",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "nickbrazeau",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-46",
      "n": 7
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "nickbrazeau",
      "count": 43,
      "uuid": 12299990
    },
    {
      "user": "bobverity",
      "count": 10,
      "uuid": 9216594
    }
  ],
  "_userbio": {
    "uuid": 140542976,
    "type": "organization",
    "name": "PlasmoGenEpi",
    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/polySimIBD"
  },
  "_devurl": "https://github.com/nickbrazeau/polysimibd",
  "_searchresults": 10,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/polySimIBD.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "%>%",
    "bvtreeToNewick",
    "get_arg",
    "get_bvibd",
    "get_effective_coi",
    "get_within_ibd",
    "sim_swf",
    "subset_bvtree"
  ],
  "_help": [
    {
      "page": "argraph",
      "title": "The Ancestral Recombination Graph This S3 class represents the ARG from the realized simulation",
      "topics": [
        "argraph"
      ]
    },
    {
      "page": "bvtree",
      "title": "A Simplified Tree: bvtree This S3 class represents the bvtree which is a simple marginal tree representation",
      "topics": [
        "bvtree"
      ]
    },
    {
      "page": "bvtreeToNewick",
      "title": "Convert 'bvtree' to Newick Tree Format",
      "topics": [
        "bvtreeToNewick"
      ]
    },
    {
      "page": "get_arg",
      "title": "Get ancestral recombination graph from forward simulations",
      "topics": [
        "get_arg"
      ]
    },
    {
      "page": "get_bvibd",
      "title": "Get Between-Host Identity by Descent from forward simulations",
      "topics": [
        "get_bvibd"
      ]
    },
    {
      "page": "get_effective_coi",
      "title": "Extract Effective COI by Loci from SWF Simulation for a Single Host",
      "topics": [
        "get_effective_coi"
      ]
    },
    {
      "page": "get_within_ibd",
      "title": "Calculate Within-Host IBD",
      "topics": [
        "get_within_ibd"
      ]
    },
    {
      "page": "polySimIBD",
      "title": "Structured Wright Fisher Simulator for Malaria Genetics",
      "topics": [
        "polySimIBD"
      ]
    },
    {
      "page": "sim_swf",
      "title": "The Structured Wright Fisher Model for IBD",
      "topics": [
        "sim_swf"
      ]
    },
    {
      "page": "subset_bvtree",
      "title": "Subset an object of class bvtree",
      "topics": [
        "subset_bvtree"
      ]
    },
    {
      "page": "swfsim",
      "title": "The Structured Wright Fisher Model Output This S3 class represents realization of the Spatial Discrete-Time Discrete-Loci Structured Wright Fisher Malaria Model.",
      "topics": [
        "swfsim"
      ]
    }
  ],
  "_readme": "https://github.com/nickbrazeau/polySimIBD/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "goodegg",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "orig_mod_framework.Rmd",
      "filename": "orig_mod_framework.html",
      "title": "Discrete-Time Discrete-Loci Structured Wright Fisher Malaria Model Overview",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Purpose",
        "A Primer on Malaria Genetics",
        "A Primer on the Coalescent",
        "Model Formulation",
        "Understanding the Simulator",
        "Getting the ARG",
        "bv_tree Class",
        "Tree Conversions",
        "Conclusion"
      ],
      "created": "2023-06-11 02:32:32",
      "modified": "2024-07-01 15:00:51",
      "commits": 6
    },
    {
      "source": "spatial_extension.Rmd",
      "filename": "spatial_extension.html",
      "title": "Extension of Structured Model for Spacee",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Extending the Model for Space",
        "Forwards-in-time Description",
        "A Note on the Migration Matrix",
        "Island Case",
        "Conclusion"
      ],
      "created": "2023-06-11 02:32:32",
      "modified": "2024-07-01 15:00:51",
      "commits": 5
    },
    {
      "source": "installation.Rmd",
      "filename": "installation.html",
      "title": "Installing polySimIBD",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installing and Loading polySimIBD",
        "Dependencies"
      ],
      "created": "2023-06-11 02:32:32",
      "modified": "2024-07-01 15:00:51",
      "commits": 2
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": false,
  "_nocasepkg": "polysimibd",
  "_universes": [
    "plasmogenepi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:46.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "aa269364e405166aa9e5a5312963afa8441e3d7bafe9a13da2d7bd38975adfa0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:45.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "4be18d452821cd9dbc2467d1edcab26755d1bf64fdd3cdb3f8fa852ce1e0cec0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:35.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "6a18096b764492286f98f250ca82e5407495e70fdf04781fcfe8b237b17626fe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:31.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "ef844f98e4325c4ecff6f85e1799458965079a1c05e0fae6428e36fb1a38ba25",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:05.000Z",
      "arch": "aarch64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "c463733eccf48be77e27670f2db66982df599d06ef2f9d12abbad7a593272699",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-12T09:14:07.000Z",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "fb89432004d465a70e4bb29b30b69c3929ea5b75fe13d4d2470118db7b058211",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:52.000Z",
      "arch": "aarch64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "5db9dacbe9243a81ac8c9b7dc5f60f232bfc9977e4f1b24bed931cce4c65c45d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-12T09:13:51.000Z",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "167ef41102c9ea070b23c46e5076d9ee5092dcbdc7652337a0b1a2688b39a7c7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:42.000Z",
      "arch": "emscripten",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "370ab6ef72127e888eb72d785d59ddab101f87c2016723694eb06cc097f6cdfd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:27.000Z",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "d825043d6ae52af653046d6f7b500f9ff6ead0d7c522b36c75ca0bc3d140d460",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-12T09:10:51.000Z",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "ae4f94107581d955c75a35ead272591445c46d035bb1c0a7f97f806ca2992e70",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-12T09:11:33.000Z",
      "arch": "x86_64",
      "commit": "9046b62014229d14220b457176658875965c7fc3",
      "fileid": "171236291a4cc5676a05bc34dbf1a7834f78f96ffba2e9e6f71bf03e2f240547",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27406032384"
    }
  ]
}