{
  "_id": "6aae40293d719c1f8407a1d1",
  "Package": "Pv3Rs",
  "Title": "Estimate the Cause of Recurrent Vivax Malaria using Genetic Data",
  "Version": "1.0.0.9000",
  "Authors@R": "c(\nperson(\"Aimee\", \"Taylor\", email = \"aimee.taylor@pasteur.fr\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2337-8992\")),\nperson(\"Yong See\", \"Foo\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3010-9106\")),\nperson(\"Tymoteusz\", \"Kwiecinski\", role = \"com\", comment = \"compiled included macros.Rd\"),\nperson(\"Duncan\", \"Murdoch\", role = \"ctb\", comment = \"author of included macros.Rd\"),\nperson(\"Mans\", \"Magnusson\", role = \"ctb\", comment = \"author of included msg_progress_bar.R\"),\nperson(\"Institut Pasteur\", role = \"cph\"),\nperson(\"European Union, Project 101110393\", role = \"fnd\")\n)",
  "Description": "Plot malaria parasite genetic data on two or more\nepisodes. Compute per-person posterior probabilities that each\nPlasmodium vivax (Pv) recurrence is a recrudescence, relapse,\nor reinfection (3Rs) using per-person P. vivax genetic data on\ntwo or more episodes and a statistical model described in\nTaylor, Foo and White (2022) <doi:10.1101/2022.11.23.22282669>.\nPlot per-recurrence posterior probabilities.",
  "License": "GPL (>= 3)",
  "URL": "https://aimeertaylor.github.io/Pv3Rs/,\nhttps://github.com/aimeertaylor/Pv3Rs",
  "BugReports": "https://github.com/aimeertaylor/Pv3Rs/issues",
  "VignetteBuilder": "knitr",
  "Config/Needs/website": "rmarkdown",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libglpk-dev libgmp3-dev libxml2-dev",
  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2026-05-22 14:28:35 UTC",
  "RemoteUrl": "https://github.com/aimeertaylor/Pv3Rs",
  "RemoteRef": "HEAD",
  "RemoteSha": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-19 07:49:28 UTC",
    "User": "root"
  },
  "Author": "Aimee Taylor [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2337-8992>),\nYong See Foo [aut] (ORCID: <https://orcid.org/0000-0003-3010-9106>),\nTymoteusz Kwiecinski [com] (compiled included macros.Rd),\nDuncan Murdoch [ctb] (author of included macros.Rd),\nMans Magnusson [ctb] (author of included msg_progress_bar.R),\nInstitut Pasteur [cph],\nEuropean Union, Project 101110393 [fnd]",
  "Maintainer": "Aimee Taylor <aimee.taylor@pasteur.fr>",
  "_user": "plasmogenepi",
  "_type": "src",
  "_file": "Pv3Rs_1.0.0.9000.tar.gz",
  "_fileid": "https://r2.ropensci.org/7457c285a6c58e22c7409c9af47d45816735f002323cf1cca09eeb26df755447",
  "_filesize": 504436,
  "_sha256": "7457c285a6c58e22c7409c9af47d45816735f002323cf1cca09eeb26df755447",
  "_expires": "2026-12-28T07:56:23.000Z",
  "_created": "2026-09-19T07:49:28.000Z",
  "_published": "2026-09-19T07:56:25.268Z",
  "_jobs": [
    {
      "job": 105863748389,
      "time": 131,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10580646830"
    },
    {
      "job": 105863748424,
      "time": 144,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10580966348"
    },
    {
      "job": 105863748421,
      "time": 109,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10580566887"
    },
    {
      "job": 105863748415,
      "time": 120,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10580507173"
    },
    {
      "job": 105863374256,
      "time": 193,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10580023074"
    },
    {
      "job": 105863748388,
      "time": 152,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10580686662"
    },
    {
      "job": 105863748435,
      "time": 91,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10580881482"
    },
    {
      "job": 105863748456,
      "time": 87,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10580188046"
    },
    {
      "job": 105863748400,
      "time": 84,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10580313044"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889",
  "_status": "success",
  "_upstream": "https://github.com/aimeertaylor/Pv3Rs",
  "_commit": {
    "id": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
    "author": "aimeertaylor <aimee.r.taylor.85@gmail.com>",
    "committer": "aimeertaylor <aimee.r.taylor.85@gmail.com>",
    "message": "Compile new pdf\n",
    "time": 1779460115
  },
  "_maintainer": {
    "name": "Aimee Taylor",
    "email": "aimee.taylor@pasteur.fr",
    "login": "aimeertaylor",
    "orcid": "0000-0002-2337-8992",
    "description": "Researcher Interested in malaria, statistical and population genetics, visualisation and art.",
    "uuid": 19333433
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "fields",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "multicool",
      "role": "Imports"
    },
    {
      "package": "partitions",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "codetools",
      "role": "Suggests"
    },
    {
      "package": "gtools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "plyr",
      "role": "Suggests"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tictoc",
      "role": "Suggests"
    },
    {
      "package": "utils",
      "role": "Suggests"
    }
  ],
  "_owner": "aimeertaylor",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-39",
      "n": 7
    },
    {
      "week": "2025-40",
      "n": 5
    },
    {
      "week": "2025-41",
      "n": 4
    },
    {
      "week": "2025-42",
      "n": 3
    },
    {
      "week": "2025-47",
      "n": 8
    },
    {
      "week": "2025-48",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-21",
      "n": 6
    }
  ],
  "_tags": [
    {
      "name": "v1.0.0",
      "date": "2025-11-20"
    }
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "aimeertaylor",
      "count": 455,
      "uuid": 19333433
    },
    {
      "user": "ysfoo",
      "count": 96,
      "uuid": 48265443
    },
    {
      "user": "fersoil",
      "count": 4,
      "uuid": 31191783
    }
  ],
  "_userbio": {
    "uuid": 140542976,
    "type": "organization",
    "name": "PlasmoGenEpi",
    "followers": 1,
    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
  },
  "_downloads": {
    "count": 201,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Pv3Rs"
  },
  "_devurl": "https://github.com/aimeertaylor/pv3rs",
  "_pkgdown": "https://aimeertaylor.github.io/Pv3Rs/",
  "_searchresults": 51,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/Pv3Rs.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/aimeertaylor/pv3rs",
  "_realowner": "aimeertaylor",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.0.2",
      "date": "2025-08-01"
    },
    {
      "version": "1.0.0",
      "date": "2025-11-20"
    }
  ],
  "_exports": [
    "compute_posterior",
    "determine_MOIs",
    "enumerate_RGs",
    "plot_data",
    "plot_RG",
    "plot_simplex",
    "project2D",
    "RG_to_igraph",
    "sample_RG"
  ],
  "_datasets": [
    {
      "name": "fs_VHX_BPD",
      "title": "Allele frequencies computed using example _Plasmodium vivax_ data",
      "object": "fs_VHX_BPD",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ys_VHX_BPD",
      "title": "Example _Plasmodium vivax_ data",
      "object": "ys_VHX_BPD",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "compute_posterior",
      "title": "Compute posterior probabilities of _P. vivax_ recurrence states",
      "topics": [
        "compute_posterior"
      ]
    },
    {
      "page": "determine_MOIs",
      "title": "Determine multiplicities of infection (MOIs)",
      "topics": [
        "determine_MOIs"
      ]
    },
    {
      "page": "enumerate_RGs",
      "title": "Enumerate relationship graphs (RGs)",
      "topics": [
        "enumerate_RGs"
      ]
    },
    {
      "page": "fs_VHX_BPD",
      "title": "Allele frequencies computed using example _Plasmodium vivax_ data",
      "topics": [
        "fs_VHX_BPD"
      ]
    },
    {
      "page": "plot_data",
      "title": "Plots the data",
      "topics": [
        "plot_data"
      ]
    },
    {
      "page": "plot_RG",
      "title": "Plot a relationship graph (RG)",
      "topics": [
        "plot_RG"
      ]
    },
    {
      "page": "plot_simplex",
      "title": "Plots a 2D simplex",
      "topics": [
        "plot_simplex"
      ]
    },
    {
      "page": "project2D",
      "title": "Project 3D probability coordinates onto 2D simplex coordinates",
      "topics": [
        "project2D"
      ]
    },
    {
      "page": "RG_to_igraph",
      "title": "Converts a relationship graph (RG) encoded as a list to an 'igraph' object",
      "topics": [
        "RG_to_igraph"
      ]
    },
    {
      "page": "sample_RG",
      "title": "Sample a relationship graph (RG)",
      "topics": [
        "sample_RG"
      ]
    },
    {
      "page": "ys_VHX_BPD",
      "title": "Example _Plasmodium vivax_ data",
      "topics": [
        "ys_VHX_BPD"
      ]
    }
  ],
  "_pkglogo": "https://github.com/aimeertaylor/Pv3Rs/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/aimeertaylor/Pv3Rs/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dotCall64",
    "dplyr",
    "fields",
    "generics",
    "glue",
    "gmp",
    "igraph",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "Matrix",
    "matrixStats",
    "multicool",
    "partitions",
    "pillar",
    "pkgconfig",
    "polynom",
    "purrr",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "Rdpack",
    "rlang",
    "sets",
    "spam",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "demonstrate-usage.Rmd",
      "filename": "demonstrate-usage.html",
      "title": "Demonstrate Pv3Rs usage",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Basic workflow",
        "1) Plot data",
        "2) Compute recurrence state posterior probabilities",
        "3) Plot per-recurrence probabilities",
        "Exploration of relationship graphs"
      ],
      "created": "2025-03-10 15:41:47",
      "modified": "2025-09-10 13:25:33",
      "commits": 34
    }
  ],
  "_score": 5.661812685537261,
  "_indexed": false,
  "_nocasepkg": "pv3rs",
  "_universes": [
    "plasmogenepi"
  ],
  "_indexurl": "https://aimeertaylor.r-universe.dev/Pv3Rs",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:51:39.000Z",
      "distro": "resolute",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/26fff806c60aa212d6afe103221e8ad6ef52edb64466953b2360f59c0c167d1e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:51:45.000Z",
      "distro": "resolute",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/80230d716aadced61574ad47977bef9316047dc0b8c65ae6a4ab62ffa2038e19",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:52:47.000Z",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/f5f30222bef352eda35b4103760d8eaf485067ec7e6324a8d54fe4f812f2699f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:55:41.000Z",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/81db2727daf94ce1fcb33080c0c31a0f017fe35fb9f9924be253ae73b9e4d1ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:51:46.000Z",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/c4d45473587fb070c1fcafcf253fd8da021ad8b1baf1a0f6fa56ca94594271ad",
      "status": "success",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:50:39.000Z",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/b9e1cf3b3d2dea44362e831ec7efbbbe17610891c1e68bc81ceb581d0402a852",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:50:42.000Z",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/54f184ab866b2f1f163bf23be418f30ea649d1cea26fa3199bc95a0f797d9683",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.0.9000",
      "date": "2026-09-19T07:50:36.000Z",
      "commit": "680b4c5a23b2f8e6ced0bcb5209ec82ff5b36243",
      "fileid": "https://r2.ropensci.org/a2ba3026d8bd111eace56933a4c8076d2831f54a9235406b6a559b7d4cbcbd7b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/35430217889"
    }
  ]
}