{
  "_id": "6a478ec06527f6f71fa0f3a4",
  "Package": "moire",
  "Title": "Multiplicity of Infection and Allele Frequency Recovery from\nNoisy Polyallelic Genetics Data",
  "Version": "3.5.0",
  "Authors@R": "c(\nperson(given = \"Maxwell\",\nfamily = \"Murphy\",\nrole = c(\"aut\", \"cre\"),\nemail = \"murphy2122@berkeley.edu\",\ncomment = c(ORCID = \"0000-0003-0332-4388\")),\nperson(given = \"Bryan\",\nfamily = \"Greenhouse\",\nrole = c(\"aut\", \"ths\"),\nemail = \"bryan.greenhouse@ucsf.edu\",\ncomment = c(ORCID = \"0000-0003-0287-9111\")))",
  "Description": "A Markov Chain Monte Carlo (MCMC) based approach to\nBayesian estimation of individual level multiplicity of\ninfection, within host relatedness, and population allele\nfrequencies from polyallelic genetic data.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "bzip2",
  "SystemRequirements": "C++17, GNU make",
  "URL": "https://github.com/EPPIcenter/moire,\nhttps://eppicenter.github.io/moire/,\nhttps://eppicenter.ucsf.edu/resources",
  "BugReports": "https://github.com/EPPIcenter/moire/issues",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "make libicu-dev",
  "Repository": "https://eppicenter.r-universe.dev",
  "Date/Publication": "2024-11-06 21:35:57 UTC",
  "RemoteUrl": "https://github.com/eppicenter/moire",
  "RemoteRef": "HEAD",
  "RemoteSha": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-02 07:29:45 UTC",
    "User": "root"
  },
  "Author": "Maxwell Murphy [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0332-4388>),\nBryan Greenhouse [aut, ths] (ORCID:\n<https://orcid.org/0000-0003-0287-9111>)",
  "Maintainer": "Maxwell Murphy <murphy2122@berkeley.edu>",
  "_user": "eppicenter",
  "_type": "src",
  "_file": "moire_3.5.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/1fab0391cc58df45e23e02ab21ea639a4c8c96b7c52bb0a0f5107850e9f7d66a",
  "_filesize": 4489665,
  "_sha256": "1fab0391cc58df45e23e02ab21ea639a4c8c96b7c52bb0a0f5107850e9f7d66a",
  "_expires": "2026-10-11T10:28:15.000Z",
  "_created": "2026-07-02T07:29:45.000Z",
  "_published": "2026-07-03T10:28:16.459Z",
  "_jobs": [
    {
      "job": 84980645200,
      "time": 210,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8031890763"
    },
    {
      "job": 84980645199,
      "time": 222,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8031893344"
    },
    {
      "job": 84980645461,
      "time": 205,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031888961"
    },
    {
      "job": 84980645215,
      "time": 245,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031901892"
    },
    {
      "job": 84980644724,
      "time": 214,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8031881860"
    },
    {
      "job": 84980645234,
      "time": 526,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8031986342"
    },
    {
      "job": 84980644998,
      "time": 214,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031901024"
    },
    {
      "job": 84980644670,
      "time": 359,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031943602"
    },
    {
      "job": 84980644669,
      "time": 251,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031817746"
    },
    {
      "job": 84980644890,
      "time": 193,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8031883584"
    },
    {
      "job": 84980645298,
      "time": 185,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8031881964"
    },
    {
      "job": 84980645371,
      "time": 210,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8031889622"
    },
    {
      "job": 84980645108,
      "time": 190,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031883239"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416",
  "_status": "success",
  "_upstream": "https://github.com/eppicenter/moire",
  "_commit": {
    "id": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
    "author": "Maxwell Murphy <murphy2122@berkeley.edu>",
    "committer": "Maxwell Murphy <murphy2122@berkeley.edu>",
    "message": "update article\n",
    "time": 1730928957
  },
  "_maintainer": {
    "name": "Maxwell Murphy",
    "email": "murphy2122@berkeley.edu",
    "login": "m-murphy",
    "orcid": "0000-0003-0332-4388",
    "twitter": "@MxMrphy",
    "description": "",
    "uuid": 5225200
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppProgress",
      "role": "LinkingTo"
    },
    {
      "package": "RcppParallel",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "RcppProgress",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "forcats",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "parallelly",
      "role": "Suggests"
    }
  ],
  "_owner": "eppicenter",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "genomics",
    "malaria",
    "mcmc",
    "cpp",
    "openmp"
  ],
  "_stars": 7,
  "_contributors": [
    {
      "user": "m-murphy",
      "count": 149,
      "uuid": 5225200
    }
  ],
  "_userbio": {
    "uuid": 14140677,
    "type": "organization",
    "name": "EPPIcenter",
    "followers": 23,
    "description": "A systems epidemiology approach to  complex infectious disease dynamics:  state-of-the-art data collection, molecular technologies, & computational analysis"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/moire"
  },
  "_devurl": "https://github.com/eppicenter/moire",
  "_pkgdown": "https://eppicenter.github.io/moire/",
  "_searchresults": 28,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/moire.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "calculate_he",
    "calculate_med_allele_freqs",
    "calculate_naive_allele_frequencies",
    "calculate_naive_coi",
    "calculate_naive_coi_offset",
    "load_delimited_data",
    "load_long_form_data",
    "plot_chain_swaps",
    "rdirichlet",
    "run_mcmc",
    "simulate_allele_frequencies",
    "simulate_data",
    "simulate_observed_allele",
    "simulate_observed_genotype",
    "simulate_sample_coi",
    "simulate_sample_genotype",
    "summarize_allele_freq_fn",
    "summarize_allele_freqs",
    "summarize_coi",
    "summarize_effective_coi",
    "summarize_epsilon_neg",
    "summarize_epsilon_pos",
    "summarize_he",
    "summarize_relatedness"
  ],
  "_datasets": [
    {
      "name": "mcmc_results",
      "title": "MCMC results from using the packaged simulated data and calling 'run_mcmc()'",
      "object": "mcmc_results",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "namibia_data",
      "title": "Genetic and epidemiological data from Namibia",
      "object": "namibia_data",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sample_id",
        "HealthFacility",
        "HealthDistrict",
        "Region",
        "Country",
        "locus",
        "allele"
      ],
      "rows": 97214,
      "table": true,
      "tojson": true
    },
    {
      "name": "regional_allele_frequencies",
      "title": "Allele frequencies for different regions",
      "object": "regional_allele_frequencies",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "simulated_data",
      "title": "Simulated genotyping data",
      "object": "simulated_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculate_he",
      "title": "Calculate the expected heterozygosity from allele frequencies",
      "topics": [
        "calculate_he"
      ]
    },
    {
      "page": "calculate_med_allele_freqs",
      "title": "Calculate the geometric median of the posterior distribution of allele frequencies",
      "topics": [
        "calculate_med_allele_freqs"
      ]
    },
    {
      "page": "calculate_naive_allele_frequencies",
      "title": "Calculate naive allele frequencies",
      "topics": [
        "calculate_naive_allele_frequencies"
      ]
    },
    {
      "page": "calculate_naive_coi",
      "title": "Calculate naive COI",
      "topics": [
        "calculate_naive_coi"
      ]
    },
    {
      "page": "calculate_naive_coi_offset",
      "title": "Calculate naive COI offset",
      "topics": [
        "calculate_naive_coi_offset"
      ]
    },
    {
      "page": "load_delimited_data",
      "title": "Load delimited data",
      "topics": [
        "load_delimited_data"
      ]
    },
    {
      "page": "load_long_form_data",
      "title": "Load long form data",
      "topics": [
        "load_long_form_data"
      ]
    },
    {
      "page": "mcmc_results",
      "title": "MCMC results from using the packaged simulated data and calling 'run_mcmc()'",
      "topics": [
        "mcmc_results"
      ]
    },
    {
      "page": "namibia_data",
      "title": "Genetic and epidemiological data from Namibia",
      "topics": [
        "namibia_data"
      ]
    },
    {
      "page": "plot_chain_swaps",
      "title": "Plot chain swap acceptance rates",
      "topics": [
        "plot_chain_swaps"
      ]
    },
    {
      "page": "rdirichlet",
      "title": "Dirichlet distribution",
      "topics": [
        "rdirichlet"
      ]
    },
    {
      "page": "regional_allele_frequencies",
      "title": "Allele frequencies for different regions",
      "topics": [
        "regional_allele_frequencies"
      ]
    },
    {
      "page": "run_mcmc",
      "title": "Sample from the target distribution using MCMC",
      "topics": [
        "run_mcmc"
      ]
    },
    {
      "page": "simulate_allele_frequencies",
      "title": "Simulate allele frequencies",
      "topics": [
        "simulate_allele_frequencies"
      ]
    },
    {
      "page": "simulate_data",
      "title": "Simulate data generated according to the assumed model",
      "topics": [
        "simulate_data"
      ]
    },
    {
      "page": "simulate_observed_allele",
      "title": "Simulates the observation process",
      "topics": [
        "simulate_observed_allele"
      ]
    },
    {
      "page": "simulate_observed_genotype",
      "title": "Simulate observed genotypes",
      "topics": [
        "simulate_observed_genotype"
      ]
    },
    {
      "page": "simulate_sample_coi",
      "title": "Simulate sample COI",
      "topics": [
        "simulate_sample_coi"
      ]
    },
    {
      "page": "simulate_sample_genotype",
      "title": "Simulate sample genotype",
      "topics": [
        "simulate_sample_genotype"
      ]
    },
    {
      "page": "simulated_data",
      "title": "Simulated genotyping data",
      "topics": [
        "simulated_data"
      ]
    },
    {
      "page": "summarize_allele_freq_fn",
      "title": "Summarize Function of Allele Frequencies",
      "topics": [
        "summarize_allele_freq_fn"
      ]
    },
    {
      "page": "summarize_allele_freqs",
      "title": "Summarize allele frequencies",
      "topics": [
        "summarize_allele_freqs"
      ]
    },
    {
      "page": "summarize_coi",
      "title": "Summarize COI",
      "topics": [
        "summarize_coi"
      ]
    },
    {
      "page": "summarize_effective_coi",
      "title": "Summarize effective COI",
      "topics": [
        "summarize_effective_coi"
      ]
    },
    {
      "page": "summarize_epsilon_neg",
      "title": "Summarize epsilon_neg",
      "topics": [
        "summarize_epsilon_neg"
      ]
    },
    {
      "page": "summarize_epsilon_pos",
      "title": "Summarize epsilon_pos",
      "topics": [
        "summarize_epsilon_pos"
      ]
    },
    {
      "page": "summarize_he",
      "title": "Summarize locus heterozygosity",
      "topics": [
        "summarize_he"
      ]
    },
    {
      "page": "summarize_relatedness",
      "title": "Summarize relatedness",
      "topics": [
        "summarize_relatedness"
      ]
    }
  ],
  "_pkglogo": "https://github.com/eppicenter/moire/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/eppicenter/moire/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppParallel",
    "RcppProgress",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "namibia.Rmd",
      "filename": "namibia.html",
      "title": "Application to Namibia",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Running MOIRE on Namibia data"
      ],
      "created": "2024-03-18 22:03:28",
      "modified": "2024-08-01 01:36:32",
      "commits": 3
    },
    {
      "source": "mcmc_demo.Rmd",
      "filename": "mcmc_demo.html",
      "title": "MCMC Demonstration",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulation and MCMC",
        "Estimating COI",
        "Estimating effective COI",
        "What is effective COI?",
        "Estimating Relatedness",
        "Estimating allele frequencies",
        "Estimating expected heterozygosity"
      ],
      "created": "2020-08-24 22:23:04",
      "modified": "2023-12-19 19:37:25",
      "commits": 14
    }
  ],
  "_score": 4.292256071356476,
  "_indexed": true,
  "_nocasepkg": "moire",
  "_universes": [
    "eppicenter",
    "m-murphy"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.5.0",
      "date": "2026-07-02T07:33:18.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/2e3b9e854916fae8fbae413cb57efbc246b0ae9ec725b7df30887c092d0a7d1d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.5.0",
      "date": "2026-07-02T07:33:19.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/14c2a5475120de8b3526c4a1810a35d6d3b49ac4a3f487a792556c25daa3eca0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.5.0",
      "date": "2026-07-02T07:33:15.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/fb00d9b5ede9bf27e915d4b250d2865ad54805fea670d9dc771f0af1f22b56bc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.5.0",
      "date": "2026-07-02T07:33:40.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/49498ccf0b8480149c63dba6e8d1091f4af8ad8de44d8ca0ad9357636aa377d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.5.0",
      "date": "2026-07-02T07:32:34.000Z",
      "arch": "aarch64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/68f32fc37c2c3f8da210e438b564e2901fded6dca2d61cf40c0ffaa7322c57a0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.5.0",
      "date": "2026-07-02T07:35:54.000Z",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/5384d3c720ff0700fe0e0a888c8956c54ad569b2d2019408936145cb435ae1b2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.5.0",
      "date": "2026-07-02T07:33:45.000Z",
      "arch": "aarch64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/1dbb6bf3db51de11272838ab4de6f7b281eef3f0077b96c3d57df2e1ebab808a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.5.0",
      "date": "2026-07-02T07:34:49.000Z",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/2c3458c94d84120802cce572db3130d6e7a3282b37fbd4352158998438ceb829",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.5.0",
      "date": "2026-07-02T07:33:19.000Z",
      "arch": "emscripten",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/e4411c9c322a7008856376a6ea11dfced05ada923cdc7afb841e0cf647049485",
      "status": "success",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.5.0",
      "date": "2026-07-02T07:31:59.000Z",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/ce2ef7852559eb053da5bb1b88b5e69dd06d3598e190259fff1236604adbcc18",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.5.0",
      "date": "2026-07-02T07:31:48.000Z",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/35838dd67fb39a7288bb7170335907fac7cd314749ec147ade7ed5b91405144f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.5.0",
      "date": "2026-07-02T07:31:58.000Z",
      "arch": "x86_64",
      "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd",
      "fileid": "https://r2.ropensci.org/991b7e7caaed71bd3e02edd9b7903b2888775151bd88088026f087d980af41b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/28572989416"
    }
  ]
}