{
  "_id": "6a61d24e768d0b54cfc790f7",
  "Package": "DirichletMultinomial",
  "Type": "Package",
  "Title": "Dirichlet-Multinomial Mixture Model Machine Learning for\nMicrobiome Data",
  "Version": "1.55.0",
  "Authors@R": "person(\n\"Martin\", \"Morgan\", role = c(\"aut\", \"cre\"),\nemail = \"mtmorgan.xyz@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5874-8148\"))",
  "Description": "Dirichlet-multinomial mixture models can be used to\ndescribe variability in microbial metagenomic data. This\npackage is an interface to code originally made available by\nHolmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as\ndiscussed further in the man page for this package,\n?DirichletMultinomial.",
  "License": "LGPL-3",
  "Collate": "AllGenerics.R dmn.R dmngroup.R roc.R util.R",
  "SystemRequirements": "gsl",
  "biocViews": "ImmunoOncology, Microbiome, Sequencing, Clustering,\nClassification, Metagenomics",
  "VignetteBuilder": "knitr",
  "URL": "https://mtmorgan.github.io/DirichletMultinomial/",
  "BugReports": "https://github.com/mtmorgan/DirichletMultinomial/issues",
  "Config/pak/sysreqs": "libgsl0-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:30 UTC",
  "RemoteUrl": "https://github.com/bioc/DirichletMultinomial",
  "RemoteRef": "HEAD",
  "RemoteSha": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-23 08:14:14 UTC",
    "User": "root"
  },
  "Author": "Martin Morgan [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5874-8148>)",
  "Maintainer": "Martin Morgan <mtmorgan.xyz@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "DirichletMultinomial_1.55.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7236a4d2d8423cfeeaf34aac32bb3cf3452f9df76372c97cbcf08d56244d6f60",
  "_filesize": 896610,
  "_sha256": "7236a4d2d8423cfeeaf34aac32bb3cf3452f9df76372c97cbcf08d56244d6f60",
  "_expires": "2026-10-31T08:35:24.000Z",
  "_created": "2026-07-23T08:14:14.000Z",
  "_published": "2026-07-23T08:35:25.993Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 12
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582",
  "_status": "success",
  "_upstream": "https://github.com/bioc/DirichletMultinomial",
  "_commit": {
    "id": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379790
  },
  "_maintainer": {
    "name": "Martin Morgan",
    "email": "mtmorgan.xyz@gmail.com",
    "login": "mtmorgan",
    "orcid": "0000-0002-5874-8148",
    "description": "",
    "uuid": 118552
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 89152347800,
      "time": 164,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8556943695"
    },
    {
      "job": 89152347880,
      "time": 131,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8556932779"
    },
    {
      "job": 89152347843,
      "time": 255,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8556972652"
    },
    {
      "job": 89152347874,
      "time": 126,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8556931203"
    },
    {
      "job": 89152347853,
      "time": 181,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8556949280"
    },
    {
      "job": 89152347823,
      "time": 85,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8556920796"
    },
    {
      "job": 89152347842,
      "time": 185,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8556950165"
    },
    {
      "job": 89152347895,
      "time": 89,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8556925007"
    },
    {
      "job": 89152347855,
      "time": 240,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8556970323"
    },
    {
      "job": 89151816314,
      "time": 204,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8556888622"
    },
    {
      "job": 89152347784,
      "time": 124,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8556930615"
    },
    {
      "job": 89152347834,
      "time": 157,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8556941352"
    },
    {
      "job": 89152347829,
      "time": 100,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8556922799"
    },
    {
      "job": 89152347814,
      "time": 123,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8556929972"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "stats4",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "lattice",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 29,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.55.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.54.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "microbiome",
    "sequencing",
    "clustering",
    "classification",
    "metagenomics",
    "gsl"
  ],
  "_stars": 12,
  "_contributors": [
    {
      "user": "dtenenba",
      "count": 19,
      "uuid": 2286826
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "mtmorgan",
      "count": 11,
      "uuid": 118552
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    },
    {
      "user": "sonali-bioc",
      "count": 1,
      "uuid": 6373953
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 450,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 9202,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DirichletMultinomial"
  },
  "_mentions": 9,
  "_devurl": "https://github.com/mtmorgan/dirichletmultinomial",
  "_pkgdown": "https://mtmorgan.github.io/DirichletMultinomial/",
  "_searchresults": 154,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DirichletMultinomial.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/mtmorgan/dirichletmultinomial",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AIC",
    "BIC",
    "csubset",
    "cvdmngroup",
    "dmn",
    "dmngroup",
    "fitted",
    "goodnessOfFit",
    "heatmapdmn",
    "laplace",
    "mixture",
    "mixturewt",
    "predict",
    "roc",
    "show",
    "summary"
  ],
  "_datasets": [
    {
      "name": "bestgrp",
      "title": "Data objects used for examples and the vignette",
      "object": "bestgrp",
      "file": "bestgrp.rda",
      "class": [
        "DMNGroup"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "fit",
      "title": "Data objects used for examples and the vignette",
      "object": "fit",
      "file": "fit.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "xval",
      "title": "Data objects used for examples and the vignette",
      "object": "xval",
      "file": "xval.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "group",
        "Lean",
        "Obese"
      ],
      "rows": 254,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "DirichletMultinomial-package",
      "title": "Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data",
      "topics": [
        "DirichletMultinomial-package"
      ]
    },
    {
      "page": "cvdmngroup",
      "title": "Cross-validation on Dirichlet-Multinomial classifiers.",
      "topics": [
        "cvdmngroup"
      ]
    },
    {
      "page": "dataobjects",
      "title": "Data objects used for examples and the vignette",
      "topics": [
        "bestgrp",
        "fit",
        "xval"
      ]
    },
    {
      "page": "dmn",
      "title": "Fit Dirichlet-Multinomial models to count data.",
      "topics": [
        "dmn"
      ]
    },
    {
      "page": "DMN-class",
      "title": "Class '\"DMN\"'",
      "topics": [
        "DMN-class"
      ]
    },
    {
      "page": "dmngroup",
      "title": "Dirichlet-Multinomial generative classifiers.",
      "topics": [
        "dmngroup"
      ]
    },
    {
      "page": "DMNGroup-class",
      "title": "Class '\"DMNGroup\"'",
      "topics": [
        "DMNGroup-class"
      ]
    },
    {
      "page": "heatmapdmn",
      "title": "Heatmap representation of samples assigned to Dirichlet components.",
      "topics": [
        "heatmapdmn"
      ]
    },
    {
      "page": "fitted",
      "title": "Access model components.",
      "topics": [
        "AIC,DMN-method",
        "BIC,DMN-method",
        "fitted,DMN-method",
        "fitted,DMNGroup-method",
        "goodnessOfFit",
        "laplace",
        "mixture",
        "mixturewt",
        "predict,DMN-method",
        "predict,DMNGroup-method",
        "show,DMN-method",
        "show,DMNGroup-method",
        "summary,DMNGroup-method"
      ]
    },
    {
      "page": "roc",
      "title": "Summarize receiver-operator characteristics",
      "topics": [
        "roc"
      ]
    },
    {
      "page": "util",
      "title": "Helpful utility functions",
      "topics": [
        "csubset"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DirichletMultinomial/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "generics",
    "IRanges",
    "S4Vectors"
  ],
  "_sysdeps": [
    {
      "shlib": "libgsl",
      "package": "libgsl28",
      "headers": "libgsl-dev",
      "source": "gsl",
      "version": "2.8+dfsg-6",
      "name": "gsl",
      "homepage": "https://www.gnu.org/software/gsl",
      "description": "GNU Scientific Library (GSL) -- library package"
    }
  ],
  "_vignettes": [
    {
      "source": "DirichletMultinomial.Rmd",
      "filename": "DirichletMultinomial.html",
      "title": "DirichletMultinomial for Clustering and Classification of Microbiome Data",
      "author": "Martin Morgan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data",
        "Clustering",
        "Generative classifier"
      ],
      "created": "2024-10-19 16:42:23",
      "modified": "2024-10-19 16:42:23",
      "commits": 1
    }
  ],
  "_score": 10.969443997885067,
  "_indexed": true,
  "_nocasepkg": "dirichletmultinomial",
  "_universes": [
    "bioc",
    "mtmorgan"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-07-23T08:16:24.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/51c89e326dce00a92c019088e26bf437188bf2982c19dfe239bbfe03e7226feb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-07-23T08:18:19.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/545e04ac02749e77a41c28800752187068383be59270ad2ab074195d7e583026",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-07-23T08:16:19.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/0860f948c72303218b64fb300b3e9a8a4165450b25a0893fdb3efb3795dc09a8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-07-23T08:17:02.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/de8c551c5939db3da5cbccabb8a3fcaef0b85377837f22ae44bd7ca0b3af522f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-07-23T08:15:49.000Z",
      "arch": "aarch64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/881f3e73853953a6224ffae1515d58a1cba3968175e21f190fdf22a1866c2992",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-07-23T08:16:54.000Z",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/5afd6dabb156c7a168fc6d1c13bd3e15f41a68e60c039343fce7cebf0b5e3413",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-07-23T08:16:02.000Z",
      "arch": "aarch64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/50e1602b5bcf2dab54c488d8186a27f19516c095573706ee49068d83a9ef2e13",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-07-23T08:17:29.000Z",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/ef043be4ebd5bf4342d377faf59f08cac8889ee6e7bc9bd5f3b2d6ad9350f662",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.55.0",
      "date": "2026-07-23T08:16:40.000Z",
      "arch": "emscripten",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/99c01d055d587dbb9d007ea46807aa1f1ef4794c033c5703902c7bd01e4566af",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-07-23T08:16:07.000Z",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/ce46c304f26e020ddf982e161b26229b79c18a5c7d6f19d3508ab217d0351453",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-07-23T08:15:29.000Z",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/f9f41dfe639112f6e34112921dd713c93ae5b14c4418c8536d670305dd11d504",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-07-23T08:15:38.000Z",
      "arch": "x86_64",
      "commit": "15e0e5b4fbc6c98fa78194b795cc379afef9d436",
      "fileid": "https://r2.ropensci.org/581e6df44240748fec32051c2fb1e45a1ad25a35a0ce2c5b3ab4e1686afe21f4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990434582"
    }
  ]
}