{
  "_id": "6a104f93acfb0bcc41ca0e69",
  "Package": "lnmCluster",
  "Type": "Package",
  "Title": "Perform Logistic Normal Multinomial Clustering for Microbiome\nCompositional Data",
  "Version": "0.3.1",
  "Authors@R": "c(\nperson(\"Wangshu\",\"Tu\",email=\"wangshu.tu@carleton.ca\",role=c(\"aut\",\"cre\")),\nperson(\"Sanjeena\",\"Dang\",email=\"sanjeena.dang@carleton.ca\",role=c(\"aut\")),\nperson(\"Yuan\",\"Fang\",email=\"yuanf@bu.edu\",role=c(\"aut\")))",
  "Maintainer": "Wangshu Tu <wangshu.tu@carleton.ca>",
  "Description": "An implementation of logistic normal multinomial (LNM)\nclustering. It is an extension of LNM mixture model proposed by\nFang and Subedi (2020) <arXiv:2011.06682>, and is designed for\nclustering compositional data. The package includes 3 extended\nmodels: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture\nModel (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA).\nThere are several advantages of LNM models: 1. LNM provides\nmore flexible covariance structure; 2. Factor analyzer can\nreduce the number of parameters to estimate; 3. Bicluster can\nsimultaneously cluster subjects and taxa, and provides\nsignificant biological insights; 4. Penalty term allows sparse\nestimation in the covariance matrix. Details for model\nassumptions and interpretation can be found in papers: Tu and\nSubedi (2021) <arXiv:2101.01871> and Tu and Subedi (2022)\n<doi:10.1002/sam.11555>.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.2",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-10 05:55:53 UTC",
    "User": "root"
  },
  "Author": "Wangshu Tu [aut, cre], Sanjeena Dang [aut], Yuan Fang [aut]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2022-07-20 16:50:02 UTC",
  "RemoteUrl": "https://github.com/cran/lnmCluster",
  "RemoteRef": "HEAD",
  "RemoteSha": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
  "MD5sum": "8fc1441a148f560232b96006175b79eb",
  "_user": "cran",
  "_type": "src",
  "_file": "lnmCluster_0.3.1.tar.gz",
  "_fileid": "c786b0723e48ace61cd06edf486c0bf5a81570d15cfc96052bcf4ae599d135f1",
  "_filesize": 143488,
  "_sha256": "c786b0723e48ace61cd06edf486c0bf5a81570d15cfc96052bcf4ae599d135f1",
  "_created": "2026-05-10T05:55:53.000Z",
  "_published": "2026-05-22T12:44:03.940Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77381775684,
      "time": 155,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6901405618"
    },
    {
      "job": 77381775601,
      "time": 168,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6901406724"
    },
    {
      "job": 77381775725,
      "time": 156,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901405768"
    },
    {
      "job": 77381775919,
      "time": 164,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901406419"
    },
    {
      "job": 77381774972,
      "time": 188,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901390500"
    },
    {
      "job": 77381774960,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160761895"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/25621198610",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/lnmCluster",
  "_commit": {
    "id": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
    "author": "Wangshu Tu <wangshu.tu@carleton.ca>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.3.1\n",
    "time": 1658335802
  },
  "_maintainer": {
    "name": "Wangshu Tu",
    "email": "wangshu.tu@carleton.ca"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.50",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "mclust",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "pgmm",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "mvtnorm",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 192,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/lnmCluster"
  },
  "_searchresults": 2,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/lnmCluster.html",
    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.3.1",
      "date": "2022-07-20"
    }
  ],
  "_exports": [
    "lnmbiclust",
    "lnmfa",
    "plnmfa"
  ],
  "_help": [
    {
      "page": "initial_variational_gaussian",
      "title": "Gives default initial guesses for logistic-normal multinomial biclustering algorithm.",
      "topics": [
        "initial_variational_gaussian"
      ]
    },
    {
      "page": "initial_variational_lasso",
      "title": "Gives default initial guesses for penalized logistic-normal multinomial Factor analyzer algorithm.",
      "topics": [
        "initial_variational_lasso"
      ]
    },
    {
      "page": "initial_variational_PGMM",
      "title": "Gives default initial guesses for logistic-normal multinomial Factor analyzer algorithm.",
      "topics": [
        "initial_variational_PGMM"
      ]
    },
    {
      "page": "lnmbiclust",
      "title": "Logistic Normal Multinomial Biclustering algorithm",
      "topics": [
        "lnmbiclust"
      ]
    },
    {
      "page": "lnmfa",
      "title": "Logistic Normal Multinomial factor analyzer algorithm",
      "topics": [
        "lnmfa"
      ]
    },
    {
      "page": "Mico_bi_jensens",
      "title": "run main microbiome bicluster algorithm.",
      "topics": [
        "Mico_bi_jensens"
      ]
    },
    {
      "page": "Mico_bi_lasso",
      "title": "Penalized Logistic Normal Multinomial factor analyzer main estimation process",
      "topics": [
        "Mico_bi_lasso"
      ]
    },
    {
      "page": "Mico_bi_PGMM",
      "title": "run main microbiome Factor Analyzer algorithm.",
      "topics": [
        "Mico_bi_PGMM"
      ]
    },
    {
      "page": "model_selection",
      "title": "Model selections for 'lnmbicluster'",
      "topics": [
        "model_selection"
      ]
    },
    {
      "page": "model_selection_lasso",
      "title": "Model selections for 'plnmfa'",
      "topics": [
        "model_selection_lasso"
      ]
    },
    {
      "page": "model_selection_PGMM",
      "title": "Model selections for 'lnmfa'",
      "topics": [
        "model_selection_PGMM"
      ]
    },
    {
      "page": "plnmfa",
      "title": "Penalized Logistic Normal Multinomial factor analyzer algorithm",
      "topics": [
        "plnmfa"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "codetools",
    "foreach",
    "glue",
    "gtools",
    "iterators",
    "lifecycle",
    "magrittr",
    "MASS",
    "mclust",
    "pgmm",
    "Rcpp",
    "rlang",
    "stringi",
    "stringr",
    "vctrs"
  ],
  "_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": "lnm-bicluster.Rmd",
      "filename": "lnm-bicluster.html",
      "title": "lnmCluster",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Main functions"
      ],
      "created": "2022-07-20 16:50:02",
      "modified": "2022-07-20 16:50:02",
      "commits": 1
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "lnmcluster",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.1",
      "date": "2026-05-10T05:57:57.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
      "fileid": "a54725af7d65d9262b3b05ca600f240c37f8fc683a15a987ca03ee3e72a8e222",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25621198610"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.1",
      "date": "2026-05-10T05:58:01.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
      "fileid": "928a27853754416f1262dbe0449175c05f692b7497a6ddbc046e7dfaa275c87d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25621198610"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.1",
      "date": "2026-05-10T05:57:58.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
      "fileid": "1487e30ac4cb583a8e2d71604c9a8dcd9019e60d437e079dcf3a9e7394ac2196",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25621198610"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.1",
      "date": "2026-05-10T05:57:58.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
      "fileid": "f1ed7102adc9ffc2e22c241a2fc97e482e464a82354bd67c4f8a85d7684bc66c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25621198610"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.3.1",
      "date": "2026-05-22T12:43:45.000Z",
      "arch": "emscripten",
      "commit": "d9d56eee60b7ae036c80e22daf23ac001c6de151",
      "fileid": "a8d9badfef7c0788657d57eab48d79b224612b7def8deb413d5e4234424a7bf3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25621198610"
    }
  ]
}