{
  "_id": "6adb336409e55c840020885a",
  "Package": "BAREB",
  "Type": "Package",
  "Title": "A Bayesian Repulsive Biclustering Model for Periodontal Data",
  "Version": "0.1.2",
  "Authors@R": "c( person(\"Yuliang\", \"Li\", email = \"yli193@jhu.edu\", role = c(\"aut\")),\nperson(\"Yanxun\", \"Xu\", email = \"yxu.jhu@gmail.com\", role = c(\"aut\")),\nperson(\"Dipankar\", \"Bandyopadhyay\", email = \"bandyopd@gmail.com\", role = c(\"aut\")),\nperson(\"John\", \"Burkardt\", email = \"burkardt@vt.edu\", role = c(\"ctb\")),\nperson(\"Qingyang\", \"Liu\", email = \"rh8liuqy@gmail.com\", role = c(\"aut\", \"cre\"))\n)",
  "Description": "Simultaneously clusters the Periodontal diseases (PD)\npatients and their tooth sites after taking the patient- and\nsite-level covariates into consideration. 'BAREB' uses the\ndeterminantal point process (DPP) prior to induce diversity\namong different biclusters to facilitate parsimony and\ninterpretability. Essentially, 'BAREB' is a cluster-wise linear\nmodel based on Yuliang (2020) <doi:10.1002/sim.8536>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-23 10:09:32 UTC",
    "User": "root"
  },
  "Author": "Yuliang Li [aut], Yanxun Xu [aut], Dipankar Bandyopadhyay\n[aut], John Burkardt [ctb], Qingyang Liu [aut, cre]",
  "Maintainer": "Qingyang Liu <rh8liuqy@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-12-18 16:42:16 UTC",
  "RemoteUrl": "https://github.com/cran/BAREB",
  "RemoteRef": "HEAD",
  "RemoteSha": "6112efd66d49c8e5b673c457ee564f3b333fb620",
  "_user": "cran",
  "_type": "src",
  "_file": "BAREB_0.1.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/baf3b65b3deff7c7302233592fb42164b505f9e01d7d85516adde0ad52a5c202",
  "_filesize": 517287,
  "_sha256": "baf3b65b3deff7c7302233592fb42164b505f9e01d7d85516adde0ad52a5c202",
  "_expires": "2027-01-31T10:13:55.000Z",
  "_created": "2026-10-23T10:09:32.000Z",
  "_published": "2026-10-23T10:13:56.642Z",
  "_upstream": "https://github.com/cran/BAREB",
  "_status": "success",
  "_maintainer": {
    "name": "Qingyang Liu",
    "email": "rh8liuqy@gmail.com",
    "login": "rh8liuqy",
    "description": "",
    "uuid": 39319788
  },
  "_jobs": [
    {
      "job": 120359414309,
      "time": 128,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12494526424"
    },
    {
      "job": 120359414290,
      "time": 133,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12494526429"
    },
    {
      "job": 120359414280,
      "time": 120,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12494975004"
    },
    {
      "job": 120359414385,
      "time": 122,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12494322642"
    },
    {
      "job": 120357911231,
      "time": 224,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12494013191"
    },
    {
      "job": 120359414277,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12493744243"
    },
    {
      "job": 120359414268,
      "time": 208,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12494820626"
    },
    {
      "job": 120359414284,
      "time": 154,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12494217941"
    },
    {
      "job": 120359414401,
      "time": 202,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12494456691"
    },
    {
      "job": 120359414344,
      "time": 111,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12494591671"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369",
  "_commit": {
    "id": "6112efd66d49c8e5b673c457ee564f3b333fb620",
    "author": "Qingyang Liu <rh8liuqy@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.2\n",
    "time": 1734540136
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "rh8liuqy",
      "count": 1,
      "uuid": 39319788
    },
    {
      "user": "bruce1995",
      "count": 1,
      "uuid": 43858439
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 634,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 297,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BAREB"
  },
  "_searchresults": 3,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BAREB.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf"
  ],
  "_realowner": "rh8liuqy",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-03-06"
    },
    {
      "version": "0.1.2",
      "date": "2024-12-18"
    }
  ],
  "_exports": [
    "const",
    "kernelC",
    "likeli_theta",
    "RJi",
    "RJi_empty",
    "update_RJ",
    "update_sigma_squre",
    "update_theta_beta",
    "update_theta_gamma",
    "update_w",
    "update_w_beta",
    "updateBeta",
    "updatec",
    "updateC",
    "updateE",
    "updateGamma",
    "updatemu",
    "updatemustar",
    "updateR",
    "updateZstar"
  ],
  "_datasets": [
    {
      "name": "Init",
      "title": "The initial value of patient- and site-level covariates for simulation",
      "object": "Init",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "obs",
      "title": "The simulation observation",
      "object": "obs",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "truth",
      "title": "The simulation truth",
      "object": "truth",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BAREB",
      "title": "The BAREB package: summary information",
      "topics": [
        "BAREB"
      ]
    },
    {
      "page": "const",
      "title": "const",
      "topics": [
        "const"
      ]
    },
    {
      "page": "Init",
      "title": "The initial value of patient- and site-level covariates for simulation",
      "topics": [
        "Init"
      ]
    },
    {
      "page": "kernelC",
      "title": "The function to get the kernel function value",
      "topics": [
        "kernelC"
      ]
    },
    {
      "page": "likeli_theta",
      "title": "likeli_theta",
      "topics": [
        "likeli_theta"
      ]
    },
    {
      "page": "obs",
      "title": "The simulation observation",
      "topics": [
        "obs"
      ]
    },
    {
      "page": "RJi",
      "title": "Function to update the number of site level clusters for one patient level cluster via RJMCMC",
      "topics": [
        "RJi"
      ]
    },
    {
      "page": "RJi_empty",
      "title": "Function to update the number of site level clusters for one patient level cluster via RJMCMC, when there is no patient in this cluster",
      "topics": [
        "RJi_empty"
      ]
    },
    {
      "page": "truth",
      "title": "The simulation truth",
      "topics": [
        "truth"
      ]
    },
    {
      "page": "update_RJ",
      "title": "update_RJ",
      "topics": [
        "update_RJ"
      ]
    },
    {
      "page": "update_sigma_squre",
      "title": "update_sigma_squre",
      "topics": [
        "update_sigma_squre"
      ]
    },
    {
      "page": "update_theta_beta",
      "title": "update_theta_beta",
      "topics": [
        "update_theta_beta"
      ]
    },
    {
      "page": "update_theta_gamma",
      "title": "update_theta_gamma",
      "topics": [
        "update_theta_gamma"
      ]
    },
    {
      "page": "update_w",
      "title": "update_w",
      "topics": [
        "update_w"
      ]
    },
    {
      "page": "update_w_beta",
      "title": "update_w_beta",
      "topics": [
        "update_w_beta"
      ]
    },
    {
      "page": "updateBeta",
      "title": "Function to update patient level linear coefficients in the BAREB model",
      "topics": [
        "updateBeta"
      ]
    },
    {
      "page": "update.c",
      "title": "Function to update c in missingess model",
      "topics": [
        "updatec"
      ]
    },
    {
      "page": "updateC",
      "title": "Function to obtain the kernel matrix of the determinantal point process",
      "topics": [
        "updateC"
      ]
    },
    {
      "page": "updateE",
      "title": "Function to update patient level clustering in the BAREB model",
      "topics": [
        "updateE"
      ]
    },
    {
      "page": "updateGamma",
      "title": "Function to update site level linear coefficients in the BAREB model",
      "topics": [
        "updateGamma"
      ]
    },
    {
      "page": "updatemu",
      "title": "Function to update estimated mean CAL values based on current parameters",
      "topics": [
        "updatemu"
      ]
    },
    {
      "page": "updatemustar",
      "title": "Function to update mean latent values for missingness model",
      "topics": [
        "updatemustar"
      ]
    },
    {
      "page": "updateR",
      "title": "Function to update site level clustering in the BAREB model",
      "topics": [
        "updateR"
      ]
    },
    {
      "page": "updateZstar",
      "title": "Function to generate new latent values for missingness model",
      "topics": [
        "updateZstar"
      ]
    }
  ],
  "_rundeps": [
    "Rcpp",
    "RcppArmadillo"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "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"
    }
  ],
  "_score": 1,
  "_indexed": false,
  "_nocasepkg": "bareb",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://rh8liuqy.r-universe.dev/BAREB",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-10-23T10:11:47.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/7b2219b39489ee55f11378b995d264d38e7a31d02682a5090643876f38c3bc53",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-10-23T10:11:45.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/2c9075a1bd035533a7cb30f814a459593afb751535401ad72cdb1af8d1fa0909",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-10-23T10:11:42.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/ba780df1043cfd967e5085a2e79ed9a4162f530ef7d1a9190b8380f58663ac2b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-10-23T10:11:35.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/71406cb7dcf0fad18ac070ca00d92eea71fe7145a8f53661129f9aa50f845755",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-10-23T10:11:41.000Z",
      "arch": "emscripten",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/74356c828b6274c4afeb09028b505d5b08f29dc1070234ee1d19c352f0258f8b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-23T10:12:50.000Z",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/3741bf51d9a956d9c01d9a8221470c6920c8efd8f2d891c09cc90d7bdc45f986",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-23T10:10:50.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/214bef84cebcbf41f6bf33de03507eaa24453b4fa830b5ebe55f338ab7a7d39b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-23T10:12:47.000Z",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/e60a2eee40d0277ed452fa1ebc6b670aeb86ad0e7fa33701710309e0b700e826",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-10-23T10:10:53.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "https://r2.ropensci.org/fc6ee5baa3cce3ce32ed7a754ef0ba876ddb811dfe5045a31739b9f4a81c0c1b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/39936657369"
    }
  ]
}