{
  "_id": "6a1edc5db401979e7340fc85",
  "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": "2026-05-20 08:33:45 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://rh8liuqy.r-universe.dev",
  "Date/Publication": "2024-12-18 16:42:16 UTC",
  "RemoteUrl": "https://github.com/cran/BAREB",
  "RemoteRef": "HEAD",
  "RemoteSha": "6112efd66d49c8e5b673c457ee564f3b333fb620",
  "MD5sum": "40fb8cd7c0ffa812a17e57e59444a0af",
  "_user": "rh8liuqy",
  "_type": "src",
  "_file": "BAREB_0.1.2.tar.gz",
  "_fileid": "f6cc179a9291bc021345faa33e44b271874dcccc32874462c0fac3590174970a",
  "_filesize": 520105,
  "_sha256": "f6cc179a9291bc021345faa33e44b271874dcccc32874462c0fac3590174970a",
  "_created": "2026-05-20T08:33:45.000Z",
  "_published": "2026-06-02T13:36:29.360Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79083236470,
      "time": 128,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7105141442"
    },
    {
      "job": 79083236798,
      "time": 114,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7105136261"
    },
    {
      "job": 79083236422,
      "time": 118,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105138036"
    },
    {
      "job": 79083236642,
      "time": 110,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105135483"
    },
    {
      "job": 79083236998,
      "time": 102,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7105130368"
    },
    {
      "job": 79083236605,
      "time": 172,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7105156274"
    },
    {
      "job": 79083236308,
      "time": 121,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105138399"
    },
    {
      "job": 79083236327,
      "time": 288,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105195547"
    },
    {
      "job": 79083235637,
      "time": 146,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105096820"
    },
    {
      "job": 79083235300,
      "time": 128,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7359218417"
    },
    {
      "job": 79083236687,
      "time": 155,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7105150166"
    },
    {
      "job": 79083236542,
      "time": 151,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7105149193"
    },
    {
      "job": 79083236610,
      "time": 131,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105143067"
    }
  ],
  "_buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/BAREB",
  "_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
  },
  "_maintainer": {
    "name": "Qingyang Liu",
    "email": "rh8liuqy@gmail.com",
    "login": "rh8liuqy",
    "description": "",
    "uuid": 39319788
  },
  "_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": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "rh8liuqy",
      "count": 1,
      "uuid": 39319788
    },
    {
      "user": "bruce1995",
      "count": 1,
      "uuid": 43858439
    }
  ],
  "_userbio": {
    "uuid": 39319788,
    "type": "user",
    "name": "Qingyang(Kevin) Liu"
  },
  "_downloads": {
    "count": 203,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BAREB"
  },
  "_searchresults": 3,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BAREB.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "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": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "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"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_score": 1,
  "_indexed": true,
  "_nocasepkg": "bareb",
  "_universes": [
    "rh8liuqy"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:58.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "d1bffb8e2ccc963659f3fe652cc112341bab1c5b55f04dbe5967669b23fcfafc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:41.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "06e821339c2501238a5bc4cdc2a0cba4498d29eea2cd9dd199cdc37c163e6d48",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:48.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "4fc39bba4f7e6057771165ce4ecc0ee8cb3d081b4331693c6051f448df5adf4c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:42.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "558166c5047ae7099b9355c87d0e508d871deb8463467a3a5bd3c765c7df6605",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:31.000Z",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "46b55663a272a2c8c042659ccfb69d2d55443423d958762d4b30edc9f8ca9954",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-20T08:36:24.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "421848f3dae19a95307dd2e5630eb0be8787303fb9b93e575b2020d16365e8c3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:46.000Z",
      "arch": "aarch64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "51200a2996b31e2763ef2568c953e8a381d7b6e5f8adf3de3f671c5334137862",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-20T08:37:49.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "26ca1993addc3badc65e6f13166bba4c973d27feb5094b29679ec5fcbe375999",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:44.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "0b554993f52125453fa7c8ee6c605b5ed8895ae2b04c3ff38a3bb1de64b29fd6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:23.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "ac9ef54f1e3f073128d4fa727d7cfeaad81ab95a99876188aa8eaab043fb7a1b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-20T08:35:27.000Z",
      "arch": "x86_64",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "8c979edd650d0d3e44a250d28b1f1377805b0cf93447615efe21eb9fb402ef0b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-06-02T13:35:17.000Z",
      "arch": "emscripten",
      "commit": "6112efd66d49c8e5b673c457ee564f3b333fb620",
      "fileid": "5f2609cb31ef134279764cda9312afb4f60784a2f53bf097d747481a2b6b2c7e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rh8liuqy/actions/runs/26150994786"
    }
  ]
}