{
  "_id": "6abe1ca999f7aa8c6aa52387",
  "Package": "MetabolSSMF",
  "Type": "Package",
  "Title": "Simplex-Structured Matrix Factorisation for Metabolomics\nAnalysis",
  "Version": "0.1.0",
  "Authors@R": "c(person(given = \"Wenxuan\",\nfamily = \"Liu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"wenxuan.liu@ucdconnect.ie\"),\nperson(given = c(\"Thomas\", \"Brendan\"),\nfamily = \"Murphy\",\nrole = \"aut\"),\nperson(given = \"Lorraine\",\nfamily = \"Brennan\",\nrole = \"aut\"))",
  "Maintainer": "Wenxuan Liu <wenxuan.liu@ucdconnect.ie>",
  "Description": "Provides a framework to perform soft clustering using\nsimplex-structured matrix factorisation (SSMF). The package\ncontains a set of functions for determining the optimal number\nof prototypes, the optimal algorithmic parameters, the\nestimation confidence intervals and the diversity of clusters.\nAbdolali, Maryam & Gillis, Nicolas (2020)\n<doi:10.1137/20M1354982>.",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "VignetteBuilder": "knitr",
  "License": "MIT + file LICENSE",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-01 08:31:36 UTC",
    "User": "root"
  },
  "Author": "Wenxuan Liu [aut, cre], Thomas Brendan Murphy [aut], Lorraine\nBrennan [aut]",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://wenxuanliu1996.r-universe.dev",
  "Date/Publication": "2025-03-04 12:34:16 UTC",
  "RemoteUrl": "https://github.com/wenxuanliu1996/metabolssmf",
  "RemoteRef": "HEAD",
  "RemoteSha": "847c65f3373742a31964772898210f0341d93d4f",
  "_user": "wenxuanliu1996",
  "_type": "src",
  "_file": "MetabolSSMF_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d795e9a9201525a4f37cd00b960ba888808dacbb3afd9331a52ba39825008a72",
  "_filesize": 1743732,
  "_sha256": "d795e9a9201525a4f37cd00b960ba888808dacbb3afd9331a52ba39825008a72",
  "_expires": "2027-01-09T08:41:11.000Z",
  "_created": "2026-10-01T08:31:36.000Z",
  "_published": "2026-10-01T08:41:13.031Z",
  "_jobs": [
    {
      "job": 110286339968,
      "time": 195,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11149628148"
    },
    {
      "job": 110286339994,
      "time": 163,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11149527554"
    },
    {
      "job": 110286340113,
      "time": 202,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11149349457"
    },
    {
      "job": 110286339898,
      "time": 196,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11150146166"
    },
    {
      "job": 110284889927,
      "time": 249,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11149597028"
    },
    {
      "job": 110286339850,
      "time": 235,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11150205626"
    },
    {
      "job": 110286340088,
      "time": 107,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11149048249"
    },
    {
      "job": 110286339928,
      "time": 112,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11149517325"
    },
    {
      "job": 110286339936,
      "time": 97,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11149612217"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735",
  "_status": "success",
  "_upstream": "https://github.com/wenxuanliu1996/metabolssmf",
  "_commit": {
    "id": "847c65f3373742a31964772898210f0341d93d4f",
    "author": "WenxuanLiu1996 <wenxuan.liu@ucdconnect.ie>",
    "committer": "WenxuanLiu1996 <wenxuan.liu@ucdconnect.ie>",
    "message": "updated\n",
    "time": 1741091656
  },
  "_maintainer": {
    "name": "Wenxuan Liu",
    "email": "wenxuan.liu@ucdconnect.ie",
    "login": "wenxuanliu1996",
    "description": "",
    "uuid": 92734645
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "LaplacesDemon",
      "role": "Imports"
    },
    {
      "package": "NMF",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "lsei",
      "role": "Imports"
    },
    {
      "package": "mclust",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "caroline",
      "role": "Suggests"
    },
    {
      "package": "ggsci",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "Biobase",
      "role": "Suggests"
    }
  ],
  "_owner": "wenxuanliu1996",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "wenxuanliu1996",
      "count": 16,
      "uuid": 92734645
    }
  ],
  "_userbio": {
    "uuid": 92734645,
    "type": "user",
    "name": "WenxuanLiu1996",
    "followers": 0
  },
  "_downloads": {
    "count": 230,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MetabolSSMF"
  },
  "_devurl": "https://github.com/wenxuanliu1996/metabolssmf",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/MetabolSSMF.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/wenxuanliu1996/metabolssmf",
  "_realowner": "wenxuanliu1996",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-03-05"
    }
  ],
  "_exports": [
    "bootstrap",
    "diversity",
    "gap",
    "init",
    "sARI",
    "ssmf"
  ],
  "_datasets": [
    {
      "name": "fit_boot",
      "title": "Example results of bootstrap.",
      "object": "fit_boot",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "fit_gap",
      "title": "Example results of gap statistic.",
      "object": "fit_gap",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "fit_SSMF",
      "title": "Example results of SSMF.",
      "object": "fit_ssmf",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "SimulatedDataset",
      "title": "A simulated metabolomic dataset.",
      "object": "SimulatedDataset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Var1",
        "Var2",
        "Var3",
        "Var4",
        "Var5",
        "Var6",
        "Var7",
        "Var8",
        "Var9",
        "Var10",
        "Var11",
        "Var12",
        "Var13",
        "Var14",
        "Var15",
        "Var16",
        "Var17",
        "Var18",
        "Var19",
        "Var20",
        "Var21",
        "Var22",
        "Var23",
        "Var24",
        "Var25",
        "Var26",
        "Var27",
        "Var28",
        "Var29",
        "Var30",
        "Var31",
        "Var32",
        "Var33",
        "Var34",
        "Var35",
        "Var36",
        "Var37",
        "Var38",
        "Var39",
        "Var40",
        "Var41",
        "Var42",
        "Var43",
        "Var44",
        "Var45",
        "Var46",
        "Var47",
        "Var48",
        "Var49",
        "Var50",
        "Var51",
        "Var52",
        "Var53",
        "Var54",
        "Var55",
        "Var56",
        "Var57",
        "Var58",
        "Var59",
        "Var60",
        "Var61",
        "Var62",
        "Var63",
        "Var64",
        "Var65",
        "Var66",
        "Var67",
        "Var68",
        "Var69",
        "Var70",
        "Var71",
        "Var72",
        "Var73",
        "Var74",
        "Var75",
        "Var76",
        "Var77",
        "Var78",
        "Var79",
        "Var80",
        "Var81",
        "Var82",
        "Var83",
        "Var84",
        "Var85",
        "Var86",
        "Var87",
        "Var88",
        "Var89",
        "Var90",
        "Var91",
        "Var92",
        "Var93",
        "Var94",
        "Var95",
        "Var96",
        "Var97",
        "Var98",
        "Var99",
        "Var100",
        "Var101",
        "Var102",
        "Var103",
        "Var104",
        "Var105",
        "Var106",
        "Var107",
        "Var108",
        "Var109",
        "Var110",
        "Var111",
        "Var112",
        "Var113",
        "Var114",
        "Var115",
        "Var116",
        "Var117",
        "Var118",
        "Var119",
        "Var120",
        "Var121",
        "Var122",
        "Var123",
        "Var124",
        "Var125",
        "Var126",
        "Var127",
        "Var128",
        "Var129",
        "Var130",
        "Var131",
        "Var132",
        "Var133",
        "Var134",
        "Var135",
        "Var136",
        "Var137",
        "Var138"
      ],
      "rows": 177,
      "table": true,
      "tojson": true
    },
    {
      "name": "SimulatedMemberships",
      "title": "A simulated membership matrix.",
      "object": "SimulatedMemberships",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Pty1",
        "Pty2",
        "Pty3",
        "Pty4"
      ],
      "rows": 177,
      "table": true,
      "tojson": true
    },
    {
      "name": "SimulatedPrototypes",
      "title": "A simulated prototype matrix.",
      "object": "SimulatedPrototypes",
      "class": [
        "data.frame"
      ],
      "fields": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6",
        "7",
        "8",
        "9",
        "10",
        "11",
        "12",
        "13",
        "14",
        "15",
        "16",
        "17",
        "18",
        "19",
        "20",
        "21",
        "22",
        "23",
        "24",
        "25",
        "26",
        "27",
        "28",
        "29",
        "30",
        "31",
        "32",
        "33",
        "34",
        "35",
        "36",
        "37",
        "38",
        "39",
        "40",
        "41",
        "42",
        "43",
        "44",
        "45",
        "46",
        "47",
        "48",
        "49",
        "50",
        "51",
        "52",
        "53",
        "54",
        "55",
        "56",
        "57",
        "58",
        "59",
        "60",
        "61",
        "62",
        "63",
        "64",
        "65",
        "66",
        "67",
        "68",
        "69",
        "70",
        "71",
        "72",
        "73",
        "74",
        "75",
        "76",
        "77",
        "78",
        "79",
        "80",
        "81",
        "82",
        "83",
        "84",
        "85",
        "86",
        "87",
        "88",
        "89",
        "90",
        "91",
        "92",
        "93",
        "94",
        "95",
        "96",
        "97",
        "98",
        "99",
        "100",
        "101",
        "102",
        "103",
        "104",
        "105",
        "106",
        "107",
        "108",
        "109",
        "110",
        "111",
        "112",
        "113",
        "114",
        "115",
        "116",
        "117",
        "118",
        "119",
        "120",
        "121",
        "122",
        "123",
        "124",
        "125",
        "126",
        "127",
        "128",
        "129",
        "130",
        "131",
        "132",
        "133",
        "134",
        "135",
        "136",
        "137",
        "138"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bootstrap",
      "title": "Bootstrap algorithm function.",
      "topics": [
        "bootstrap"
      ]
    },
    {
      "page": "diversity",
      "title": "Shannon diversity index",
      "topics": [
        "diversity"
      ]
    },
    {
      "page": "fit_boot",
      "title": "Example results of bootstrap.",
      "topics": [
        "fit_boot"
      ]
    },
    {
      "page": "fit_gap",
      "title": "Example results of gap statistic.",
      "topics": [
        "fit_gap"
      ]
    },
    {
      "page": "fit_SSMF",
      "title": "Example results of SSMF.",
      "topics": [
        "fit_SSMF"
      ]
    },
    {
      "page": "gap",
      "title": "Gap statistic algorithm.",
      "topics": [
        "gap"
      ]
    },
    {
      "page": "init",
      "title": "Initialise the membership matrix H or prototype matrix W.",
      "topics": [
        "init"
      ]
    },
    {
      "page": "sARI",
      "title": "Soft adjusted Rand index.",
      "topics": [
        "sARI"
      ]
    },
    {
      "page": "SimulatedDataset",
      "title": "A simulated metabolomic dataset.",
      "topics": [
        "SimulatedDataset"
      ]
    },
    {
      "page": "SimulatedMemberships",
      "title": "A simulated membership matrix.",
      "topics": [
        "SimulatedMemberships"
      ]
    },
    {
      "page": "SimulatedPrototypes",
      "title": "A simulated prototype matrix.",
      "topics": [
        "SimulatedPrototypes"
      ]
    },
    {
      "page": "ssmf",
      "title": "Simplex-structured matrix factorisation algorithm (SSMF).",
      "topics": [
        "ssmf"
      ]
    }
  ],
  "_readme": "https://github.com/wenxuanliu1996/metabolssmf/raw/HEAD/README.md",
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "digest",
    "doParallel",
    "dplyr",
    "farver",
    "foreach",
    "generics",
    "ggplot2",
    "glue",
    "gridBase",
    "gtable",
    "isoband",
    "iterators",
    "labeling",
    "LaplacesDemon",
    "lifecycle",
    "lsei",
    "magrittr",
    "mclust",
    "NMF",
    "pillar",
    "pkgconfig",
    "plyr",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "registry",
    "reshape2",
    "rlang",
    "rngtools",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "MetabolSSMF.Rmd",
      "filename": "MetabolSSMF.pdf",
      "title": "MetabolSSMF",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Data",
        "Visualise the simulated data",
        "Choose the number of clusters",
        "Bootstrap",
        "Soft Adjusted Rand Index (sARI)",
        "Shannon diversity index",
        "Additional NOTE"
      ],
      "created": "2025-02-17 07:49:21",
      "modified": "2025-03-04 12:34:16",
      "commits": 7
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "metabolssmf",
  "_universes": [
    "wenxuanliu1996"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-01T08:34:34.000Z",
      "distro": "resolute",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/2fbb1f5d4f436da69fde261cce2f5b81d38407302c660b61761e9a1b3b90dbfc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-01T08:33:58.000Z",
      "distro": "resolute",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/5aef24d866509297a86d3ad44df0c6ba465398d7b7de918fdc0acd114b564c51",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-01T08:39:38.000Z",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/61613207c3a8e1b9ba5bcfccd0d2d8542d9fa0bb09e8e33dc360bc5758c53135",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-01T08:36:51.000Z",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/2b0178be361b26850b44bd31f17d2943f1cc069714c9543264d336dfb419448b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-10-01T08:35:49.000Z",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/4f05bfdae85e21cd09e54c6bb68855957722edf2cb73cc7ab3a0c49b4396df00",
      "status": "success",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-01T08:32:50.000Z",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/bcbbf16151e7035700fc18378c69191b704ee93666a1bdad111d77c71f7ceb2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-01T08:32:58.000Z",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/e44ffbaf94f8b3a0c1d0243ef4a9ae76fa95fd81d136f7b978818d74fdd69664",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-01T08:32:50.000Z",
      "commit": "847c65f3373742a31964772898210f0341d93d4f",
      "fileid": "https://r2.ropensci.org/999af752496876b68019dfa0eb01f144da0e598ead10a43e40c44de660ec005a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wenxuanliu1996/actions/runs/36836390735"
    }
  ]
}