{
  "_id": "6a1e859f1d7bb097a0a670a2",
  "Package": "libdr",
  "Type": "Package",
  "Title": "Support Functions used by the LIBDR LCMM Analysis",
  "Version": "1.0.1",
  "Authors@R": "c(\nperson(\"Nathan\", \"Constantine-Cooke\", , \"nathan.constantine-cooke@ed.ac.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4437-8713\")),\nperson(\"Catalina\", \"Vallejos\", , \"catalina.vallejos@ed.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3638-1960\")))",
  "Description": "This package provides support functions frequently used by\nConstantine et al. for their paper, \"Large-scale clustering of\nlongitudinal faecal calprotectin and C-reactive protein\nprofiles in inflammatory bowel disease\". These functions are\nprimarily used to manipulate data and visualise findings.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libicu-dev libpng-dev perl",
  "Repository": "https://vallejosgroup.r-universe.dev",
  "Date/Publication": "2025-07-07 16:11:37 UTC",
  "RemoteUrl": "https://github.com/VallejosGroup/Lothian-IBDR",
  "RemoteRef": "HEAD",
  "RemoteSha": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
  "RemoteSubdir": "libdr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 07:23:08 UTC",
    "User": "root"
  },
  "Author": "Nathan Constantine-Cooke [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4437-8713>),\nCatalina Vallejos [aut] (ORCID:\n<https://orcid.org/0000-0003-3638-1960>)",
  "Maintainer": "Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>",
  "MD5sum": "5fe06a231499b2b08040e65e469004b8",
  "_user": "vallejosgroup",
  "_type": "src",
  "_file": "libdr_1.0.1.tar.gz",
  "_fileid": "0dbc5ad538be7cb4944f6a7295de30e2032c0b0543fa3f7746d5f110d312aa6b",
  "_filesize": 114806,
  "_sha256": "0dbc5ad538be7cb4944f6a7295de30e2032c0b0543fa3f7746d5f110d312aa6b",
  "_created": "2026-06-02T07:23:08.000Z",
  "_published": "2026-06-02T07:26:23.948Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79019982076,
      "time": 142,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7351454461"
    },
    {
      "job": 79019982072,
      "time": 152,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7351457613"
    },
    {
      "job": 79019982096,
      "time": 98,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7351441198"
    },
    {
      "job": 79019982083,
      "time": 113,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7351445787"
    },
    {
      "job": 79019453168,
      "time": 214,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351411168"
    },
    {
      "job": 79019982080,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7351449721"
    },
    {
      "job": 79019982122,
      "time": 102,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7351442558"
    },
    {
      "job": 79019982128,
      "time": 95,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7351440642"
    },
    {
      "job": 79019982070,
      "time": 102,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7351443128"
    }
  ],
  "_buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/VallejosGroup/Lothian-IBDR",
  "_commit": {
    "id": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
    "author": "Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>",
    "committer": "Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>",
    "message": "Merge branch 'main' of https://github.com/VallejosGroup/IBD-Inflammatory-Patterns\n",
    "time": 1751904697
  },
  "_maintainer": {
    "name": "Nathan Constantine-Cooke",
    "email": "nathan.constantine-cooke@ed.ac.uk",
    "login": "nathansam",
    "orcid": "0000-0002-4437-8713",
    "twitter": "@IBDNathan",
    "description": "Postdoctoral researcher at the University of Edinburgh and member of the @VallejosGroup and Lees group. Longitudinal modelling of Inflammatory Bowel Disease.",
    "uuid": 10416927
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "splines",
      "role": "Depends"
    },
    {
      "package": "patchwork",
      "role": "Depends"
    },
    {
      "package": "magrittr",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Depends"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "forcats",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "lcmm",
      "role": "Imports"
    },
    {
      "package": "nnet",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "pracma",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Imports"
    },
    {
      "package": "magick",
      "role": "Suggests"
    }
  ],
  "_owner": "vallejosgroup",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v1.0.0",
      "date": "2025-10-03"
    }
  ],
  "_topics": [
    "clustering",
    "crp",
    "denmark",
    "fcal",
    "ibd",
    "lcmm",
    "scotland"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "nathansam",
      "count": 167,
      "uuid": 10416927
    },
    {
      "user": "catavallejos",
      "count": 53,
      "uuid": 7511093
    },
    {
      "user": "marievibeke",
      "count": 1,
      "uuid": 62746303
    }
  ],
  "_userbio": {
    "uuid": 38918233,
    "type": "organization",
    "name": "VallejosGroup"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/libdr"
  },
  "_devurl": "https://github.com/vallejosgroup/lothian-ibdr",
  "_searchresults": 17,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/libdr.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "buildDT",
    "compareClustering",
    "describe_cat",
    "lcmmHeatmap",
    "makeMetrics",
    "mlrPlot",
    "plotCat",
    "rankCumulative",
    "reLabel",
    "spaghettiPlot"
  ],
  "_help": [
    {
      "page": "buildDT",
      "title": "Build DT::datatable objects from matrix of fit statistics",
      "topics": [
        "buildDT"
      ]
    },
    {
      "page": "compareClustering",
      "title": "Create co-clustering matrix for FCAL and CRP models",
      "topics": [
        "compareClustering"
      ]
    },
    {
      "page": "describe_cat",
      "title": "Produce descriptive analysis of categorical variables",
      "topics": [
        "describe_cat"
      ]
    },
    {
      "page": "lcmmHeatmap",
      "title": "Produce a heatmap of LCMM cluster assignments across multiple lcmm::hlme fit objects",
      "topics": [
        "lcmmHeatmap"
      ]
    },
    {
      "page": "makeMetrics",
      "title": "Produce table of model fit metrics (AIC, BIC, Log-likelihood) for LCMMs",
      "topics": [
        "makeMetrics"
      ]
    },
    {
      "page": "mlrPlot",
      "title": "Forest plot of multinomial logistic regression model",
      "topics": [
        "mlrPlot"
      ]
    },
    {
      "page": "plotCat",
      "title": "Percentage bar plots for categorical data",
      "topics": [
        "plotCat"
      ]
    },
    {
      "page": "rankCumulative",
      "title": "Rank clusters by the area under their mean trajectories",
      "topics": [
        "rankCumulative"
      ]
    },
    {
      "page": "reLabel",
      "title": "relabel alluvial class labels ensuring consistency.",
      "topics": [
        "reLabel"
      ]
    },
    {
      "page": "spaghettiPlot",
      "title": "Spaghetti plots of each class",
      "topics": [
        "spaghettiPlot"
      ]
    }
  ],
  "_readme": "https://github.com/VallejosGroup/Lothian-IBDR/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "digest",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "forcats",
    "foreach",
    "generics",
    "GetoptLong",
    "ggplot2",
    "GlobalOptions",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "IRanges",
    "isoband",
    "iterators",
    "knitr",
    "labeling",
    "lattice",
    "lcmm",
    "lifecycle",
    "magrittr",
    "marqLevAlg",
    "Matrix",
    "matrixStats",
    "mvtnorm",
    "nlme",
    "nnet",
    "numDeriv",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "pracma",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rjson",
    "rlang",
    "S4Vectors",
    "S7",
    "scales",
    "shape",
    "spacefillr",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_score": 2.230448921378274,
  "_indexed": true,
  "_nocasepkg": "libdr",
  "_universes": [
    "vallejosgroup",
    "nathansam"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-02T07:25:28.000Z",
      "distro": "noble",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "1c19819a336284ea58e6be8805003c630783a6e5c9fb9374af49487acac14d88",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-02T07:25:37.000Z",
      "distro": "noble",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "2919cd0d79e5577149dbfc352531a9224dc14ae87f447b6971fc3e8ddd319028",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-02T07:24:49.000Z",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "f72220a8a0c659e66e95e70d70b5a1afbdb7b4c96e0fb50269dba6b2191645e6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-02T07:25:02.000Z",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "824b9a2a133df5a238ace218b418fe73e402c0cf250e41320ac5f2962065dc91",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-06-02T07:25:36.000Z",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "0d2aa82bf7cbf1343c9c5fd8023a021d4d9a56afc4bafc803251ea4f1b5db9a3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-02T07:24:44.000Z",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "3af83ea9be0acd5685ad37556a6e40c11fe4dcd31dc9215384d47fee08cba7f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-02T07:24:36.000Z",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "4b85e36a6b4913e8dde0f89af367cc35751f37f8ace537a1347ec830181a2d50",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-02T07:24:44.000Z",
      "commit": "e44d6362ea97b4d5d368d4c7b78c89f177791103",
      "fileid": "57de7df0cfeff3cd008751436f9bbf45ae7391edf07d8d817919b5cce8d80172",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26804751851"
    }
  ]
}