{
  "_id": "6a10309aacfb0bcc41c958d0",
  "Package": "ukbnmr",
  "Type": "Package",
  "Title": "Removal of Unwanted Technical Variation from UK Biobank NMR\nMetabolomics Biomarker Data",
  "Version": "3.3.2",
  "Authors@R": "person(given=c(\"Scott\", \"C\"), family=\"Ritchie\", email=\"sritchie73@gmail.com\",\nrole=c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-8454-9548\"))",
  "BugReports": "https://github.com/sritchie73/ukbnmr/issues",
  "Description": "A suite of utilities for working with the UK Biobank\n<https://www.ukbiobank.ac.uk/> Nuclear Magnetic Resonance\nspectroscopy (NMR) metabolomics data\n<https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220>.\nIncludes functions for extracting biomarkers from decoded UK\nBiobank field data, removing unwanted technical variation from\nbiomarker concentrations, computing an extended set of lipid,\nfatty acid, and cholesterol fractions, and for re-deriving\ncomposite biomarkers and ratios after adjusting data for\nunwanted biological variation. For further details on methods\nsee Ritchie SC et al. Sci Data (2023)\n<doi:10.1038/s41597-023-01949-y>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/Needs/development": "roxygen2",
  "Repository": "https://sritchie73.r-universe.dev",
  "Date/Publication": "2026-04-12 10:09:32 UTC",
  "RemoteUrl": "https://github.com/sritchie73/ukbnmr",
  "RemoteRef": "HEAD",
  "RemoteSha": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-12 09:24:15 UTC",
    "User": "root"
  },
  "Author": "Scott C Ritchie [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8454-9548>)",
  "Maintainer": "Scott C Ritchie <sritchie73@gmail.com>",
  "MD5sum": "7e15ed7a2c755f0a3b4612f564fe177e",
  "_user": "sritchie73",
  "_type": "src",
  "_file": "ukbnmr_3.3.2.tar.gz",
  "_fileid": "fb0577f5657056c6f2d848ea32c68cab781e73736205c92f10955b71f947db4e",
  "_filesize": 3889027,
  "_sha256": "fb0577f5657056c6f2d848ea32c68cab781e73736205c92f10955b71f947db4e",
  "_created": "2026-05-12T09:24:15.000Z",
  "_published": "2026-05-22T10:31:54.437Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77362256811,
      "time": 126,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6940437885"
    },
    {
      "job": 77362256997,
      "time": 127,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940437244"
    },
    {
      "job": 77362257168,
      "time": 271,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6940598571"
    },
    {
      "job": 77362256849,
      "time": 132,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940503936"
    },
    {
      "job": 77362256302,
      "time": 194,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940392436"
    },
    {
      "job": 77362256406,
      "time": 100,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158405593"
    },
    {
      "job": 77362256936,
      "time": 100,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6940428132"
    },
    {
      "job": 77362257163,
      "time": 76,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6940419916"
    },
    {
      "job": 77362257229,
      "time": 85,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940423251"
    }
  ],
  "_buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/sritchie73/ukbnmr",
  "_commit": {
    "id": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
    "author": "Dr. Scott C. Ritchie <sr827@medschl.cam.ac.uk>",
    "committer": "Dr. Scott C. Ritchie <sr827@medschl.cam.ac.uk>",
    "message": "Bugfix #17 and new CRAN NOTE\n",
    "time": 1775988572
  },
  "_maintainer": {
    "name": "Scott C Ritchie",
    "email": "sritchie73@gmail.com",
    "login": "sritchie73",
    "orcid": "0000-0002-8454-9548",
    "uuid": 1674387
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "bit64",
      "role": "Imports"
    },
    {
      "package": "lubridate",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "sritchie73",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-34",
      "n": 2
    },
    {
      "week": "2025-48",
      "n": 3
    },
    {
      "week": "2026-15",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v3.3.0",
      "date": "2025-11-27"
    },
    {
      "name": "v3.3.1",
      "date": "2025-11-28"
    },
    {
      "name": "v3.3.2",
      "date": "2026-04-12"
    }
  ],
  "_stars": 64,
  "_contributors": [
    {
      "user": "sritchie73",
      "count": 106,
      "uuid": 1674387
    },
    {
      "user": "michaelchirico",
      "count": 2,
      "uuid": 7606389
    }
  ],
  "_userbio": {
    "uuid": 1674387,
    "type": "user",
    "name": "Scott Ritchie"
  },
  "_downloads": {
    "count": 584,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ukbnmr"
  },
  "_devurl": "https://github.com/sritchie73/ukbnmr",
  "_searchresults": 27,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/ukbnmr.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/sritchie73/ukbnmr",
  "_realowner": "sritchie73",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.4",
      "date": "2023-01-09"
    },
    {
      "version": "1.5",
      "date": "2023-01-31"
    },
    {
      "version": "2.1.3",
      "date": "2023-08-21"
    },
    {
      "version": "2.2",
      "date": "2023-08-24"
    },
    {
      "version": "3.2.0",
      "date": "2024-11-14"
    },
    {
      "version": "3.3.0",
      "date": "2025-11-28"
    },
    {
      "version": "3.3.1",
      "date": "2025-11-30"
    },
    {
      "version": "3.3.2",
      "date": "2026-04-12"
    }
  ],
  "_exports": [
    "compute_extended_ratio_qc_flags",
    "compute_extended_ratios",
    "extract_biomarker_qc_flags",
    "extract_biomarkers",
    "extract_sample_qc_flags",
    "recompute_derived_biomarker_qc_flags",
    "recompute_derived_biomarkers",
    "remove_technical_variation"
  ],
  "_datasets": [
    {
      "name": "nmr_info",
      "title": "Nightingale biomarker information",
      "object": "nmr_info",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Biomarker",
        "Description",
        "Units",
        "Group",
        "Sub.Group",
        "Type",
        "Nightingale",
        "UKB.Field.ID",
        "QC.Flag.Field.ID",
        "Full.Formula",
        "Simplified.Formula"
      ],
      "rows": 327,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_qc_info",
      "title": "Nightingale biomarker sample processing information",
      "object": "sample_qc_info",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Name",
        "Description",
        "UKB.Field.ID"
      ],
      "rows": 21,
      "table": true,
      "tojson": true
    },
    {
      "name": "test_data",
      "title": "Data for testing package functions",
      "object": "test_data",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "eid",
        "p20282_i0",
        "p20282_i1",
        "p23444_i0",
        "p23444_i1",
        "p23445_i0",
        "p23445_i1",
        "p23446_i0",
        "p23446_i1",
        "p23459_i0",
        "p23459_i1",
        "p23464_i0",
        "p23464_i1",
        "p23465_i0",
        "p23465_i1",
        "p23466_i0",
        "p23466_i1",
        "p23467_i0",
        "p23467_i1",
        "p23649_i0",
        "p23649_i1",
        "p23650_i0",
        "p23650_i1",
        "p23658_i0",
        "p23658_i1",
        "p23659_i0",
        "p23659_i1",
        "p23660_i0",
        "p23660_i1",
        "p23746_i0",
        "p23751_i0",
        "p23752_i0",
        "p23759_i0",
        "p23764_i0",
        "p23766_i0",
        "p23767_i0",
        "p23765_i0",
        "p23765_i1",
        "p23744_i0"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "compute_extended_ratio_qc_flags",
      "title": "Aggregate QC Flags when computing the extended set of biomarker ratios",
      "topics": [
        "compute_extended_ratio_qc_flags"
      ]
    },
    {
      "page": "compute_extended_ratios",
      "title": "Compute extended set of biomarker ratios",
      "topics": [
        "compute_extended_ratios"
      ]
    },
    {
      "page": "extract_biomarker_qc_flags",
      "title": "Extract NMR biomarker QC flags from a data.frame of UK Biobank fields",
      "topics": [
        "extract_biomarker_qc_flags"
      ]
    },
    {
      "page": "extract_biomarkers",
      "title": "Extract NMR metabolomic biomarkers from a data.frame of UK Biobank fields",
      "topics": [
        "extract_biomarkers"
      ]
    },
    {
      "page": "extract_sample_qc_flags",
      "title": "Extract NMR sample QC flags from a data.frame of UK Biobank fields",
      "topics": [
        "extract_sample_qc_flags"
      ]
    },
    {
      "page": "nmr_info",
      "title": "Nightingale biomarker information",
      "topics": [
        "nmr_info"
      ]
    },
    {
      "page": "recompute_derived_biomarker_qc_flags",
      "title": "Aggregate QC Flags when recomputing all composite and derived biomarkers",
      "topics": [
        "recompute_derived_biomarker_qc_flags"
      ]
    },
    {
      "page": "recompute_derived_biomarkers",
      "title": "Recompute composite biomarkers and ratios from the 107 non-derived biomarkers",
      "topics": [
        "recompute_derived_biomarkers"
      ]
    },
    {
      "page": "remove_technical_variation",
      "title": "Remove technical variation from NMR biomarker data in UK Biobank.",
      "topics": [
        "remove_technical_variation"
      ]
    },
    {
      "page": "sample_qc_info",
      "title": "Nightingale biomarker sample processing information",
      "topics": [
        "sample_qc_info"
      ]
    },
    {
      "page": "test_data",
      "title": "Data for testing package functions",
      "topics": [
        "test_data"
      ]
    },
    {
      "page": "ukbnmr",
      "title": "Tools for processing the UK Biobank NMR metabolomics biomarker data",
      "topics": [
        "ukbnmr-package",
        "ukbnmr"
      ]
    }
  ],
  "_readme": "https://github.com/sritchie73/ukbnmr/raw/HEAD/README.md",
  "_rundeps": [
    "bit",
    "bit64",
    "cpp11",
    "data.table",
    "generics",
    "lubridate",
    "MASS",
    "timechange"
  ],
  "_vignettes": [
    {
      "source": "ukbnmr.Rmd",
      "filename": "ukbnmr.html",
      "title": "Guide to using the ukbnmr package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Citation",
        "Data Extraction Functions",
        "Removal of technical variation",
        "Algorithms for removing technical variation",
        "Algorithm version 1",
        "Algorithm version 2",
        "Algorithm version 3",
        "Technical variation in the full UK Biobank NMR data",
        "Technical variation in the phase 2 release of UK Biobank NMR data",
        "Justification for algorithm version 2 updates",
        "Methods for computing derived biomarkers and ratios after adjusting for biological variation"
      ],
      "created": "2022-12-21 09:55:47",
      "modified": "2024-11-14 18:06:50",
      "commits": 14
    }
  ],
  "_score": 6.413634997198556,
  "_indexed": true,
  "_nocasepkg": "ukbnmr",
  "_universes": [
    "sritchie73"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.3.2",
      "date": "2026-05-12T09:26:14.000Z",
      "distro": "noble",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "7888dc298e95bf5fd610e8c32335bc55384b1ad2b3e98a744e374fc5f8dd00dd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.3.2",
      "date": "2026-05-12T09:26:21.000Z",
      "distro": "noble",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "b27038eeb6ce135444094c2bcf940fb4c6b7e3f4ee5c2ab69946de5e36c1fdeb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.3.2",
      "date": "2026-05-12T09:33:49.000Z",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "d7ccdfd2d7db296aa61d4c08efdc1d52499d7bd6fa8e66795bcaead0c039abac",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.3.2",
      "date": "2026-05-12T09:29:40.000Z",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "640b7f64c2175c1599b71d92b9a747229161ef5942f23c49975407fc76d864dc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.3.2",
      "date": "2026-05-12T09:25:41.000Z",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "91c2cdb94552137c1d2e36b7076882def5f6599aad58b0a27938636751bdc79e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.3.2",
      "date": "2026-05-12T09:25:22.000Z",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "fe844e6e54b7e8070c1ed5d3a21388cc24c54b878dabeab5b1420934417f3cbb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "3.3.2",
      "date": "2026-05-12T09:25:31.000Z",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "c0f39799eef9cbf27316cb97beaceb99ecbbc50004de527ad7b48d2e8effd0a8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.3.2",
      "date": "2026-05-22T10:31:36.000Z",
      "commit": "a14a6b6fd2c011b8287a7270a1465ac2bc9679d0",
      "fileid": "97827243c0ef9c8a48bd04b085f063737d56f4d7e1c3020d8a3c85be2520e507",
      "status": "success",
      "buildurl": "https://github.com/r-universe/sritchie73/actions/runs/25725390467"
    }
  ]
}