{
  "_id": "6a15b67dacfb0bcc41d66c88",
  "Package": "SUMnlmr",
  "Title": "Non-Linear Mendelian Randomization On Partially Summarized Data",
  "Version": "0.0.0.9000",
  "Authors@R": "c( person(given = \"Amy\",\nfamily = \"Mason\",\nrole = c(\"aut\", \"cre\"),\nemail = \"am2609@medschl.cam.ac.uk\",\ncomment = c(ORCID = \"0000-0002-8019-0777\") ),\nperson(given = \"Stephen\",\nfamily = \"Burgess\",\nrole = \"aut\",\nemail= \"sb432@cam.ac.uk\"),\nperson(given = \"James\",\nfamily = \"Staley\",\nrole = \"aut\",\nemail= \"jrstaley95@gmail.com\"),\nperson(given = \"Matt\",\nfamily = \"Arnold\",\nrole = \"aut\",\nemail= \"\")  )",
  "Description": "Runs non-linear MR calculations on partly-summarized data.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2026-05-26 12:52:16 UTC",
  "RemoteUrl": "https://github.com/amymariemason/SUMnlmr",
  "RemoteRef": "HEAD",
  "RemoteSha": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-26 14:59:55 UTC",
    "User": "root"
  },
  "Author": "Amy Mason [aut, cre] (ORCID: <https://orcid.org/0000-0002-8019-0777>),\nStephen Burgess [aut],\nJames Staley [aut],\nMatt Arnold [aut]",
  "Maintainer": "Amy Mason <am2609@medschl.cam.ac.uk>",
  "MD5sum": "5ca55fc9fba30f983ee22244fb4c51ec",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "SUMnlmr_0.0.0.9000.tar.gz",
  "_fileid": "ca805bd41db567ebf0781cf15216a7e3e13097781dd608d697ee8b4384e10bd4",
  "_filesize": 2071929,
  "_sha256": "ca805bd41db567ebf0781cf15216a7e3e13097781dd608d697ee8b4384e10bd4",
  "_created": "2026-05-26T14:59:55.000Z",
  "_published": "2026-05-26T15:04:29.370Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77891369479,
      "time": 226,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7218235574"
    },
    {
      "job": 77891369514,
      "time": 186,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218218654"
    },
    {
      "job": 77891369390,
      "time": 99,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7218201054"
    },
    {
      "job": 77891369969,
      "time": 96,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218200478"
    },
    {
      "job": 77890681954,
      "time": 176,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218135125"
    },
    {
      "job": 77891369465,
      "time": 135,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218197272"
    },
    {
      "job": 77891369553,
      "time": 128,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7218194277"
    },
    {
      "job": 77891369784,
      "time": 106,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7218182861"
    },
    {
      "job": 77891369565,
      "time": 122,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218190645"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/amymariemason/SUMnlmr",
  "_commit": {
    "id": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
    "author": "Amy Mason <amymariemason@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Upgrade checkout action from v2 to v4",
    "time": 1779799936
  },
  "_maintainer": {
    "name": "Amy Mason",
    "email": "am2609@medschl.cam.ac.uk",
    "login": "amymariemason",
    "description": "",
    "uuid": 19505214,
    "orcid": "0000-0002-8019-0777"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "metafor",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "amymariemason",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-19",
      "n": 3
    },
    {
      "week": "2026-22",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v1.2",
      "date": "2026-05-06"
    }
  ],
  "_stars": 22,
  "_contributors": [
    {
      "user": "amymariemason",
      "count": 106,
      "uuid": 19505214
    },
    {
      "user": "sb452",
      "count": 9,
      "uuid": 14124649
    },
    {
      "user": "pc494",
      "count": 5,
      "uuid": 32455330
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SUMnlmr"
  },
  "_devurl": "https://github.com/amymariemason/sumnlmr",
  "_searchresults": 21,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SUMnlmr.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "create_ind_data",
    "create_nlmr_summary",
    "create_summary_data",
    "frac_poly_summ_mr",
    "getGRvalues",
    "iv_free",
    "lowfun",
    "piecewise_summ_figure",
    "piecewise_summ_mr",
    "reprow",
    "upfun"
  ],
  "_datasets": [
    {
      "name": "bmi_acm",
      "title": "Hunt dataset containing the allele score-associations with bmi and all cause mortality, by 100 quantiles of residual BMI. As used in the paper \"Body mass index and all cause mortality in HUNT and UK Biobank studies: linear and non-linear mendelian randomisation analyses\" https://doi.org/10.1136/bmj.l1042",
      "object": "bmi_acm",
      "class": [
        "data.frame"
      ],
      "fields": [
        "beta_bmi",
        "se_bmi",
        "beta_acm",
        "se_acm",
        "mean_bmi"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "generated_data",
      "title": "Artificial genetic & phenotype data, for purposes of package tests",
      "object": "generated_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "g",
        "u",
        "errorX",
        "errorY",
        "X",
        "linear.Y",
        "quadratic.Y",
        "sqrt.Y",
        "log.Y",
        "threshold.Y",
        "y.bin",
        "fracpoly.Y"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
    {
      "name": "LDL_CAD",
      "title": "UK Biobank dataset containing the allele score-associations with ldl-cholesterol and CAD diagnosis, by 10 quantiles of residual ldl.",
      "object": "LDL_CAD",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "bx",
        "by",
        "bxse",
        "byse",
        "xmean",
        "xmin",
        "xmax"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "LDL_CAD_covar",
      "title": "UK Biobank dataset containing the allele score-associations with ldl-cholesterol and CAD diagnosis adjusted for age, sex and first 10 principle components, by 10 quantiles of residual ldl.",
      "object": "LDL_CAD_covar",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "bx",
        "by",
        "bxse",
        "byse",
        "xmean",
        "xmin",
        "xmax"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bmi_acm",
      "title": "Hunt dataset containing the allele score-associations with bmi and all cause mortality, by 100 quantiles of residual BMI. As used in the paper \"Body mass index and all cause mortality in HUNT and UK Biobank studies: linear and non-linear mendelian randomisation analyses\" https://doi.org/10.1136/bmj.l1042",
      "topics": [
        "bmi_acm"
      ]
    },
    {
      "page": "create_ind_data",
      "title": "Generation of individual level data",
      "topics": [
        "create_ind_data"
      ]
    },
    {
      "page": "create_nlmr_summary",
      "title": "Creation of summarized Mendelian randomization local estimates",
      "topics": [
        "create_nlmr_summary"
      ]
    },
    {
      "page": "create_summary_data",
      "title": "generation of summary level data",
      "topics": [
        "create_summary_data"
      ]
    },
    {
      "page": "frac_poly_summ_mr",
      "title": "Instrumental variable analysis using fractional polynomials based on summary data",
      "topics": [
        "frac_poly_summ_mr"
      ]
    },
    {
      "page": "generated_data",
      "title": "Artificial genetic & phenotype data, for purposes of package tests",
      "topics": [
        "generated_data"
      ]
    },
    {
      "page": "getGRvalues",
      "title": "Gelman-Rubin (GR) Statistics",
      "topics": [
        "getGRvalues"
      ]
    },
    {
      "page": "iv_free",
      "title": "IV-free exposure",
      "topics": [
        "iv_free"
      ]
    },
    {
      "page": "LDL_CAD",
      "title": "UK Biobank dataset containing the allele score-associations with ldl-cholesterol and CAD diagnosis, by 10 quantiles of residual ldl.",
      "topics": [
        "LDL_CAD"
      ]
    },
    {
      "page": "LDL_CAD_covar",
      "title": "UK Biobank dataset containing the allele score-associations with ldl-cholesterol and CAD diagnosis adjusted for age, sex and first 10 principle components, by 10 quantiles of residual ldl.",
      "topics": [
        "LDL_CAD_covar"
      ]
    },
    {
      "page": "lowfun",
      "title": "Lower Coefficient value",
      "topics": [
        "lowfun"
      ]
    },
    {
      "page": "piecewise_summ_figure",
      "title": "Piecewise linear figure",
      "topics": [
        "piecewise_summ_figure"
      ]
    },
    {
      "page": "piecewise_summ_mr",
      "title": "Instrumental variable analysis using piecewise linear method based on summary data",
      "topics": [
        "piecewise_summ_mr"
      ]
    },
    {
      "page": "print.frac_poly_mr",
      "title": "Create plot of Fractional Polynomial Fit",
      "topics": [
        "print.frac_poly_mr"
      ]
    },
    {
      "page": "print.summary.frac_poly_mr",
      "title": "Print Summary Fractional Polynomial Fits",
      "topics": [
        "print.summary.frac_poly_mr"
      ]
    },
    {
      "page": "print.summary.piecewise_summ_mr",
      "title": "Print summary of piecewise linear fits",
      "topics": [
        "print.summary.piecewise_summ_mr"
      ]
    },
    {
      "page": "reprow",
      "title": "Repeat rows",
      "topics": [
        "reprow"
      ]
    },
    {
      "page": "summary.frac_poly_mr",
      "title": "Summarizing Fractional Polynomial Fits",
      "topics": [
        "summary.frac_poly_mr"
      ]
    },
    {
      "page": "summary.piecewise_summ_mr",
      "title": "Summary of piecewise linear fits",
      "topics": [
        "summary.piecewise_summ_mr"
      ]
    },
    {
      "page": "upfun",
      "title": "Upper Coefficient value",
      "topics": [
        "upfun"
      ]
    }
  ],
  "_readme": "https://github.com/amymariemason/SUMnlmr/raw/HEAD/README.md",
  "_rundeps": [
    "assertthat",
    "cli",
    "cpp11",
    "digest",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "mathjaxr",
    "Matrix",
    "matrixStats",
    "metadat",
    "metafor",
    "nlme",
    "numDeriv",
    "pbapply",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "survival",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 3.9656719712201065,
  "_indexed": false,
  "_nocasepkg": "sumnlmr",
  "_universes": [
    "mrcieu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:03:16.000Z",
      "distro": "noble",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "e6f6797d031bedc711ca9a468770ee9a932144fb8709b7121ba22d202de45b8a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:02:37.000Z",
      "distro": "noble",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "d37c2fb87f85db57670f022c718bf68fea2e2699208ccad197a7b7e442b95ccf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:02:17.000Z",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "1726aaae511a5a720947e5207b4a5f5c0318eed284c5044995b9adb5cc8d1474",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:02:09.000Z",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "980212227368081e92daaa2d5b53f71dcfb954b62d2e69d2bbf1df330a8702f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:02:34.000Z",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "11a1f08ba0341873b1f47961df7b773cb1b61e44011884423e2323939634d91f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:01:33.000Z",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "8f77ef11ea9292d47fee98630ee7c41c615b79d1690f91f2d8ba3a6c6574fb19",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:01:19.000Z",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "534e79486be12706717f3b04c0c7ed3b125daf9e89b6f1fe1cd79cf238b2c39a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-26T15:01:27.000Z",
      "commit": "be863b426ecef2b2baaad65d9a4800fbc0e6e766",
      "fileid": "8ba6ee52b7f270926935d672ebaacbdd124aed008ecd9ce6c1175bea08a8b3d4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26456153172"
    }
  ]
}