{
  "_id": "6abcd73399f7aa8c6aa4cae6",
  "Package": "smcfcs",
  "Title": "Multiple Imputation of Covariates by Substantive Model\nCompatible Fully Conditional Specification",
  "Version": "2.0.2",
  "Authors@R": "c(person(\"Jonathan\", \"Bartlett\", email = \"jonathan.bartlett1@lshtm.ac.uk\",role = c(\"aut\", \"cre\")),\nperson(\"Ruth\", \"Keogh\", email = \"ruth.keogh@lshtm.ac.uk\",role = c(\"aut\")),\nperson(\"Edouard F.\", \"Bonneville\",role = c(\"aut\")),\nperson(\"Lars\", \"van der Burg\",role = c(\"aut\")),\nperson(\"Claus Thorn\", \"Ekstrøm\",role = c(\"ctb\")))",
  "URL": "https://github.com/jwb133/smcfcs",
  "Description": "Implements multiple imputation of missing covariates by\nSubstantive Model Compatible Fully Conditional Specification.\nThis is a modification of the popular FCS/chained equations\nmultiple imputation approach, and allows imputation of missing\ncovariate values from models which are compatible with the user\nspecified substantive model.",
  "License": "GPL-3",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "BugReports": "https://github.com/jwb133/smcfcs/issues",
  "Repository": "https://jwb133.r-universe.dev",
  "Date/Publication": "2026-04-30 11:32:23 UTC",
  "RemoteUrl": "https://github.com/jwb133/smcfcs",
  "RemoteRef": "HEAD",
  "RemoteSha": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-30 08:53:57 UTC",
    "User": "root"
  },
  "Author": "Jonathan Bartlett [aut, cre],\nRuth Keogh [aut],\nEdouard F. Bonneville [aut],\nLars van der Burg [aut],\nClaus Thorn Ekstrøm [ctb]",
  "Maintainer": "Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>",
  "_user": "jwb133",
  "_type": "src",
  "_file": "smcfcs_2.0.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/c3aab51cd84e89873945c2667d172c2b42e466f87e44e0062948c41365874f5a",
  "_filesize": 587909,
  "_sha256": "c3aab51cd84e89873945c2667d172c2b42e466f87e44e0062948c41365874f5a",
  "_expires": "2027-01-08T09:32:34.000Z",
  "_created": "2026-09-30T08:53:57.000Z",
  "_published": "2026-09-30T09:32:35.816Z",
  "_jobs": [
    {
      "job": 109813191289,
      "time": 164,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11086990818"
    },
    {
      "job": 109813191281,
      "time": 157,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11087030447"
    },
    {
      "job": 109813191239,
      "time": 188,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11087958048"
    },
    {
      "job": 109813191321,
      "time": 204,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11087168636"
    },
    {
      "job": 109811692964,
      "time": 263,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11085813405"
    },
    {
      "job": 109813191363,
      "time": 117,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11086701666"
    },
    {
      "job": 109813191264,
      "time": 104,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11085743884"
    },
    {
      "job": 109813191399,
      "time": 75,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11086003216"
    },
    {
      "job": 109813191691,
      "time": 89,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11086402697"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943",
  "_status": "success",
  "_upstream": "https://github.com/jwb133/smcfcs",
  "_commit": {
    "id": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
    "author": "Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>",
    "committer": "Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>",
    "message": "Adding BugReports to DESCRIPTION\n",
    "time": 1777548743
  },
  "_maintainer": {
    "name": "Jonathan Bartlett",
    "email": "jonathan.bartlett1@lshtm.ac.uk",
    "login": "jwb133",
    "twitter": "@TheStatsGeek",
    "description": "Professor in Medical Statistics at the Department of Medical Statistics, London School of Hygiene & Tropical Medicine, UK.",
    "uuid": 10440582
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.2",
      "role": "Depends"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "VGAM",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "brglm2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "mitools",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "kmi",
      "role": "Suggests"
    },
    {
      "package": "flexsurv",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    }
  ],
  "_owner": "jwb133",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2026-18",
      "n": 3
    }
  ],
  "_tags": [],
  "_stars": 14,
  "_contributors": [
    {
      "user": "jwb133",
      "count": 83,
      "uuid": 10440582
    },
    {
      "user": "ekstroem",
      "count": 1,
      "uuid": 6160801
    },
    {
      "user": "tom-metherell",
      "count": 1,
      "uuid": 102831716
    }
  ],
  "_userbio": {
    "uuid": 10440582,
    "type": "user",
    "name": "Jonathan Bartlett",
    "followers": 79,
    "description": "Professor in Medical Statistics at the Department of Medical Statistics, London School of Hygiene & Tropical Medicine, UK."
  },
  "_downloads": {
    "count": 2695,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/smcfcs"
  },
  "_mentions": 8,
  "_devurl": "https://github.com/jwb133/smcfcs",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/smcfcs.html"
  ],
  "_homeurl": "https://github.com/jwb133/smcfcs",
  "_realowner": "jwb133",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2015-05-12"
    },
    {
      "version": "1.1.0",
      "date": "2015-08-21"
    },
    {
      "version": "1.1.1",
      "date": "2015-11-23"
    },
    {
      "version": "1.2.0",
      "date": "2016-01-30"
    },
    {
      "version": "1.2.1",
      "date": "2016-02-04"
    },
    {
      "version": "1.3.0",
      "date": "2017-06-03"
    },
    {
      "version": "1.3.1",
      "date": "2018-10-10"
    },
    {
      "version": "1.4.0",
      "date": "2019-04-08"
    },
    {
      "version": "1.4.1",
      "date": "2020-03-30"
    },
    {
      "version": "1.4.2",
      "date": "2020-12-07"
    },
    {
      "version": "1.5.0",
      "date": "2021-04-01"
    },
    {
      "version": "1.6.0",
      "date": "2021-06-17"
    },
    {
      "version": "1.6.1",
      "date": "2022-01-18"
    },
    {
      "version": "1.6.2",
      "date": "2022-05-16"
    },
    {
      "version": "1.7.0",
      "date": "2022-06-22"
    },
    {
      "version": "1.7.1",
      "date": "2022-11-07"
    },
    {
      "version": "1.8.0",
      "date": "2024-06-04"
    },
    {
      "version": "1.9.0",
      "date": "2024-11-07"
    },
    {
      "version": "1.9.1",
      "date": "2024-12-04"
    },
    {
      "version": "1.9.2",
      "date": "2025-01-21"
    },
    {
      "version": "2.0.0",
      "date": "2025-03-25"
    },
    {
      "version": "2.0.1",
      "date": "2025-07-17"
    },
    {
      "version": "2.0.2",
      "date": "2026-05-01"
    }
  ],
  "_exports": [
    "smcfcs",
    "smcfcs.casecohort",
    "smcfcs.dtsam",
    "smcfcs.finegray",
    "smcfcs.flexsurv",
    "smcfcs.nestedcc",
    "smcfcs.parallel"
  ],
  "_datasets": [
    {
      "name": "ex_cc",
      "title": "Simulated case cohort data",
      "object": "ex_cc",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "x",
        "z",
        "in.subco",
        "id",
        "entertime"
      ],
      "rows": 1565,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_coarsening",
      "title": "Simulated example data with a coarsened factor covariate",
      "object": "ex_coarsening",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x",
        "xobs",
        "z",
        "y"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_compet",
      "title": "Simulated example data with competing risks outcome and partially observed covariates",
      "object": "ex_compet",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "x1",
        "x2"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_coxquad",
      "title": "Simulated example data with time to event outcome and quadratic covariate effects",
      "object": "ex_coxquad",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "z",
        "x",
        "v"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_dtsam",
      "title": "Simulated discrete time survival data set",
      "object": "ex_dtsam",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x1",
        "x2",
        "failtime",
        "d"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_finegray",
      "title": "Simulated example data with competing risks outcome and partially observed covariates",
      "object": "ex_finegray",
      "class": [
        "data.frame"
      ],
      "fields": [
        "times",
        "d",
        "x1",
        "x2"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_flexsurv",
      "title": "Simulated example data with time-to-event Weibull outcome and two covariates",
      "object": "ex_flexsurv",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "x",
        "z"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_lininter",
      "title": "Simulated example data with continuous outcome and interaction between two partially observed covariates",
      "object": "ex_lininter",
      "class": [
        "data.frame"
      ],
      "fields": [
        "y",
        "x1",
        "x2"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_linquad",
      "title": "Simulated example data with continuous outcome and quadratic covariate effects",
      "object": "ex_linquad",
      "class": [
        "data.frame"
      ],
      "fields": [
        "y",
        "z",
        "x",
        "v"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_logisticquad",
      "title": "Simulated example data with binary outcome and quadratic covariate effects",
      "object": "ex_logisticquad",
      "class": [
        "data.frame"
      ],
      "fields": [
        "y",
        "z",
        "x",
        "v"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_ncc",
      "title": "Simulated nested case-control data",
      "object": "ex_ncc",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "x",
        "z",
        "id",
        "numrisk",
        "setno",
        "case"
      ],
      "rows": 700,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_poisson",
      "title": "Simulated example data with count outcome, modelled using Poisson regression",
      "object": "ex_poisson",
      "class": [
        "data.frame"
      ],
      "fields": [
        "y",
        "x",
        "z"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ex_cc",
      "title": "Simulated case cohort data",
      "topics": [
        "ex_cc"
      ]
    },
    {
      "page": "ex_coarsening",
      "title": "Simulated example data with a coarsened factor covariate",
      "topics": [
        "ex_coarsening"
      ]
    },
    {
      "page": "ex_compet",
      "title": "Simulated example data with competing risks outcome and partially observed covariates",
      "topics": [
        "ex_compet"
      ]
    },
    {
      "page": "ex_coxquad",
      "title": "Simulated example data with time to event outcome and quadratic covariate effects",
      "topics": [
        "ex_coxquad"
      ]
    },
    {
      "page": "ex_dtsam",
      "title": "Simulated discrete time survival data set",
      "topics": [
        "ex_dtsam"
      ]
    },
    {
      "page": "ex_finegray",
      "title": "Simulated example data with competing risks outcome and partially observed covariates",
      "topics": [
        "ex_finegray"
      ]
    },
    {
      "page": "ex_flexsurv",
      "title": "Simulated example data with time-to-event Weibull outcome and two covariates",
      "topics": [
        "ex_flexsurv"
      ]
    },
    {
      "page": "ex_lininter",
      "title": "Simulated example data with continuous outcome and interaction between two partially observed covariates",
      "topics": [
        "ex_lininter"
      ]
    },
    {
      "page": "ex_linquad",
      "title": "Simulated example data with continuous outcome and quadratic covariate effects",
      "topics": [
        "ex_linquad"
      ]
    },
    {
      "page": "ex_logisticquad",
      "title": "Simulated example data with binary outcome and quadratic covariate effects",
      "topics": [
        "ex_logisticquad"
      ]
    },
    {
      "page": "ex_ncc",
      "title": "Simulated nested case-control data",
      "topics": [
        "ex_ncc"
      ]
    },
    {
      "page": "ex_poisson",
      "title": "Simulated example data with count outcome, modelled using Poisson regression",
      "topics": [
        "ex_poisson"
      ]
    },
    {
      "page": "plot.smcfcs",
      "title": "Assess convergence of a smcfcs object",
      "topics": [
        "plot.smcfcs"
      ]
    },
    {
      "page": "smcfcs",
      "title": "Substantive model compatible fully conditional specification imputation of covariates.",
      "topics": [
        "smcfcs"
      ]
    },
    {
      "page": "smcfcs.casecohort",
      "title": "Substantive model compatible fully conditional specification imputation of covariates for case cohort studies",
      "topics": [
        "smcfcs.casecohort"
      ]
    },
    {
      "page": "smcfcs.dtsam",
      "title": "Substantive model compatible fully conditional specification imputation of covariates for discrete time survival analysis",
      "topics": [
        "smcfcs.dtsam"
      ]
    },
    {
      "page": "smcfcs.finegray",
      "title": "Substantive model compatible fully conditional specification imputation of covariates for a Fine-Gray model",
      "topics": [
        "smcfcs.finegray"
      ]
    },
    {
      "page": "smcfcs.flexsurv",
      "title": "Substantive model compatible fully conditional specification imputation of covariates and event times using flexible parametric survival models",
      "topics": [
        "smcfcs.flexsurv"
      ]
    },
    {
      "page": "smcfcs.nestedcc",
      "title": "Substantive model compatible fully conditional specification imputation of covariates for nested case control studies",
      "topics": [
        "smcfcs.nestedcc"
      ]
    },
    {
      "page": "smcfcs.parallel",
      "title": "Parallel substantive model compatible imputation",
      "topics": [
        "smcfcs.parallel"
      ]
    }
  ],
  "_readme": "https://github.com/jwb133/smcfcs/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "brglm2",
    "checkmate",
    "enrichwith",
    "lattice",
    "MASS",
    "Matrix",
    "nleqslv",
    "nnet",
    "numDeriv",
    "rlang",
    "statmod",
    "survival",
    "VGAM"
  ],
  "_vignettes": [
    {
      "source": "coarsening.Rmd",
      "filename": "coarsening.html",
      "title": "smcfcs for coarsened factor covariates",
      "author": "Jonathan Bartlett and Lars van der Burg",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2025-03-13 20:55:37",
      "modified": "2025-03-18 09:00:25",
      "commits": 3
    },
    {
      "source": "smcfcs-vignette.Rmd",
      "filename": "smcfcs-vignette.html",
      "title": "smcfcs",
      "author": "Jonathan Bartlett",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Joint model and FCS multiple imputation",
        "Imputation model compatibility",
        "Substantive Model Compatible Fully Conditional Specification multiple imputation",
        "Sampling from the imputation distribution",
        "Statistical properties",
        "When SMC-FCS may be preferable to FCS/MICE",
        "The smcfcs package",
        "Example - linear regression substantive model with quadratic covariate effects",
        "Imputing using auxiliary variables with smcfcs",
        "Rejection sampling warnings",
        "Assessing convergence"
      ],
      "created": "2015-01-15 18:17:17",
      "modified": "2025-03-18 09:21:31",
      "commits": 27
    },
    {
      "source": "coverror.Rmd",
      "filename": "coverror.html",
      "title": "smcfcs for covariate measurement error correction",
      "author": "Jonathan Bartlett",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Validation data",
        "Replication data",
        "Multiple covariates measured with error"
      ],
      "created": "2025-03-13 21:12:17",
      "modified": "2025-03-13 21:12:17",
      "commits": 1
    }
  ],
  "_score": 7.434019301632265,
  "_indexed": true,
  "_nocasepkg": "smcfcs",
  "_universes": [
    "jwb133"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.2",
      "date": "2026-09-30T08:56:25.000Z",
      "distro": "resolute",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/badcf52722e350bfed13eb627a41020146bbe8c0f49c7fc18a3f3c91ddeffeb7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.0.2",
      "date": "2026-09-30T08:56:23.000Z",
      "distro": "resolute",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/459f3aaa760d30a41e5acaaf95f1fb9bd1ab6565db910a374c7d5e0e92a5e586",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.0.2",
      "date": "2026-09-30T09:26:45.000Z",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/bf5c3ac1281fbff683e6de507928ca641fbbb0178a13bd01e102efe415a9637b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.0.2",
      "date": "2026-09-30T09:31:01.000Z",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/3d42ec2b53df8a68ba8319fb1fa3e7c0e4276de11cf65b65efc2c981f9c3b8cd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.2",
      "date": "2026-09-30T08:56:18.000Z",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/78c5e63ceffc8d49df0f141674d0cd3071bfa614cd57eb88e5a92ed833dc4383",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.2",
      "date": "2026-09-30T08:55:21.000Z",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/03439e646cceb5b3617591159559a5698daba564aa6118e5cd01cd4519f69f82",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.0.2",
      "date": "2026-09-30T08:55:06.000Z",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/c06383b80adbc529be1eb2da2d26bd43587ec9f218b035cd770429e96c8a2351",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.0.2",
      "date": "2026-09-30T08:55:08.000Z",
      "commit": "789bbcdeecad2ee303bac7f97c43c216e7326fb9",
      "fileid": "https://r2.ropensci.org/9a3cf9e93c2d323dee0bc312be12bdd1f4bee707bb1a77f63037a50215c33938",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jwb133/actions/runs/36692140943"
    }
  ]
}