{
  "_id": "6a48aa03e06c18f0a6545eb4",
  "Package": "cit",
  "Type": "Package",
  "Title": "Causal Inference Test",
  "Version": "2.4.0",
  "Date": "2024-06-26",
  "Authors@R": "person(\"Joshua\", \"Millstein\", email = \"joshua.millstein@usc.edu\", role =\nc(\"aut\", \"cre\"), comment = c(ORCID=\"0000-0001-7961-8943\"))",
  "Description": "A likelihood-based hypothesis testing approach is\nimplemented for assessing causal mediation. Described in\nMillstein, Chen, and Breton (2016),\n<DOI:10.1093/bioinformatics/btw135>, it could be used to test\nfor mediation of a known causal association between a DNA\nvariant, the 'instrumental variable', and a clinical outcome or\nphenotype by gene expression or DNA methylation, the potential\nmediator. Another example would be testing mediation of the\neffect of a drug on a clinical outcome by the molecular target.\nThe hypothesis test generates a p-value or permutation-based\nFDR value with confidence intervals to quantify uncertainty in\nthe causal inference. The outcome can be represented by either\na continuous or binary variable, the potential mediator is\ncontinuous, and the instrumental variable can be continuous or\nbinary and is not limited to a single variable but may be a\ndesign matrix representing multiple variables.",
  "SystemRequirements": "gsl (with development libraries libgsl-dev)",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "LazyLoad": "yes",
  "BugReports": "https://github.com/USCbiostats/cit/issues",
  "URL": "https://github.com/USCbiostats/cit",
  "Config/pak/sysreqs": "libgsl0-dev",
  "Repository": "https://uscbiostats.r-universe.dev",
  "Date/Publication": "2024-06-27 04:50:38 UTC",
  "RemoteUrl": "https://github.com/uscbiostats/cit",
  "RemoteRef": "HEAD",
  "RemoteSha": "620f42dc9195d73b391497b6f1fccf6794756d67",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 06:08:46 UTC",
    "User": "root"
  },
  "Author": "Joshua Millstein [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7961-8943>)",
  "Maintainer": "Joshua Millstein <joshua.millstein@usc.edu>",
  "_user": "uscbiostats",
  "_type": "src",
  "_file": "cit_2.4.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/9d3970ab6546a03297690efc529f5a80757aa3463c3c7eacba7446ea5c18cea3",
  "_filesize": 186874,
  "_sha256": "9d3970ab6546a03297690efc529f5a80757aa3463c3c7eacba7446ea5c18cea3",
  "_expires": "2026-10-12T06:36:49.000Z",
  "_created": "2026-07-04T06:08:46.000Z",
  "_published": "2026-07-04T06:36:51.228Z",
  "_jobs": [
    {
      "job": 85109022554,
      "time": 183,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8079016208"
    },
    {
      "job": 85109022556,
      "time": 180,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8079015446"
    },
    {
      "job": 85109022552,
      "time": 209,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8079019669"
    },
    {
      "job": 85109022567,
      "time": 215,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8079020244"
    },
    {
      "job": 85109022563,
      "time": 146,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8079194040"
    },
    {
      "job": 85109022564,
      "time": 244,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8079024088"
    },
    {
      "job": 85109022560,
      "time": 180,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8079193284"
    },
    {
      "job": 85109022568,
      "time": 383,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8079043187"
    },
    {
      "job": 85108705384,
      "time": 287,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078989857"
    },
    {
      "job": 85109022541,
      "time": 192,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8079016892"
    },
    {
      "job": 85109022570,
      "time": 178,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8079015149"
    },
    {
      "job": 85109022555,
      "time": 164,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8079013098"
    },
    {
      "job": 85109022561,
      "time": 190,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8079016809"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615",
  "_status": "success",
  "_upstream": "https://github.com/uscbiostats/cit",
  "_commit": {
    "id": "620f42dc9195d73b391497b6f1fccf6794756d67",
    "author": "MingzhiYe16 <yemingzhis@gmail.com>",
    "committer": "MingzhiYe16 <yemingzhis@gmail.com>",
    "message": "change DESCRIPTIOON file\n",
    "time": 1719463838
  },
  "_maintainer": {
    "name": "Joshua Millstein",
    "email": "joshua.millstein@usc.edu",
    "login": "millstei",
    "description": "",
    "uuid": 23107824,
    "orcid": "0000-0001-7961-8943"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "uscbiostats",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "millstei",
      "count": 13,
      "uuid": 23107824
    },
    {
      "user": "gvegayon",
      "count": 9,
      "uuid": 893619
    },
    {
      "user": "mingzhiye16",
      "count": 5,
      "uuid": 45770554
    }
  ],
  "_userbio": {
    "uuid": 10712919,
    "type": "organization",
    "name": "USC Division of Biostatistics",
    "followers": 43,
    "description": "Organization for USC Division of Biostatistics"
  },
  "_downloads": {
    "count": 386,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cit"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/uscbiostats/cit",
  "_searchresults": 36,
  "_topics": [
    "gsl",
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/cit.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/uscbiostats/cit",
  "_realowner": "uscbiostats",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2011-09-07"
    },
    {
      "version": "1.1",
      "date": "2011-12-10"
    },
    {
      "version": "1.2",
      "date": "2013-12-20"
    },
    {
      "version": "1.3",
      "date": "2014-12-10"
    },
    {
      "version": "1.4",
      "date": "2015-03-10"
    },
    {
      "version": "1.5",
      "date": "2015-10-25"
    },
    {
      "version": "1.7",
      "date": "2015-10-28"
    },
    {
      "version": "1.8",
      "date": "2016-01-09"
    },
    {
      "version": "1.9",
      "date": "2016-01-10"
    },
    {
      "version": "2.0",
      "date": "2016-03-07"
    },
    {
      "version": "2.1",
      "date": "2016-11-15"
    },
    {
      "version": "2.2",
      "date": "2017-12-15"
    },
    {
      "version": "2.3.1",
      "date": "2021-05-25"
    },
    {
      "version": "2.3.2",
      "date": "2024-06-28"
    }
  ],
  "_exports": [
    "cit.bp",
    "cit.bp.m.v1",
    "cit.bp.m.v2",
    "cit.bp.v1",
    "cit.bp.v2",
    "cit.cp",
    "cit.cp.m.v1",
    "cit.cp.m.v2",
    "cit.cp.v1",
    "cit.cp.v2",
    "fdr.cit",
    "fdr.od",
    "fdr.q.para",
    "fdr.q.perm",
    "iuq",
    "linregM.nc",
    "ms_f"
  ],
  "_help": [
    {
      "page": "cit-package",
      "title": "Causal Inference Test",
      "topics": [
        "cit-package"
      ]
    },
    {
      "page": "cit.bp",
      "title": "Causal Inference Test for a Binary Outcome",
      "topics": [
        "cit.bp"
      ]
    },
    {
      "page": "cit.cp",
      "title": "Causal Inference Test for a Continuous Outcome",
      "topics": [
        "cit.cp"
      ]
    },
    {
      "page": "fdr.cit",
      "title": "Omnibus FDR Values for CIT",
      "topics": [
        "fdr.cit"
      ]
    },
    {
      "page": "fdr.od",
      "title": "Permutation-Based FDR and Confidence Interval",
      "topics": [
        "fdr.od"
      ]
    },
    {
      "page": "fdr.q.para",
      "title": "Parametric tail-area FDR Values, q-values",
      "topics": [
        "fdr.q.para"
      ]
    },
    {
      "page": "fdr.q.perm",
      "title": "Nonparametric permutation-based tail-area FDR Values, q-values",
      "topics": [
        "fdr.q.perm"
      ]
    },
    {
      "page": "iuq",
      "title": "Intersection/Union Q-Value",
      "topics": [
        "iuq"
      ]
    },
    {
      "page": "linreg",
      "title": "F Test for Linear Model",
      "topics": [
        "linreg"
      ]
    }
  ],
  "_readme": "https://github.com/uscbiostats/cit/raw/HEAD/README.md",
  "_rundeps": [
    "Rcpp"
  ],
  "_sysdeps": [
    {
      "shlib": "libgsl",
      "package": "libgsl28",
      "headers": "libgsl-dev",
      "source": "gsl",
      "version": "2.8+dfsg-6",
      "name": "gsl",
      "homepage": "https://www.gnu.org/software/gsl",
      "description": "GNU Scientific Library (GSL) -- library package"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 4.033423755486949,
  "_indexed": true,
  "_nocasepkg": "cit",
  "_universes": [
    "uscbiostats",
    "millstei"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-04T06:12:05.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/8757d55cbae2317e2c37b548b6e9127e7f418f2c4efa53b571fee1425d1e44cb",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-04T06:11:49.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/480e116f541b941bc943c7a24bf443f77a8f8404532fcd2b7030ac31f9ab176e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-04T06:12:29.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/cae961d1d0a4d0ed4fc5c5906f1ef9571114e58d9d6783692aa1145bac82108c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-04T06:12:22.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/34519117281f474fbbb21a765970df0c3e30a4b6aefd8ccf4776058bff1469ce",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-04T06:35:31.000Z",
      "arch": "aarch64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/eeb6c83f5bc5d92f5978e53cd84851a09aa20c68402f9b7325596b40c8ea3499",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-04T06:12:26.000Z",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/914a8d6416e4be92d7757c0448cfef15e2b2ffb9c14595a4ecda697082b733c1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-04T06:35:02.000Z",
      "arch": "aarch64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/56f347e67615fe2866d52c7e96bb4c00c2d9f780bb81e3acf5807ec06a3e2fb8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-04T06:13:33.000Z",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/a681cbb0797ff8fadf3f5fe20b25f587b87c7cb7deed3637463f61446de7abfd",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.4.0",
      "date": "2026-07-04T06:12:10.000Z",
      "arch": "emscripten",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/4bbf818007185b5b6f85de840aa173f5ff1b39be8d585e499dd3e1baaa772078",
      "status": "success",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.4.0",
      "date": "2026-07-04T06:10:46.000Z",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/e7a079e797240fb90253114ef6fad0d5e36ef7ceb2bd130c6d1fcd74fba24459",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.4.0",
      "date": "2026-07-04T06:10:41.000Z",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/ad5b5371695a5c57be1e204ba92d626707e4be5f91590f95277a9aa40e5b85d7",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.4.0",
      "date": "2026-07-04T06:10:55.000Z",
      "arch": "x86_64",
      "commit": "620f42dc9195d73b391497b6f1fccf6794756d67",
      "fileid": "https://r2.ropensci.org/807fbef4a58417bb8dddd6141699897a9b07ceeb98d45c518b0634a52398a7ae",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/28697144615"
    }
  ]
}