{ "_id": "6a157063acfb0bcc41d64e31", "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, 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": "2026-05-26 09:57:10 UTC", "User": "root" }, "Author": "Joshua Millstein [aut, cre] (ORCID:\n)", "Maintainer": "Joshua Millstein ", "MD5sum": "c67c387e6fbee89111bd241bc0bbeebb", "_user": "uscbiostats", "_type": "src", "_file": "cit_2.4.0.tar.gz", "_fileid": "5586bfce47ffc448bdd121e010e2b941d27f8583dca43f1701fc467881c7d455", "_filesize": 184934, "_sha256": "5586bfce47ffc448bdd121e010e2b941d27f8583dca43f1701fc467881c7d455", "_created": "2026-05-26T09:57:10.000Z", "_published": "2026-05-26T10:05:23.155Z", "_distro": "noble", "_jobs": [ { "job": 77850686668, "time": 218, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7214192999" }, { "job": 77850686697, "time": 163, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7214175320" }, { "job": 77850686685, "time": 177, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7214179320" }, { "job": 77850686652, "time": 153, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7214171542" }, { "job": 77850686720, "time": 101, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7214155607" }, { "job": 77850686713, "time": 404, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7214255688" }, { "job": 77850686703, "time": 129, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7214164242" }, { "job": 77850686684, "time": 255, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7214205985" }, { "job": 77849925519, "time": 274, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7214120138" }, { "job": 77850686670, "time": 151, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7214171350" }, { "job": 77850686705, "time": 176, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7214179468" }, { "job": 77850686785, "time": 177, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7214179805" }, { "job": 77850686735, "time": 127, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7214163529" } ], "_buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/uscbiostats/cit", "_commit": { "id": "620f42dc9195d73b391497b6f1fccf6794756d67", "author": "MingzhiYe16 ", "committer": "MingzhiYe16 ", "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" }, "_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": 2, "_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", "description": "Organization for USC Division of Biostatistics" }, "_downloads": { "count": 289, "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": "4.6.0", "_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": "libgsl27", "headers": "libgsl-dev", "source": "gsl", "version": "2.7.1+dfsg-6ubuntu2", "name": "gsl", "homepage": "https://www.gnu.org/software/gsl", "description": "GNU Scientific Library (GSL) -- library package" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.8573324964312685, "_indexed": true, "_nocasepkg": "cit", "_universes": [ "uscbiostats", "millstei" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.4.0", "date": "2026-05-26T10:00:47.000Z", "distro": "noble", "arch": "aarch64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "24ade89908af3025c7c2d23298e75139574c424435f38d33ec59d9422a5f415c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.7.0", "os": "linux", "version": "2.4.0", "date": "2026-05-26T09:59:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "cbbd15ffc29417ee46b59f8fe43d1ceb6a4974a1a51f13159f944eb6ebd7752c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.6.0", "os": "linux", "version": "2.4.0", "date": "2026-05-26T10:00:08.000Z", "distro": "noble", "arch": "aarch64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "430fa28ad87a647794eabeb30ef347bbdd84f008c4b83492cb82c796e98f826b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.6.0", "os": "linux", "version": "2.4.0", "date": "2026-05-26T09:59:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "d1901d64708deef3fae851acfa769c819b4db849038b0fc49fbb96bbd78f169c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.5.3", "os": "mac", "version": "2.4.0", "date": "2026-05-26T09:59:20.000Z", "arch": "aarch64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "8dccd16cf17d8d3e9d700dfdc43fdeaa794cc97db36276c5ee768aa65c8a62cf", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.5.3", "os": "mac", "version": "2.4.0", "date": "2026-05-26T10:02:16.000Z", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "08d2a4cb46bc2f3b8189a4a265401618e1e9653a83fee59ffc2e5b9f64829bee", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.6.0", "os": "mac", "version": "2.4.0", "date": "2026-05-26T09:59:40.000Z", "arch": "aarch64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "1672df3975c8476766eea128ed5c4594c27433689c0fe4ba885ddd2a8e9bda29", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.6.0", "os": "mac", "version": "2.4.0", "date": "2026-05-26T10:00:41.000Z", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "96b7057a824063bd277077c0ca713c62eedb78b3835fcaa9d5065670eb2d74cd", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.6.0", "os": "wasm", "version": "2.4.0", "date": "2026-05-26T09:59:55.000Z", "arch": "emscripten", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "c5b465a6270783958f0a7e1b2fddaf3e2863d64d48ba5bdbfd3d4fdcbbd4ffbd", "status": "success", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.7.0", "os": "win", "version": "2.4.0", "date": "2026-05-26T09:59:17.000Z", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "03f5cb90bedbacbb489e0697ee0fee4af93837502dabee4fc32d0bac225220c4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.5.3", "os": "win", "version": "2.4.0", "date": "2026-05-26T09:59:08.000Z", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "355c9a7d8c22911f7d58388bc2eb840e79c54b2a07e2d318dc211f41120233b3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" }, { "r": "4.6.0", "os": "win", "version": "2.4.0", "date": "2026-05-26T09:59:07.000Z", "arch": "x86_64", "commit": "620f42dc9195d73b391497b6f1fccf6794756d67", "fileid": "ae2ef975d2a052e8b4deb662beb37764596fab186a9d8d5eddcb80d2b5a687ec", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26445277071" } ] }