{ "_id": "6a1014c9acfb0bcc41c83c5b", "Package": "CIVMR", "Title": "Constrained Instrumental Variables in Mendelian Randomization\nwith Pleiotropy", "Version": "0.0.1", "Authors@R": "person(\"Lai\", \"Jiang\", email = \"jianglai1987@gmail.com\", role = c(\"aut\", \"cre\"))", "Description": "In Mendelian randomization (MR), genetic variants are used\nto construct instrumental variables that then enable inference\nabout the causal relationship between a phenotype of interest\nand a response or disease outcome. However, valid MR inference\nrequires several assumptions, including the assumption that the\ngenetic variants only influence the response through the\nphenotype of interest.Pleiotropy occurs when a genetic variant\nhas an effect on more than one different phenotypes, and\ntherefore a pleiotropic genetic variant may be an invalid\ninstrumental variable.Hence, a naive method for constructing an\ninstrumental variables may lead to biased estimation of the\nassociation between the phenotype and the response. Here, we\nencode a new and intuitive method (Constrained Instrumental\nVariable method [CIV]) to construct valid instrumental\nvariables and perform adjusted causal effect estimation when\npleiotropic exists, focusing particularly on the situation\nwhere pleiotropic phenotypes have been measured. Our approach\nis theoretically guaranteed to perform an automatic and valid\nselection of genetic variants when building the instrumental\nvariable. We also provide details of the features of many\nexisting methods, together with a comparison of their\nperformance in a large series of simulations. CIV performs\nrobustly across many different pleiotropic violations of the MR\nassumptions.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Repository": "https://mrcieu.r-universe.dev", "Date/Publication": "2026-03-15 11:02:29 UTC", "RemoteUrl": "https://github.com/remlapmot/CIVMR", "RemoteRef": "suggestions", "RemoteSha": "44661fac3a5b1240354aa0331eee58b2d28408ae", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-14 09:04:20 UTC", "User": "root" }, "Author": "Lai Jiang [aut, cre]", "Maintainer": "Lai Jiang ", "MD5sum": "73754d0bedc5b9c0c46ca47c19409d21", "_user": "mrcieu", "_type": "src", "_file": "CIVMR_0.0.1.tar.gz", "_fileid": "d7247e54a30ddac6a37b266841151554fc80273ec065bb8f70044e7e415bf79b", "_filesize": 385151, "_sha256": "d7247e54a30ddac6a37b266841151554fc80273ec065bb8f70044e7e415bf79b", "_created": "2026-05-14T09:04:20.000Z", "_published": "2026-05-22T08:33:13.368Z", "_distro": "noble", "_jobs": [ { "job": 77344397731, "time": 200, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6990975811" }, { "job": 77344398358, "time": 198, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6990973228" }, { "job": 77344398110, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7011039463" }, { "job": 77344397902, "time": 173, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7011063195" }, { "job": 77344397557, "time": 289, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6990914361" }, { "job": 77344397441, "time": 118, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156232258" }, { "job": 77344397714, "time": 153, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6990959533" }, { "job": 77344397771, "time": 328, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6991011711" }, { "job": 77344397888, "time": 140, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6990955814" } ], "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/remlapmot/CIVMR", "_commit": { "id": "44661fac3a5b1240354aa0331eee58b2d28408ae", "author": "Tom Palmer ", "committer": "Tom Palmer ", "message": "Update .gitignore\n", "time": 1773572549 }, "_maintainer": { "name": "Lai Jiang", "email": "jianglai1987@gmail.com", "login": "laijiang", "uuid": 27783748 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "PMA", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "foreach", "role": "Suggests" }, { "package": "caret", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "sem", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "remlapmot", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-11", "n": 24 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "laijiang", "count": 11, "uuid": 27783748 } ], "_userbio": { "uuid": 15654827, "type": "organization", "name": "MRC Integrative Epidemiology Unit" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CIVMR" }, "_devurl": "https://github.com/remlapmot/civmr", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CIVMR.html", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "allele", "boot_CIV", "CIV", "cv_CIV", "IV_reduction", "LA_decomposition", "lmp", "lmPvalue", "pcc_IV", "rm_outlier_IV", "smooth_CIV", "smooth_L0_lambda", "SNP_reduction", "solve_pcc", "TSLS_IV" ], "_datasets": [ { "name": "ADNI", "title": "ADNI Data.", "object": "ADNI", "class": [ "data.frame" ], "fields": [ "Y", "G", "X", "Z" ], "rows": 491, "table": false, "tojson": true }, { "name": "simulation", "title": "simulation Data.", "object": "simulation", "class": [ "data.frame" ], "fields": [ "Y", "y", "X", "Z", "G", "n", "p" ], "rows": 500, "table": false, "tojson": true } ], "_help": [ { "page": "ADNI", "title": "ADNI Data.", "topics": [ "ADNI" ] }, { "page": "allele", "title": "cross-validated Allele score method.", "topics": [ "allele" ] }, { "page": "boot_CIV", "title": "bootstrapped CIV (recommended).", "topics": [ "boot_CIV" ] }, { "page": "CIV", "title": "Find a unique solution of CIV.", "topics": [ "CIV" ] }, { "page": "cv_CIV", "title": "cross-validated CIV.", "topics": [ "cv_CIV" ] }, { "page": "IV_reduction", "title": "Instrumental variable reduction.", "topics": [ "IV_reduction" ] }, { "page": "LA_decomposition", "title": "linear algebra decompositions for CIV. (internal function.)", "topics": [ "LA_decomposition" ] }, { "page": "lmp", "title": "simple linear regression pvalues (internal function.)", "topics": [ "lmp" ] }, { "page": "lmPvalue", "title": "univariate T-test p-values.", "topics": [ "lmPvalue" ] }, { "page": "pcc_IV", "title": "multiple orthogonal CIV solutions. (internal function)", "topics": [ "pcc_IV" ] }, { "page": "rm_outlier_IV", "title": "select IVs from a smooth_IV object (experimental function).", "topics": [ "rm_outlier_IV" ] }, { "page": "simulation", "title": "simulation Data.", "topics": [ "simulation" ] }, { "page": "smooth_CIV", "title": "CIV_smooth solution with cross-validation.(recommended)", "topics": [ "smooth_CIV" ] }, { "page": "smooth_L0_lambda", "title": "CIV_smooth solution given lambda. (Internal function)", "topics": [ "smooth_L0_lambda" ] }, { "page": "SNP_reduction", "title": "SNP pre-processing.", "topics": [ "SNP_reduction" ] }, { "page": "solve_pcc", "title": "Find a unique solution of CIV (internal use).", "topics": [ "solve_pcc" ] }, { "page": "TSLS_IV", "title": "Two stage least square method.", "topics": [ "TSLS_IV" ] } ], "_readme": "https://github.com/remlapmot/CIVMR/raw/suggestions/README.md", "_rundeps": [], "_vignettes": [ { "source": "CIVMR.Rmd", "filename": "CIVMR.html", "title": "Package 'CIVMR'", "author": "Lai Jiang", "engine": "knitr::rmarkdown", "headings": [ "1. Constrained Instrumental Variable Methods", "2. Package Contents", "2.1 Datasets", "2.2 MR Methods", "3. Example" ], "created": "2017-09-11 22:05:10", "modified": "2026-03-15 07:55:09", "commits": 6 } ], "_score": 2.6989700043360187, "_indexed": false, "_nocasepkg": "civmr", "_universes": [ "mrcieu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.1", "date": "2026-05-14T09:06:44.000Z", "distro": "noble", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "678aa66125a70ce08adc482cbcb6b9dd68b62daff85237dc9350b8cb08f17a89", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.6.0", "os": "linux", "version": "0.0.1", "date": "2026-05-14T09:06:37.000Z", "distro": "noble", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "a3cd7fcc25f4138af0dbabb79362905e32fab408be051bcc871c881265011145", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.5.3", "os": "mac", "version": "0.0.1", "date": "2026-05-15T05:57:41.000Z", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "fc7a53935ceaed2be31af9c5960655a65c3df6010c6eb6c0afd6325857928b3a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.6.0", "os": "mac", "version": "0.0.1", "date": "2026-05-15T05:59:32.000Z", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "a287c1be6c5977d479f32e71c91eaddfbfa47d69e4e4a9a1b55349f6b3edcbbc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.7.0", "os": "win", "version": "0.0.1", "date": "2026-05-14T09:05:42.000Z", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "e4c0b594478e5a2ecd439d007e5cbe61c6386845b48cd5b1112ad8d865517d01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.5.3", "os": "win", "version": "0.0.1", "date": "2026-05-14T09:08:52.000Z", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "06adbbf0e8d980d189c65c462011bd35ef99da45f1951e92e4fef3983ef60863", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.6.0", "os": "win", "version": "0.0.1", "date": "2026-05-14T09:05:38.000Z", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "d12661b21c8564de61784f0f9d0621e92310f3e1787202a999c8a6217649efbc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.1", "date": "2026-05-22T08:32:52.000Z", "commit": "44661fac3a5b1240354aa0331eee58b2d28408ae", "fileid": "05fc60fedd13b32e84a5f46cddd980266ead25d140303658028ed3f1578788fd", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25851381143" } ] }