{ "_id": "6a1e8b2c1d7bb097a0a68abb", "Package": "compound.Cox", "Type": "Package", "Title": "Univariate Feature Selection and Compound Covariate for\nPredicting Survival, Including Copula-Based Analyses for\nDependent Censoring", "Version": "3.33", "Date": "2025-6-16", "Authors@R": "c(person(given = \"Takeshi\",\nfamily = \"Emura\",\nrole = c(\"aut\", \"cre\"),\nemail = \"takeshiemura@gmail.com\"),\nperson(given = \"Hsuan-Yu\",\nfamily = \"Chen\",\nrole = \"aut\"),\nperson(given = \"Shigeyuki\",\nfamily = \"Matsui\",\nrole = \"aut\"),\nperson(given = \"Yi-Hau\",\nfamily = \"Chen\",\nrole = \"aut\"))", "Maintainer": "Takeshi Emura ", "Description": "Univariate feature selection and compound covariate\nmethods under the Cox model with high-dimensional features\n(e.g., gene expressions). Available are survival data for\nnon-small-cell lung cancer patients with gene expressions (Chen\net al 2007 New Engl J Med) ,\nstatistical methods in Emura et al (2012 PLoS ONE)\n, Emura & Chen (2016 Stat\nMethods Med Res) , and Emura et\nal (2019). Algorithms for\ngenerating correlated gene expressions are also available.\nEstimation of survival functions via copula-graphic (CG)\nestimators is also implemented, which is useful for sensitivity\nanalyses under dependent censoring (Yeh et al 2023\nBiomedicines) and factorial\nsurvival analyses (Emura et al 2024 Stat Methods Med Res)\n.", "License": "GPL-2", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 07:47:32 UTC", "User": "root" }, "Author": "Takeshi Emura [aut, cre], Hsuan-Yu Chen [aut], Shigeyuki Matsui\n[aut], Yi-Hau Chen [aut]", "Repository": "https://takeshiemura1.r-universe.dev", "Date/Publication": "2025-06-16 04:50:02 UTC", "RemoteUrl": "https://github.com/cran/compound.Cox", "RemoteRef": "HEAD", "RemoteSha": "010105cc40c1e99c814dda5fdd278e625bcf212a", "MD5sum": "e17428ecfd36194a2f3bf7969ca7daf0", "_user": "takeshiemura1", "_type": "src", "_file": "compound.Cox_3.33.tar.gz", "_fileid": "d4e3e36316f7a96a1beba60cfc0430e0e1582cc62a03a33b5060359bcbf66570", "_filesize": 210731, "_sha256": "d4e3e36316f7a96a1beba60cfc0430e0e1582cc62a03a33b5060359bcbf66570", "_created": "2026-06-02T07:47:32.000Z", "_published": "2026-06-02T07:50:04.849Z", "_distro": "noble", "_jobs": [ { "job": 79023687659, "time": 119, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7351911924" }, { "job": 79023687654, "time": 106, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7351907217" }, { "job": 79023687668, "time": 104, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7351906767" }, { "job": 79023687761, "time": 86, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7351900576" }, { "job": 79023258513, "time": 164, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7351872146" }, { "job": 79023687758, "time": 80, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7351898937" }, { "job": 79023687722, "time": 112, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7351909297" }, { "job": 79023687674, "time": 101, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7351906264" }, { "job": 79023687689, "time": 96, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7351904049" } ], "_buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/compound.Cox", "_commit": { "id": "010105cc40c1e99c814dda5fdd278e625bcf212a", "author": "Takeshi Emura ", "committer": "cran-robot ", "message": "version 3.33\n", "time": 1750049402 }, "_maintainer": { "name": "Takeshi Emura", "email": "takeshiemura@gmail.com", "login": "takeshiemura1", "description": "", "uuid": 236010106 }, "_registered": true, "_dependencies": [ { "package": "numDeriv", "role": "Depends" }, { "package": "survival", "role": "Depends" }, { "package": "MASS", "role": "Depends" } ], "_owner": "cran", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-25", "n": 1 } ], "_tags": [ { "name": "3.33", "date": "2025-06-16" } ], "_stars": 0, "_contributors": [ { "user": "takeshiemura1", "count": 36, "uuid": 236010106 } ], "_userbio": { "uuid": 236010106, "type": "user", "name": "Takeshi Emura" }, "_downloads": { "count": 339, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/compound.Cox" }, "_searchresults": 28, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/compound.Cox.html", "extra/contents.json", "manual.pdf" ], "_realowner": "takeshiemura1", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2012-04-16" }, { "version": "1.1", "date": "2012-10-02" }, { "version": "1.2", "date": "2012-11-10" }, { "version": "1.3", "date": "2013-11-08" }, { "version": "1.4", "date": "2014-04-13" }, { "version": "2.0", "date": "2015-10-31" }, { "version": "2.1", "date": "2016-10-21" }, { "version": "3.0", "date": "2016-11-28" }, { "version": "3.1", "date": "2017-01-09" }, { "version": "3.2", "date": "2017-02-17" }, { "version": "3.3", "date": "2017-03-18" }, { "version": "3.4", "date": "2017-10-24" }, { "version": "3.5", "date": "2017-11-02" }, { "version": "3.6", "date": "2017-11-18" }, { "version": "3.7", "date": "2018-01-03" }, { "version": "3.8", "date": "2018-03-09" }, { "version": "3.9", "date": "2018-03-16" }, { "version": "3.10", "date": "2018-03-28" }, { "version": "3.11", "date": "2018-05-24" }, { "version": "3.12", "date": "2018-07-02" }, { "version": "3.13", "date": "2018-07-12" }, { "version": "3.14", "date": "2018-07-21" }, { "version": "3.15", "date": "2019-04-03" }, { "version": "3.16", "date": "2019-05-31" }, { "version": "3.17", "date": "2019-06-02" }, { "version": "3.18", "date": "2019-07-04" }, { "version": "3.19", "date": "2019-09-19" }, { "version": "3.20", "date": "2020-07-05" }, { "version": "3.21", "date": "2022-08-08" }, { "version": "3.22", "date": "2022-11-24" }, { "version": "3.23", "date": "2022-12-06" }, { "version": "3.24", "date": "2023-01-05" }, { "version": "3.25", "date": "2023-01-21" }, { "version": "3.26", "date": "2023-01-30" }, { "version": "3.27", "date": "2023-02-13" }, { "version": "3.28", "date": "2023-04-05" }, { "version": "3.29", "date": "2023-06-18" }, { "version": "3.30", "date": "2023-07-11" }, { "version": "3.31", "date": "2024-10-05" }, { "version": "3.32", "date": "2025-01-11" }, { "version": "3.33", "date": "2025-06-16" } ], "_exports": [ "CG.Clayton", "CG.Frank", "CG.Gumbel", "CG.test", "cindex.CV", "compound.reg", "dependCox.reg", "dependCox.reg.CV", "surv.factorial", "uni.score", "uni.selection", "uni.Wald", "X.pathway", "X.tag" ], "_datasets": [ { "name": "Lung", "title": "Survival data for patients with non-small-cell lung cancer.", "object": "Lung", "file": "Lung.rda", "class": [ "data.frame" ], "fields": [ "t.vec", "d.vec", "train", "VHL", "IHPK1", "HMMR", "CMKOR1", "PLAU", "IGF2", "FGB", "MYBL2", "ODC1", "MTHFD2", "GLIPR1", "EZH2", "HCK", "CCNC", "XRCC1", "CYP1B1", "CDC25A", "CD44", "LCK", "MTHFS", "PON3", "PTPN6", "KIDINS220", "KLHL22", "RBBP6", "GABARAPL2", "SEH1L", "CITED2", "BARD1", "TLX1", "CRMP1", "CTNNA1", "ANXA5", "PTGS2", "SMC4L1", "LOC285086", "ATP11B", "CDK10", "IRF4", "MYH11", "ME3", "CCT6A", "SNCG", "MAK3", "VCPIP1", "JMJD1A", "STAT2", "DDX6", "ERBB3", "PAX2", "PCTK2", "NF1", "DLG2", "JMJD1A.1", "SUCLA2", "MMP16", "AP3B2", "HGF", "MAP2K3", "CPEB4", "ZNF264", "AXL", "CDC23", "MAST3", "COX11", "PRKAG2", "MAN1B1", "F8", "RSU1", "MMD", "AK5", "IDS", "BNIP1", "ENG", "PCDHGC3", "RALY", "WDR33", "RNF4", "PRDX1", "FXN", "PTPRU", "FRAP1", "MMP7", "CST3", "TIMP2", "TAL1", "STAT1", "CCND1", "DUSP6", "SNRPF", "MMP13", "NR2F6", "HOXA1", "RIPK1", "IL7R", "SEC13L1", "RPL5" ], "rows": 125, "table": true, "tojson": true }, { "name": "PBC", "title": "Primary biliary cirrhosis (PBC) of the liver data", "object": "PBC", "file": "PBC.rda", "class": [ "data.frame" ], "fields": [ "T", "d", "trt", "age", "sex", "asc", "hep", "spi", "ede", "bil", "cho", "alb", "cop", "alk", "SGO", "tri", "pla", "pro", "gra" ], "rows": 276, "table": true, "tojson": true } ], "_help": [ { "page": "compound.Cox-package", "title": "Univariate Feature Selection and Compound Covariate for Predicting Survival, Including Copula-Based Analyses for Dependent Censoring", "topics": [ "compound.Cox-package", "compound.Cox" ] }, { "page": "CG.Clayton", "title": "Copula-graphic estimator under the Clayton copula.", "topics": [ "CG.Clayton" ] }, { "page": "CG.Frank", "title": "Copula-graphic estimator under the Frank copula.", "topics": [ "CG.Frank" ] }, { "page": "CG.Gumbel", "title": "Copula-graphic estimator under the Gumbel copula.", "topics": [ "CG.Gumbel" ] }, { "page": "CG.test", "title": "Testing survival difference of two groups via the CG estimators", "topics": [ "CG.test" ] }, { "page": "cindex.CV", "title": "Cross-validated c-index for measuring the predictive accuracy of a prognostic index under a copula-based dependent censoring model.", "topics": [ "cindex.CV" ] }, { "page": "compound.reg", "title": "Compound shrinkage estimation under the Cox model", "topics": [ "compound.reg" ] }, { "page": "dependCox.reg", "title": "Univariate Cox regression under dependent censoring.", "topics": [ "dependCox.reg" ] }, { "page": "dependCox.reg.CV", "title": "Cox regression under dependent censoring.", "topics": [ "dependCox.reg.CV" ] }, { "page": "Lung", "title": "Survival data for patients with non-small-cell lung cancer.", "topics": [ "Lung" ] }, { "page": "PBC", "title": "Primary biliary cirrhosis (PBC) of the liver data", "topics": [ "PBC" ] }, { "page": "surv.factorial", "title": "Factorial survival analysis under dependent censoring", "topics": [ "surv.factorial" ] }, { "page": "uni.score", "title": "Univariate Cox score test", "topics": [ "uni.score" ] }, { "page": "uni.selection", "title": "Univariate feature selection based on univariate significance tests", "topics": [ "uni.selection" ] }, { "page": "uni.Wald", "title": "Univariate Cox Wald test", "topics": [ "uni.Wald" ] }, { "page": "X.pathway", "title": "Generate a matrix of gene expressions in the presence of gene pathways", "topics": [ "X.pathway" ] }, { "page": "X.tag", "title": "Generate a matrix of gene expressions in the presence of tag genes", "topics": [ "X.tag" ] } ], "_rundeps": [ "lattice", "MASS", "Matrix", "numDeriv", "survival" ], "_score": 2.4014005407815437, "_indexed": true, "_nocasepkg": "compound.cox", "_universes": [ "takeshiemura1" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.33", "date": "2026-06-02T07:49:20.000Z", "distro": "noble", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "33a7d4f5b703f6176b7da8fd635de85357986ae2bd18ac7820e8adb682625501", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.6.0", "os": "linux", "version": "3.33", "date": "2026-06-02T07:49:13.000Z", "distro": "noble", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "c6a39c10ca2bf2e4951bacdb00dc423c8965dccec55db04a22bc9f569c0cdfff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.5.3", "os": "mac", "version": "3.33", "date": "2026-06-02T07:49:16.000Z", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "092eceb1716c649aaad7edc38e272e3d1c57a903480d322140274a00bec67d46", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.6.0", "os": "mac", "version": "3.33", "date": "2026-06-02T07:48:54.000Z", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "2978a243a2ab4e82fa9e2f72f045a6c14d504d6f245a79fc1d488d0c9aba7bc3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.6.0", "os": "wasm", "version": "3.33", "date": "2026-06-02T07:49:11.000Z", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "91e7c329b12f7b83c4eec4ee256e20e0883f8cf1895f509e21d52b49cfefa0d9", "status": "success", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.7.0", "os": "win", "version": "3.33", "date": "2026-06-02T07:49:03.000Z", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "b0a21094e67fbdb4aa7df63aff22721d11749ee71112205760ae9f74b3132258", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.5.3", "os": "win", "version": "3.33", "date": "2026-06-02T07:48:57.000Z", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "ad0af8cd680c7cf45881d0b64b90c86d30bec998c9b8b1b26da65510d71cd3a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" }, { "r": "4.6.0", "os": "win", "version": "3.33", "date": "2026-06-02T07:48:51.000Z", "commit": "010105cc40c1e99c814dda5fdd278e625bcf212a", "fileid": "2f59e626424b63fe6625b7d1502564f8ebc0753a65304041d1714c3826ab0a64", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/takeshiemura1/actions/runs/26805901454" } ] }