{ "_id": "6ab645c899f7aa8c6aa2d04f", "Package": "gcemod", "Type": "Package", "Title": "Generalized Competing Event Models with Lunn-McNeil Testing", "Version": "0.3.0", "Date": "2026-08-06", "Authors@R": "person(\"Loren\", \"Mell\", email = \"lmell@ucsd.edu\", role = c(\"aut\", \"cre\"))", "Description": "Tools for fitting generalized competing event (GCE) models\nand estimating covariate effects on omega-plus, the ratio of\nthe hazard for an event of interest to the hazard for a\ncompeting event, on both the cause-specific (Cox) and\nsubdistribution (Fine-Gray) hazard scales. Confidence intervals\nand p-values are obtained from the Lunn-McNeil (1995) stacked\n(augmented) data approach. The package builds GCE risk scores\nfrom the model linear predictor, identifies risk-score\ncutpoints that maximize the separation in omega-plus between\ngroups, and produces cumulative incidence (\"alligator\") plots\nby risk group and calibration plots of predicted versus\nobserved omega-plus. Methods follow Carmona et al. (2014)\n, Mell et al. (2024)\n, and Lunn and McNeil (1995)\n.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Repository": "https://lmell-source.r-universe.dev", "Date/Publication": "2026-09-14 18:59:22 UTC", "RemoteUrl": "https://github.com/lmell-source/gcemod", "RemoteRef": "HEAD", "RemoteSha": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-25 09:54:22 UTC", "User": "root" }, "Author": "Loren Mell [aut, cre]", "Maintainer": "Loren Mell ", "_user": "lmell-source", "_type": "src", "_file": "gcemod_0.3.0.tar.gz", "_fileid": "https://r2.ropensci.org/fd9a106a8bde9fe359b5250c298ab9c6ba6c77ef87b91f79b98a490a92a0ac08", "_filesize": 431873, "_sha256": "fd9a106a8bde9fe359b5250c298ab9c6ba6c77ef87b91f79b98a490a92a0ac08", "_expires": "2027-01-03T09:58:30.000Z", "_created": "2026-09-25T09:54:22.000Z", "_published": "2026-09-25T09:58:32.188Z", "_jobs": [ { "job": 108026424865, "time": 154, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10857731674" }, { "job": 108026424917, "time": 198, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10857416957" }, { "job": 108026424907, "time": 160, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10858735499" }, { "job": 108026424796, "time": 200, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10858245931" }, { "job": 108025417047, "time": 206, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10857416495" }, { "job": 108026424813, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10858395704" }, { "job": 108026424930, "time": 108, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10857546635" }, { "job": 108026424847, "time": 111, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10858145743" }, { "job": 108026424952, "time": 89, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10857626540" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548", "_status": "success", "_upstream": "https://github.com/lmell-source/gcemod", "_commit": { "id": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "author": "lmell-source ", "committer": "GitHub ", "message": "Add files via upload\n\nAdd gcemod v0.3.1 tarball", "time": 1789412362 }, "_maintainer": { "name": "Loren Mell", "email": "lmell@ucsd.edu", "login": "lmell-source", "description": "", "uuid": 246723659 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "survival", "role": "Imports" }, { "package": "cmprsk", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.2", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "lmell-source", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-32", "n": 2 }, { "week": "2026-38", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "lmell-source", "count": 3, "uuid": 246723659 } ], "_userbio": { "uuid": 246723659, "type": "user", "name": "lmell-source", "followers": 0 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gcemod" }, "_devurl": "https://github.com/lmell-source/gcemod", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gcemod.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/lmell-source/gcemod", "_realowner": "lmell-source", "_cranurl": true, "_releases": [ { "version": "0.3.0", "date": "2026-09-24" } ], "_exports": [ "gce_alligator", "gce_calibration", "gce_cutpoints", "gce_performance", "gce_riskscore", "gce_scaling", "gce_tidy", "gcecox", "gcefg", "lunnmcneil" ], "_datasets": [ { "name": "hn", "title": "Head-and-neck cancer competing-risks example dataset", "object": "hn", "class": [ "data.frame" ], "fields": [ "id", "time", "status", "age", "ps", "female", "smoker", "t_cat", "n_cat", "p16", "site" ], "rows": 1000, "table": true, "tojson": true }, { "name": "prostate", "title": "Prostate cancer competing-risks example dataset", "object": "prostate", "class": [ "data.frame" ], "fields": [ "id", "time", "status", "age", "ps", "psa", "gleason", "t2b", "comorbidity" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "gce_alligator", "title": "Alligator plot: cumulative incidence by risk group and event type", "topics": [ "gce_alligator" ] }, { "page": "gce_calibration", "title": "Calibration of predicted vs. observed omega+ by risk rank", "topics": [ "gce_calibration" ] }, { "page": "gce_cutpoints", "title": "Risk-score cutpoints for GCE risk stratification", "topics": [ "gce_cutpoints" ] }, { "page": "gce_performance", "title": "Discrimination (C-index) for a GCE model", "topics": [ "gce_performance" ] }, { "page": "gce_riskscore", "title": "Normalized risk score and relative omega+ for new subjects", "topics": [ "gce_riskscore" ] }, { "page": "gce_scaling", "title": "Covariate scaling (means and SDs) used by the GCE risk score", "topics": [ "gce_scaling" ] }, { "page": "gce_tidy", "title": "Tidy a GCE model into a data frame of estimates", "topics": [ "gce_tidy" ] }, { "page": "gcecox", "title": "Generalized competing event model via cause-specific Cox regression", "topics": [ "gcecox" ] }, { "page": "gcefg", "title": "Generalized competing event model via Fine-Gray regression", "topics": [ "gcefg" ] }, { "page": "hn", "title": "Head-and-neck cancer competing-risks example dataset", "topics": [ "hn" ] }, { "page": "lunnmcneil", "title": "Lunn-McNeil stacked-model estimation of omega+ ratios", "topics": [ "lunnmcneil" ] }, { "page": "prostate", "title": "Prostate cancer competing-risks example dataset", "topics": [ "prostate" ] } ], "_readme": "https://github.com/lmell-source/gcemod/raw/HEAD/README.md", "_rundeps": [ "cli", "cmprsk", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "patchwork", "R6", "RColorBrewer", "rlang", "S7", "scales", "survival", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "gcemod.Rmd", "filename": "gcemod.html", "title": "Generalized Competing Event Modeling with gcemod", "author": "gcemod", "engine": "knitr::rmarkdown", "headings": [ "What gcemod does", "Two contrasting cohorts", "1. Fit the GCE model (cause-specific)", "2. Risk score", "3. Cutpoints maximizing the omega+ difference", "4. Alligator plot (cumulative incidence by risk group)", "5. Calibration of predicted vs. observed omega+", "Discrimination", "The competing-dominant contrast: prostate", "References" ], "created": "2026-08-06 15:28:46", "modified": "2026-08-06 15:28:46", "commits": 1 } ], "_score": 4, "_indexed": true, "_nocasepkg": "gcemod", "_universes": [ "lmell-source" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-09-25T09:56:33.000Z", "distro": "resolute", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/8cfece4cb5cccfa547de8570ea1308fb67f614ac9a45535eee520b1c8dd27ae2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.6.1", "os": "linux", "version": "0.3.0", "date": "2026-09-25T09:57:29.000Z", "distro": "resolute", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/a0480e6e5667accf33f12fafe79a467b095c2dd44ca48d0c671d7e0018284cd7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-09-25T09:56:31.000Z", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/296544c05ec431cdfcfdf9d472dfb511f3d3ee44a1c026f419cb8e37d32d57f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.6.1", "os": "mac", "version": "0.3.0", "date": "2026-09-25T09:56:42.000Z", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/05516ce1d0bcd4d09fd4e414dd4937b223de436ac31af489cdea191c2ba9beab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0", "date": "2026-09-25T09:56:48.000Z", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/dd7cd680b4399b82f9f26858394afdef6a272b102f88e587e49e9636f6c51691", "status": "success", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-09-25T09:55:35.000Z", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/a7848d84995a9a61bf7e974074d05b9892f67dd54f023f59d69baadd253c77ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.5.3", "os": "win", "version": "0.3.0", "date": "2026-09-25T09:55:44.000Z", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/4290b5d6617ce491821b1c77d67cd826b8df7728cb5c9e6f87614b4e3bc03bd7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" }, { "r": "4.6.1", "os": "win", "version": "0.3.0", "date": "2026-09-25T09:55:26.000Z", "commit": "9423c5d56d75702cc14147fc6f3e71d004ec0ac1", "fileid": "https://r2.ropensci.org/ce679e32dc1189e65d35ac97ba0ce7a3d3586cfc38d53546100de4835dcdd067", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lmell-source/actions/runs/36120719548" } ] }