{ "_id": "6a23be65530b9bc726bdae0a", "Package": "survkl", "Title": "Estimate Survival Data with Data Integration", "Version": "1.0.0", "URL": "https://um-kevinhe.github.io/survkl/", "Authors@R": "c(\nperson(\"Yubo\",\"Shao\",role=c(\"aut\",\"cre\"),email=\"ybshao@umich.edu\"),\nperson(\"Lingfeng\",\"Luo\",role=c(\"aut\"),email=\"lfluo@umich.edu\"),\nperson(\"Xiaohan\",\"Liu\",role=c(\"aut\"),email=\"xhliuu@umich.edu\"),\nperson(\"Junyi\",\"Qiu\",role=c(\"aut\"),email=\"junyiqiu@umich.edu\"),\nperson(\"Di\",\"Wang\",role=c(\"aut\"),email=\"dwwang@umich.edu\"),\nperson(\"Kevin\",\"He\",role=c(\"aut\"),email=\"kevinhe@umich.edu\")\n)", "Description": "Provides flexible and efficient tools for integrating\nexternal risk scores into Cox proportional hazards models while\naccounting for population heterogeneity. Enables robust\nestimation, improved predictive accuracy, and user-friendly\nworkflows for modern survival analysis. For more information,\nsee Wang et al. (2023) .", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "License": "GPL-3", "VignetteBuilder": "knitr", "SystemRequirements": "GNU make", "Config/pak/sysreqs": "make", "Repository": "https://um-kevinhe.r-universe.dev", "Date/Publication": "2026-06-06 01:38:28 UTC", "RemoteUrl": "https://github.com/um-kevinhe/survkl", "RemoteRef": "HEAD", "RemoteSha": "e56d70a48f9849efd0722a02cc8adf9731185168", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-06 05:23:35 UTC", "User": "root" }, "Author": "Yubo Shao [aut, cre],\nLingfeng Luo [aut],\nXiaohan Liu [aut],\nJunyi Qiu [aut],\nDi Wang [aut],\nKevin He [aut]", "Maintainer": "Yubo Shao ", "MD5sum": "c28cd0dc0feb57c25a9e4ed9b921c998", "_user": "um-kevinhe", "_type": "src", "_file": "survkl_1.0.0.tar.gz", "_fileid": "8941f938ce4804a03a404e7646e30ab2dbd10942ffed775aa4823be0793da189", "_filesize": 1791729, "_sha256": "8941f938ce4804a03a404e7646e30ab2dbd10942ffed775aa4823be0793da189", "_created": "2026-06-06T05:23:35.000Z", "_published": "2026-06-06T06:29:57.838Z", "_distro": "noble", "_jobs": [ { "job": 79853842930, "time": 240, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7451545424" }, { "job": 79853842928, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7451538816" }, { "job": 79853842933, "time": 3923, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7451987633" }, { "job": 79853842947, "time": 168, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7451536531" }, { "job": 79853842950, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7451536678" }, { "job": 79853842958, "time": 338, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7451553370" }, { "job": 79853842953, "time": 184, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7451534600" }, { "job": 79853842952, "time": 526, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7451573433" }, { "job": 79853433959, "time": 430, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7451516382" }, { "job": 79853842935, "time": 1572, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7451693909" }, { "job": 79853842926, "time": 184, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7451538438" }, { "job": 79853842934, "time": 125, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7451531207" }, { "job": 79853842925, "time": 156, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7451534922" } ], "_buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/um-kevinhe/survkl", "_commit": { "id": "e56d70a48f9849efd0722a02cc8adf9731185168", "author": "ybshao0709 ", "committer": "ybshao0709 ", "message": "Update website: rewrite Methods vignette (de-stratified, paper-aligned) + rebuild pkgdown site\n", "time": 1780709908 }, "_maintainer": { "name": "Yubo Shao", "email": "ybshao@umich.edu", "login": "ybshao0709", "description": "", "uuid": 93620754 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "survival", "role": "Suggests" } ], "_owner": "um-kevinhe", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-33", "n": 2 }, { "week": "2025-34", "n": 2 }, { "week": "2025-37", "n": 2 }, { "week": "2025-38", "n": 3 }, { "week": "2025-40", "n": 1 }, { "week": "2025-41", "n": 10 }, { "week": "2025-48", "n": 1 }, { "week": "2025-50", "n": 19 }, { "week": "2026-03", "n": 3 }, { "week": "2026-06", "n": 3 }, { "week": "2026-07", "n": 1 }, { "week": "2026-15", "n": 2 }, { "week": "2026-16", "n": 1 }, { "week": "2026-23", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "lingfengluo0510", "count": 39, "uuid": 44854842 }, { "user": "ybshao0709", "count": 28, "uuid": 93620754 }, { "user": "emiiilyliu", "count": 16, "uuid": 130197854 }, { "user": "joey-junyi-qiu", "count": 1, "uuid": 186342255 } ], "_userbio": { "uuid": 67330286, "type": "organization", "name": "UM-KevinHe" }, "_downloads": { "count": 452, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/survkl" }, "_devurl": "https://github.com/um-kevinhe/survkl", "_pkgdown": "https://um-kevinhe.github.io/survkl/", "_searchresults": 2, "_topics": [ "openblas", "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "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", "extra/survkl.html", "manual.pdf" ], "_homeurl": "https://github.com/um-kevinhe/survkl", "_realowner": "um-kevinhe", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2026-04-21" } ], "_exports": [ "cal_surv_prob", "coxkl", "coxkl_enet", "coxkl_ridge", "cv.coxkl", "cv.coxkl_enet", "cv.coxkl_ridge", "cv.plot", "generate_eta", "loss_fn", "test_eval" ], "_datasets": [ { "name": "ExampleData_highdim", "title": "Example high-dimensional survival data", "object": "ExampleData_highdim", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ExampleData_lowdim", "title": "Example low-dimensional survival data", "object": "ExampleData_lowdim", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "support", "title": "Study to Understand Prognoses Preferences Outcomes and Risks of Treatment", "object": "support", "class": [ "data.frame" ], "fields": [ "age", "death", "sex", "slos", "d.time", "dzgroup", "dzclass", "num.co", "edu", "scoma", "avtisst", "race", "hday", "diabetes", "dementia", "ca", "meanbp", "wblc", "hrt", "resp", "temp", "pafi", "alb", "bili", "crea", "sod", "ph", "glucose", "bun", "urine", "adlp", "adlsc", "sps", "aps" ], "rows": 9104, "table": true, "tojson": true } ], "_help": [ { "page": "cal_surv_prob", "title": "Calculate Survival Probabilities", "topics": [ "cal_surv_prob" ] }, { "page": "coef.coxkl", "title": "Extract Coefficients from a 'coxkl' Object", "topics": [ "coef.coxkl" ] }, { "page": "coef.coxkl_enet", "title": "Extract Coefficients from a 'coxkl_enet' Object", "topics": [ "coef.coxkl_enet" ] }, { "page": "coef.coxkl_ridge", "title": "Extract Coefficients from a 'coxkl_ridge' Object", "topics": [ "coef.coxkl_ridge" ] }, { "page": "coxkl", "title": "Cox Proportional Hazards Model with KL Divergence for Data Integration", "topics": [ "coxkl" ] }, { "page": "coxkl_enet", "title": "Cox Proportional Hazards Model with KL Divergence for Data Integration and Lasso & Elastic Net Penalty", "topics": [ "coxkl_enet" ] }, { "page": "coxkl_ridge", "title": "Cox Proportional Hazards Model with Ridge Penalty and External Information", "topics": [ "coxkl_ridge" ] }, { "page": "cv.coxkl", "title": "Cross-Validated Selection of Integration Parameter ('eta') for the Cox–KL Model", "topics": [ "cv.coxkl" ] }, { "page": "cv.coxkl_enet", "title": "Cross-Validation for CoxKL Model with elastic net & lasso penalty", "topics": [ "cv.coxkl_enet" ] }, { "page": "cv.coxkl_ridge", "title": "Cross-Validation for CoxKL Ridge Model (eta tuning)", "topics": [ "cv.coxkl_ridge" ] }, { "page": "cv.plot", "title": "Plot Cross-Validation Results vs Eta", "topics": [ "cv.plot" ] }, { "page": "ExampleData_highdim", "title": "Example high-dimensional survival data", "topics": [ "ExampleData_highdim" ] }, { "page": "ExampleData_lowdim", "title": "Example low-dimensional survival data", "topics": [ "ExampleData_lowdim" ] }, { "page": "generate_eta", "title": "Generate a Sequence of Tuning Parameters (eta)", "topics": [ "generate_eta" ] }, { "page": "loss_fn", "title": "Calculate the Log-Partial Likelihood for a Stratified Cox Model", "topics": [ "loss_fn" ] }, { "page": "plot.coxkl", "title": "Plot Model Performance vs Eta for 'coxkl'", "topics": [ "plot.coxkl" ] }, { "page": "plot.coxkl_enet", "title": "Plot Model Performance vs Lambda for 'coxkl_enet'", "topics": [ "plot.coxkl_enet" ] }, { "page": "plot.coxkl_ridge", "title": "Plot Model Performance vs Lambda for 'coxkl_ridge'", "topics": [ "plot.coxkl_ridge" ] }, { "page": "predict.coxkl", "title": "Predict Linear Predictors from a 'coxkl' Object", "topics": [ "predict.coxkl" ] }, { "page": "predict.coxkl_enet", "title": "Predict Linear Predictors from a coxkl_enet Object", "topics": [ "predict.coxkl_enet" ] }, { "page": "predict.coxkl_ridge", "title": "Predict Linear Predictors from a coxkl_ridge Object", "topics": [ "predict.coxkl_ridge" ] }, { "page": "SUPPORT", "title": "Study to Understand Prognoses Preferences Outcomes and Risks of Treatment", "topics": [ "support" ] }, { "page": "test_eval", "title": "Evaluate model performance on test data", "topics": [ "test_eval" ] } ], "_readme": "https://github.com/um-kevinhe/survkl/raw/HEAD/README.md", "_rundeps": [ "cli", "cowplot", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppParallel", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "Methods.Rmd", "filename": "Methods.html", "title": "Methods for Transfer-learning Based Integrated Cox Models", "engine": "knitr::rmarkdown", "headings": [ "Cox Proportional Hazards Model for the Target Cohort", "External Summary Information", "Partial Likelihood-Based Transfer Learning", "Regularization for High-Dimensional Data" ], "created": "2025-12-09 02:00:16", "modified": "2026-06-06 01:38:28", "commits": 3 }, { "source": "survkl.Rmd", "filename": "survkl.html", "title": "survkl: Transfer-Learning Based Integrated Cox Models", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Key Features", "Installation", "Quick Start", "Low-Dimensional Integration", "Example data structure", "High-Dimensional Integration (Ridge, Elastic Net, and LASSO)", "High-dimensional example data", "Ridge-Penalized KL-Integrated Cox Model (coxkl_ridge)", "Elastic-Net / LASSO KL-Integrated Cox Model (coxkl_enet)" ], "created": "2025-12-09 02:00:16", "modified": "2026-06-06 01:38:28", "commits": 5 } ], "_score": 5.623249290397901, "_indexed": true, "_nocasepkg": "survkl", "_universes": [ "um-kevinhe", "ybshao0709" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-06T05:27:28.000Z", "distro": "noble", "arch": "aarch64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "348e5fad4c81c3d71e6f15c0299bac400c738391dca729e1d8f4488083b43c47", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-06T05:26:28.000Z", "distro": "noble", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "761dbe71c8ea300bd38629b6a00875449e722846aabcf4d0eff42d7d3e7017aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-06T06:28:50.000Z", "distro": "noble", "arch": "aarch64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "3168dbe85b66ec8485bae757659e6037ee75aeeb80fbd0a303feafdd15a9d433", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-06T05:26:09.000Z", "distro": "noble", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "d074eb79f7a5301a6e13e5787f4f3bf4dcfa5ea9e2c1370ca7c5989e099c297b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-06T05:26:22.000Z", "arch": "aarch64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "c9c35191622ee29141fde2b0768f800a88fc78dc02d5a27de4f7b72c3bdf3ae5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-06T05:27:57.000Z", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "95f73926d427ae4d19fbf9b412cd7cb1a058b6918eeec5bccc567615484ddc42", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-06T05:25:57.000Z", "arch": "aarch64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "1bbf685a11511645575cdb652c4480da3e8ae0a4a7695301a603a7f31730b5d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-06T05:30:17.000Z", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "f7e547d87f3c764fd03245cb649e14a996841b7b775f7e04fd1259b394e942b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-06T05:50:05.000Z", "arch": "emscripten", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "ff3a7a34a50a7695c6caaef662bc68ce6b5c4c6827a94a446e3350f43ee5467a", "status": "success", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-06-06T05:25:22.000Z", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "dd2bddab9629f74d56036c6e52c23d3ae3fbcc38a59722485535573ce042e87a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-06-06T05:25:09.000Z", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "ffb2d560221c1774f365b1f29ab22ad9839527a5bfc47340dfd76802d64ed59c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-06-06T05:25:20.000Z", "arch": "x86_64", "commit": "e56d70a48f9849efd0722a02cc8adf9731185168", "fileid": "9ed02894232f9f4982ed517c13f7a618985607f6aed308d31d816f2c15a389d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/um-kevinhe/actions/runs/27053545565" } ] }