{ "_id": "6ad3521c6fd9391477c95863", "Package": "iPEB", "Type": "Package", "Title": "Improved Parametric Empirical Bayes for Longitudinal Biomarker\nAnalysis", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Bitan\", \"Sarkar\", email = \"bitansarkar010899@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0009-0000-5178-5934\")),\nperson(c(\"Ana\", \"Maria\"), \"Kenney\", role = \"aut\"),\nperson(c(\"James\", \"P.\"), \"Long\", role = \"aut\"),\nperson(c(\"Johannes\", \"F.\"), \"Fahrmann\", role = \"aut\"),\nperson(\"Samir\", \"Hanash\", role = \"aut\"),\nperson(\"Kim-Anh\", \"Do\", role = \"aut\"),\nperson(\"Ehsan\", \"Irajizad\", role = \"aut\"))", "Description": "Extends parametric empirical Bayes (PEB) for longitudinal\nbiomarker screening with a time-gap-aware standardization\nlayer, covariate adjustment, and objective-driven multi-marker\nweighting. The layer models each subject's biomarker history\nwith a random intercept (and an optional random slope) and\nautocorrelated, gap-scaled residuals, so that prediction\nuncertainty grows with the time between visits and per-visit\nspecificity is preserved under irregular sampling. Marker\nweights are learned to optimize a user-selected clinical\nobjective -- maximizing sensitivity at a fixed specificity,\nextending detection lead time, or a combined objective -- with\noptional feature selection and a choice of scalar or\nmultivariate combiner. Functions for fitting, prediction, and\nevaluation (sensitivity, lead time, and specificity at chosen\noperating points) are provided. A manuscript describing the\nmethod is in preparation.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "URL": "https://github.com/bitansa/iPEB", "BugReports": "https://github.com/bitansa/iPEB/issues", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-17 10:44:24 UTC", "User": "root" }, "Author": "Bitan Sarkar [aut, cre, cph] (ORCID:\n), Ana Maria Kenney\n[aut], James P. Long [aut], Johannes F. Fahrmann [aut], Samir\nHanash [aut], Kim-Anh Do [aut], Ehsan Irajizad [aut]", "Maintainer": "Bitan Sarkar ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-09-17 13:20:08 UTC", "RemoteUrl": "https://github.com/cran/iPEB", "RemoteRef": "HEAD", "RemoteSha": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "_user": "cran", "_type": "src", "_file": "iPEB_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/c63d53857ba61290f1304da39642925c6776ba88f43286f96ab0762e1a016713", "_filesize": 188678, "_sha256": "c63d53857ba61290f1304da39642925c6776ba88f43286f96ab0762e1a016713", "_expires": "2027-01-25T10:46:50.000Z", "_created": "2026-10-17T10:44:24.000Z", "_published": "2026-10-17T10:46:52.673Z", "_buildurl": "https://github.com/r-universe/cran/actions/runs/39025830214", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117377159396, "time": 109, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12098672475" }, { "job": 117377159407, "time": 105, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12098836627" }, { "job": 117376579266, "time": 193, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12098766078" }, { "job": 117377159469, "time": 104, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12098667233" }, { "job": 117377159485, "time": 87, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12097888565" }, { "job": 117377159365, "time": 67, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12098945971" } ], "_upstream": "https://github.com/cran/iPEB", "_commit": { "id": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "author": "Bitan Sarkar ", "committer": "cran-robot ", "message": "version 0.1.1\n", "time": 1789651208 }, "_maintainer": { "name": "Bitan Sarkar", "email": "bitansarkar010899@gmail.com", "login": "bitansa", "description": "", "uuid": 112052702, "orcid": "0009-0000-5178-5934" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "nlme", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-38", "n": 1 } ], "_tags": [ { "name": "0.1.1", "date": "2026-09-17" } ], "_stars": 0, "_contributors": [ { "user": "bitansa", "count": 1, "uuid": 112052702 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 632, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 479, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/iPEB" }, "_devurl": "https://github.com/bitansa/ipeb", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/iPEB.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/bitansa/ipeb", "_realowner": "bitansa", "_cranurl": false, "_releases": [ { "version": "0.1.1", "date": "2026-09-17" } ], "_exports": [ "evaluate", "ipeb", "ipeb_innovations", "ipeb_run", "run_app" ], "_datasets": [ { "name": "ipeb_example", "title": "Synthetic longitudinal biomarker example", "object": "ipeb_example", "class": [ "data.frame" ], "fields": [ "id", "case", "time", "time_to_dx", "m1", "m2", "m3", "split" ], "rows": 1439, "table": true, "tojson": true } ], "_help": [ { "page": "evaluate", "title": "Evaluate a fitted iPEB model", "topics": [ "evaluate", "evaluate.ipeb" ] }, { "page": "ipeb", "title": "Fit an improved Parametric Empirical Bayes (iPEB) model", "topics": [ "ipeb" ] }, { "page": "ipeb_example", "title": "Synthetic longitudinal biomarker example", "topics": [ "ipeb_example" ] }, { "page": "ipeb_innovations", "title": "Time-gap-aware standardized innovations", "topics": [ "ipeb_innovations" ] }, { "page": "ipeb_run", "title": "Fit and evaluate iPEB in one call", "topics": [ "ipeb_run" ] }, { "page": "plot.ipeb", "title": "Plot the fitted iPEB marker weights", "topics": [ "plot.ipeb" ] }, { "page": "predict.ipeb", "title": "Score new subjects with a fitted iPEB model", "topics": [ "predict.ipeb" ] }, { "page": "run_app", "title": "Launch the iPEB Shiny explorer", "topics": [ "run_app" ] } ], "_readme": "https://github.com/cran/iPEB/raw/HEAD/README.md", "_rundeps": [ "lattice", "nlme" ], "_vignettes": [ { "source": "iPEB.Rmd", "filename": "iPEB.html", "title": "Getting started with iPEB", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Fitting a model", "Scoring and evaluating new subjects", "Changing the objective", "Feature selection", "One-call workflow", "Notes" ], "created": "2026-09-17 13:20:08", "modified": "2026-09-17 13:20:08", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": false, "_nocasepkg": "ipeb", "_universes": [ "cran" ], "_indexurl": "https://bitansa.r-universe.dev/iPEB", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-10-17T10:46:13.000Z", "distro": "resolute", "commit": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "fileid": "https://r2.ropensci.org/c17f7c9254ba67cb1cf88ee4df42a3f04f38a52363a381e427000f1dacfcb97c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39025830214" }, { "r": "4.6.1", "os": "linux", "version": "0.1.1", "date": "2026-10-17T10:46:13.000Z", "distro": "resolute", "commit": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "fileid": "https://r2.ropensci.org/9cb849423461fed2e109b4f16e0181112d937e796fd17eeae8bc270a27d34a44", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39025830214" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-10-17T10:46:22.000Z", "commit": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "fileid": "https://r2.ropensci.org/359b56a4da7f70e62f8c9ce9aab6ca948c8ff5172fb27cbbf13c8c0009a1f3a7", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/39025830214" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-10-17T10:45:46.000Z", "commit": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "fileid": "https://r2.ropensci.org/4b9d80f4879b6c222c1529ebda420d1aa2e1296381104055f3952b23eefd1de2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39025830214" }, { "r": "4.6.1", "os": "win", "version": "0.1.1", "date": "2026-10-17T10:45:28.000Z", "commit": "5ff3505a19373b8778555c4b519b7c0c426b06bd", "fileid": "https://r2.ropensci.org/c1dfd0e75a06e2fc082d639ce00ce3841832e56ff1c138d18bbacd417c19f58f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39025830214" } ] }