{ "_id": "6ac8d0cade46216d5edd7d2c", "Package": "NBvarsel", "Title": "Variable Selection via Cross-Validated Net Benefit", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Lasai\", \"Barreñada\", , \"lasai.barrenadataleb@kuleuven.be\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8020-0210\",\n\"Department of Development and Regeneration ; Leuven Unit for Health Technology Assessment Research (LUHTAR), KU Leuven, Belgium\")),\nperson(\"Laure\", \"Wynants\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3037-122X\",\n\"Department of Development and Regeneration, KU Leuven, Belgium; Leuven Unit for Health Technology Assessment Research (LUHTAR), KU Leuven, Belgium; Department of Epidemiology, CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, Netherlands\")),\nperson(\"Ewout W.\", \"Steyerberg\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-7787-0122\",\n\"Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands\")),\nperson(\"Andrew\", \"Vickers\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1525-6503\",\n\"Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA\")),\nperson(\"Ben\", \"Van Calster\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1613-7450\",\n\"Department of Development and Regeneration, KU Leuven, Belgium; Leuven Unit for Health Technology Assessment Research (LUHTAR), KU Leuven, Belgium; Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands\"))\n)", "Description": "Performs exhaustive or groupwise (backward elimination)\nvariable selection for binary outcome prediction models using\ncross-validated Net Benefit as the optimization criterion. It\nsupports predictor costs, restricted cubic splines, interaction\nterms, permutation importance, and parallel computation. It\nincludes visualizations for model comparison and variable\nimportance. References include Vickers AJ & Elkin EB (2006)\n, Van Calster B et al. (2018)\n, Vickers AJ et al. (2019)\n, and Baker SG et al. (2012)\n.", "License": "GPL (>= 3)", "URL": "https://lasaibarrenada.github.io/NB_varsel/,\nhttps://github.com/LasaiBarrenada/NB_varsel", "BugReports": "https://github.com/LasaiBarrenada/NB_varsel/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "8.0.0", "VignetteBuilder": "quarto", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://lasaibarrenada.r-universe.dev", "Date/Publication": "2026-09-09 12:39:27 UTC", "RemoteUrl": "https://github.com/lasaibarrenada/nb_varsel", "RemoteRef": "HEAD", "RemoteSha": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 11:03:11 UTC", "User": "root" }, "Author": "Lasai Barreñada [aut, cre] (ORCID:\n, Department of Development\nand Regeneration ; Leuven Unit for Health Technology Assessment\nResearch (LUHTAR), KU Leuven, Belgium),\nLaure Wynants [aut] (ORCID: ,\nDepartment of Development and Regeneration, KU Leuven, Belgium;\nLeuven Unit for Health Technology Assessment Research (LUHTAR), KU\nLeuven, Belgium; Department of Epidemiology, CAPHRI Care and Public\nHealth Research Institute, Maastricht University, Maastricht,\nNetherlands),\nEwout W. Steyerberg [aut] (ORCID:\n, Julius Centre for Health\nSciences and Primary Care, University Medical Centre Utrecht,\nUtrecht, Netherlands),\nAndrew Vickers [aut] (ORCID: ,\nDepartment of Epidemiology and Biostatistics, Memorial Sloan\nKettering Cancer Center, New York, NY, USA),\nBen Van Calster [aut] (ORCID: ,\nDepartment of Development and Regeneration, KU Leuven, Belgium;\nLeuven Unit for Health Technology Assessment Research (LUHTAR), KU\nLeuven, Belgium; Julius Centre for Health Sciences and Primary\nCare, University Medical Centre Utrecht, Utrecht, Netherlands)", "Maintainer": "Lasai Barreñada ", "_user": "lasaibarrenada", "_type": "src", "_file": "NBvarsel_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/16766d0c11173b249b2c21ee63c1cfa7c8b37a85e381c48a4c2fcf7f832bd8f0", "_filesize": 3152223, "_sha256": "16766d0c11173b249b2c21ee63c1cfa7c8b37a85e381c48a4c2fcf7f832bd8f0", "_expires": "2027-01-17T11:32:24.000Z", "_created": "2026-10-09T11:03:11.000Z", "_published": "2026-10-09T11:32:26.657Z", "_buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113789923983, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11611973378" }, { "job": 113789924035, "time": 204, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11612197878" }, { "job": 113789924078, "time": 241, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11613180625" }, { "job": 113789924077, "time": 235, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11613401051" }, { "job": 113787882437, "time": 362, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11612556366" }, { "job": 113789923998, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11612630112" }, { "job": 113789924045, "time": 161, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11612421799" }, { "job": 113789924089, "time": 154, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11612396893" }, { "job": 113789924012, "time": 180, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11611703104" } ], "_upstream": "https://github.com/lasaibarrenada/nb_varsel", "_commit": { "id": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "author": "Lasai Barreñada ", "committer": "Lasai Barreñada ", "message": "Add badges\n", "time": 1788957567 }, "_maintainer": { "name": "Lasai Barreñada", "email": "lasai.barrenadataleb@kuleuven.be", "login": "lasaibarrenada", "orcid": "0000-0001-8020-0210", "twitter": "@BarrenadaLasai", "description": "PhD Candidate in Clinical Prediction Models at KU Leuven", "uuid": 67263444 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "caret", "role": "Imports" }, { "package": "DescTools", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggtext", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "rms", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "glmnet", "role": "Suggests" }, { "package": "ggsci", "role": "Suggests" }, { "package": "gt", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "lasaibarrenada", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-13", "n": 8 }, { "week": "2026-14", "n": 5 }, { "week": "2026-20", "n": 1 }, { "week": "2026-21", "n": 2 }, { "week": "2026-23", "n": 1 }, { "week": "2026-24", "n": 2 }, { "week": "2026-34", "n": 1 }, { "week": "2026-37", "n": 1 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-03-30" }, { "name": "v0.1.1", "date": "2026-08-21" } ], "_stars": 2, "_contributors": [ { "user": "lasaibarrenada", "count": 24, "uuid": 67263444 } ], "_userbio": { "uuid": 67263444, "type": "user", "name": "Lasai Barreñada", "followers": 10, "description": "PhD Candidate in Clinical Prediction Models at KU Leuven" }, "_downloads": { "count": 331, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NBvarsel" }, "_devurl": "https://github.com/lasaibarrenada/nb_varsel", "_pkgdown": "https://lasaibarrenada.github.io/NB_varsel/", "_searchresults": 3, "_quarto": true, "_topics": [ "quarto" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NBvarsel.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/lasaibarrenada/nb_varsel", "_realowner": "lasaibarrenada", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2026-09-08" } ], "_exports": [ "all_subset_plot", "nb_varsel", "VIF_plot" ], "_datasets": [ { "name": "adnex_results", "title": "ADNEX Exhaustive Variable Selection Results", "object": "adnex_results", "class": [ "data.frame" ], "fields": [ "Model", "n_Preds", "AUC", "Brier", "Total_Cost", "Avg_Adj_Net_Benefit", "Avg_Net_Benefit", "VIF_age", "VIF_ca125", "VIF_family_history", "VIF_locules_gt_10", "VIF_oncology_center", "VIF_max_diam_lesion", "VIF_papillary_count", "VIF_acoustic_shadows", "VIF_ascites", "VIF_ireg_walls", "VIF_bilateral", "VIF_color_score", "VIF_pain", "VIF_max_diam_solid", "VIF_papillary_presence", "VIF_prop_solid" ], "rows": 293, "table": true, "tojson": true } ], "_help": [ { "page": "adnex_results", "title": "ADNEX Exhaustive Variable Selection Results", "topics": [ "adnex_results" ] }, { "page": "all_subset_plot", "title": "All-Subset Model Comparison Plot", "topics": [ "all_subset_plot" ] }, { "page": "nb_varsel", "title": "Variable Selection via Cross-Validated Net Benefit", "topics": [ "nb_varsel" ] }, { "page": "VIF_plot", "title": "Permutation Importance Bar Plot", "topics": [ "VIF_plot" ] } ], "_readme": "https://github.com/lasaibarrenada/nb_varsel/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "bit", "bit64", "boot", "bslib", "cachem", "caret", "cellranger", "checkmate", "class", "cli", "clipr", "clock", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "crayon", "curl", "data.table", "DescTools", "diagram", "digest", "doParallel", "dplyr", "e1071", "evaluate", "Exact", "expm", "farver", "fastmap", "fontawesome", "forcats", "foreach", "foreign", "Formula", "fs", "future", "future.apply", "generics", "ggplot2", "ggtext", "gld", "globals", "glue", "gower", "gridExtra", "gridtext", "gtable", "hardhat", "haven", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "ipred", "isoband", "iterators", "jpeg", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lattice", "lava", "lifecycle", "listenv", "litedown", "lmom", "lubridate", "magrittr", "markdown", "MASS", "Matrix", "MatrixModels", "memoise", "mime", "ModelMetrics", "multcomp", "mvtnorm", "nlme", "nnet", "numDeriv", "openssl", "parallelly", "patchwork", "pillar", "pkgconfig", "plyr", "png", "polspline", "prettyunits", "pROC", "prodlim", "progress", "progressr", "proxy", "purrr", "quantreg", "R6", "rappdirs", "RColorBrewer", "Rcpp", "readr", "readxl", "recipes", "rematch", "reshape2", "rlang", "rmarkdown", "rms", "rootSolve", "rpart", "rstudioapi", "S7", "sandwich", "sass", "scales", "shape", "SparseM", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "sys", "TH.data", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "xfun", "xml2", "yaml", "zoo" ], "_vignettes": [ { "source": "nb-varsel-tutorial.qmd", "filename": "nb-varsel-tutorial.html", "title": "Variable Selection via Net Benefit with NBvarsel", "engine": "quarto::html", "headings": [ "Introduction", "Simple illustration", "Data generation", "Backward elimination (baseline)", "Exhaustive net benefit variable selection", "Results", "Case study — fabricated clinical data", "Cost structure", "Best model", "All models", "Visualisation", "Groupwise net benefit variable selection", "Comparison with other methods", "Selected variables", "Discrimination", "Decision curve analysis", "Case study — ADNEX ovarian tumour data", "Predictors and cost structure", "Exhaustive search", "Top models", "Summary" ], "created": "2026-03-26 07:07:39", "modified": "2026-05-17 13:04:23", "commits": 5 } ], "_score": 4.903089986991944, "_indexed": true, "_nocasepkg": "nbvarsel", "_universes": [ "lasaibarrenada" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-10-09T11:05:53.000Z", "distro": "resolute", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/052f0f8cdbb2f088f88cb33fd55dc8d85faa6408a8fd990ae487e432609bbfad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.6.1", "os": "linux", "version": "0.1.1", "date": "2026-10-09T11:05:58.000Z", "distro": "resolute", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/29520b535ca1181d2405b1c4ffec0c53a2027c15d9f8c88a358b3887fdf0807f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.5.3", "os": "mac", "version": "0.1.1", "date": "2026-10-09T11:19:23.000Z", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/68f7d4167a196acf3d4953197200665031c8ac1781d4797b274105790bbfbc07", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.6.1", "os": "mac", "version": "0.1.1", "date": "2026-10-09T11:30:37.000Z", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/e6c3acd322725a1488c0dc2a4c876ffabd057bf8438927495bf1f868af3022d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-10-09T11:06:03.000Z", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/529813c0be6ae67f4f884dee4912a812f1d8c9e3e8f08ca8f235bee2d166d926", "status": "success", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-10-09T11:05:03.000Z", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/3b17206c337ecc940839e03accd6ac4fb87472e8acb1a09554820b1044e14dea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.5.3", "os": "win", "version": "0.1.1", "date": "2026-10-09T11:05:04.000Z", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/9ea88ff8c90f01e26b0bcff892705a171e665c01d99bd57fe543ad289eb3346a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" }, { "r": "4.6.1", "os": "win", "version": "0.1.1", "date": "2026-10-09T11:05:48.000Z", "commit": "719fb2195a05988f2c7f80bfafb24d67b1be72ac", "fileid": "https://r2.ropensci.org/8f7766b577e3964149cfc01f009c7a3b62491a89c6c0b64ef4e86d72aa664226", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/lasaibarrenada/actions/runs/37920735701" } ] }