{ "_id": "6a1864f9acfb0bcc41dbfcc3", "Package": "oscar", "Type": "Package", "Title": "Optimal Subset Cardinality Regression (OSCAR) Models Using the\nL0-Pseudonorm", "Version": "1.2.1", "Date": "2023-10-02", "Authors@R": "c(\nperson(given=c(\"Teemu\", \"Daniel\"), family=\"Laajala\", role=c(\"aut\", \"cre\"), email=\"teelaa@utu.fi\", comment = c(ORCID = \"0000-0002-7016-7354\")),\nperson(given=\"Kaisa\", family=\"Joki\", role=c(\"aut\"), email=\"kjjoki@utu.fi\"),\nperson(given=\"Anni\", family=\"Halkola\", role=c(\"aut\"), email=\"ansuha@utu.fi\"))", "Description": "Optimal Subset Cardinality Regression (OSCAR) models offer\nregularized linear regression using the L0-pseudonorm,\nconventionally known as the number of non-zero coefficients.\nThe package estimates an optimal subset of features using the\nL0-penalization via cross-validation, bootstrapping and visual\ndiagnostics. Effective Fortran implementations are offered\nalong the package for finding optima for the DC-decomposition,\nwhich is used for transforming the discrete L0-regularized\noptimization problem into a continuous non-convex optimization\ntask. These optimization modules include DBDC ('Double Bundle\nmethod for nonsmooth DC optimization' as described in Joki et\nal. (2018) ) and LMBM ('Limited Memory\nBundle Method for large-scale nonsmooth optimization' as in\nHaarala et al. (2004) ). The\nOSCAR models are comprehensively exemplified in Halkola et al.\n(2023) ). Multiple regression\nmodel families are supported: Cox, logistic, and Gaussian.", "License": "GPL-3", "LazyData": "true", "URL": "https://github.com/Syksy/oscar", "BugReports": "https://github.com/Syksy/oscar/issues", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "Repository": "https://syksy.r-universe.dev", "Date/Publication": "2023-10-02 11:18:32 UTC", "RemoteUrl": "https://github.com/syksy/oscar", "RemoteRef": "HEAD", "RemoteSha": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "Packaged": { "Date": "2026-05-28 15:00:51 UTC", "User": "root" }, "Author": "Teemu Daniel Laajala [aut, cre] (ORCID:\n),\nKaisa Joki [aut],\nAnni Halkola [aut]", "Maintainer": "Teemu Daniel Laajala ", "MD5sum": "07411ba56393ff46b73dc1bb87ab0f1c", "_user": "syksy", "_type": "src", "_file": "oscar_1.2.1.tar.gz", "_fileid": "390b6afef49d301646cb046d3c5d93978a19772dd7af64a1661bc528c5756b72", "_filesize": 659364, "_sha256": "390b6afef49d301646cb046d3c5d93978a19772dd7af64a1661bc528c5756b72", "_created": "2026-05-28T15:00:51.000Z", "_published": "2026-05-28T15:53:29.077Z", "_distro": "noble", "_jobs": [ { "job": 78320767371, "time": 160, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7269450732" }, { "job": 78320767413, "time": 245, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7269545756" }, { "job": 78320767363, "time": 154, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7269448107" }, { "job": 78320767496, "time": 279, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7269561474" }, { "job": 78320767383, "time": 178, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7270586139" }, { "job": 78320767401, "time": 363, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7270651344" }, { "job": 78320767943, "time": 172, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7270645977" }, { "job": 78320767670, "time": 337, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7270645535" }, { "job": 78319545987, "time": 253, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7269377973" }, { "job": 78320767600, "time": 213, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7269547240" }, { "job": 78320767451, "time": 216, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7269521625" }, { "job": 78320767483, "time": 242, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7269556585" }, { "job": 78320767426, "time": 164, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7269510687" } ], "_buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/syksy/oscar", "_commit": { "id": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "author": "Syksy ", "committer": "Syksy ", "message": "Fix to _R_CHECK_FORTRAN_KIND_DETAILS_ warning\n", "time": 1696245512 }, "_maintainer": { "name": "Teemu Daniel Laajala", "email": "teelaa@utu.fi", "login": "syksy", "orcid": "0000-0002-7016-7354", "description": "Finn with a knack for bioinformatics (mostly cancer), artificial intelligence, machine learning, game jams, and all that jazz.", "uuid": 36551395 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "hamlet", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "ePCR", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "syksy", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "fortran", "penalized-regression", "regression" ], "_stars": 2, "_contributors": [ { "user": "syksy", "count": 234, "uuid": 36551395 }, { "user": "nabuliini", "count": 129, "uuid": 58519381 }, { "user": "kjjoki", "count": 15, "uuid": 58545394 } ], "_userbio": { "uuid": 36551395, "type": "user", "name": "T. D. Laajala", "description": "Finn with a knack for bioinformatics (mostly cancer), artificial intelligence, machine learning, game jams, and all that jazz." }, "_downloads": { "count": 140, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/oscar" }, "_devurl": "https://github.com/syksy/oscar", "_searchresults": 11, "_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/oscar.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/syksy/oscar", "_realowner": "syksy", "_cranurl": true, "_releases": [ { "version": "1.0.3", "date": "2022-05-20" }, { "version": "1.0.4", "date": "2022-05-24" }, { "version": "1.1.2-2", "date": "2023-03-13" }, { "version": "1.1.4", "date": "2023-03-28" }, { "version": "1.1.7", "date": "2023-08-08" }, { "version": "1.2.0", "date": "2023-08-29" }, { "version": "1.2.1", "date": "2023-10-02" } ], "_exports": [ "coef", "cost", "feat", "kits", "oscar", "oscar.binarize", "oscar.binplot", "oscar.bs", "oscar.bs.boxplot", "oscar.bs.k", "oscar.bs.plot", "oscar.bs.visu", "oscar.control", "oscar.cost.after", "oscar.cv", "oscar.cv.visu", "oscar.pareto", "oscar.pareto.visu", "oscar.sparsify", "oscar.visu", "plot", "predict", "show" ], "_datasets": [ { "name": "ex_c", "title": "Example data from TYKS / HUSLAB", "object": "ex", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "ex_K", "title": "Example data from TYKS / HUSLAB", "object": "ex", "class": [ "matrix", "array" ], "fields": [ "BMI", "HEIGHTBL", "WEIGHTBL", "SYSTOLICBP", "DIASTOLICBP", "PULSE", "HB", "HEMAT", "RBC", "WBC", "PLT", "LYMperLEU", "MONOperLEU", "NEU", "POT", "MONO", "BASOperLEU", "EOSperLEU", "NEUperLEU", "NA.", "CCRC", "LDH", "AST", "ALB", "ALP", "PSA", "CREAT", "CREACL", "LYM", "PHOS", "CA", "ALT", "TPRO", "EOS", "TESTO", "GLU", "MG", "TBILI" ], "rows": 22, "table": true, "tojson": true }, { "name": "ex_X", "title": "Example data from TYKS / HUSLAB", "object": "ex", "class": [ "matrix", "array" ], "fields": [ "BMI", "HEIGHTBL", "WEIGHTBL", "SYSTOLICBP", "DIASTOLICBP", "PULSE", "HB", "HEMAT", "RBC", "WBC", "PLT", "LYMperLEU", "MONOperLEU", "NEU", "POT", "MONO", "BASOperLEU", "EOSperLEU", "NEUperLEU", "NA.", "CCRC", "LDH", "AST", "ALB", "ALP", "PSA", "CREAT", "CREACL", "LYM", "PHOS", "CA", "ALT", "TPRO", "EOS", "TESTO", "GLU", "MG", "TBILI" ], "rows": 650, "table": true, "tojson": true }, { "name": "ex_Y", "title": "Example data from TYKS / HUSLAB", "object": "ex", "class": [ "matrix", "array" ], "fields": [ "Time", "Event" ], "rows": 650, "table": true, "tojson": true } ], "_help": [ { "page": "oscar-package", "title": "oscar: Optimal Subset Cardinality Regression", "topics": [ "oscar-package" ] }, { "page": "oscar-methods", "title": "Extract coefficients of oscar-objects", "topics": [ "coef,oscar-method", "plot,oscar-method", "predict,oscar-method" ] }, { "page": "cost", "title": "Return total cost of model fit based on provided kit/variable costs vector", "topics": [ "cost", "cost,oscar-method", "cost,oscar-methods" ] }, { "page": "ex", "title": "Example data from TYKS / HUSLAB", "topics": [ "ex_c", "ex_K", "ex_X", "ex_Y" ] }, { "page": "feat", "title": "Return named vector of feature indices with a given k that are non-zero", "topics": [ "feat", "feat,oscar-method", "feat,oscar-methods" ] }, { "page": "kits", "title": "Return named vector of indices for kits with a given k that are non-zero", "topics": [ "kits", "kits,oscar-method", "kits,oscar-methods" ] }, { "page": "oscar", "title": "Main OSCAR fitting function", "topics": [ "oscar" ] }, { "page": "oscar-class", "title": "S4-class for oscar", "topics": [ "oscar-class" ] }, { "page": "oscar.binarize", "title": "Binary logical indicator matrix representation of an oscar object's coefficients (zero vs. non-zero, i.e. feature inclusion)", "topics": [ "oscar.binarize" ] }, { "page": "oscar.binplot", "title": "Visualize binary indicator matrix optionally coupled with cross-validation performance for oscar models", "topics": [ "oscar.binplot" ] }, { "page": "oscar.bs", "title": "Bootstrapping for oscar-fitted model objects", "topics": [ "oscar.bs" ] }, { "page": "oscar.bs.boxplot", "title": "Bootstrap visualization with boxplot, percentage of new additions", "topics": [ "oscar.bs.boxplot" ] }, { "page": "oscar.bs.k", "title": "Reformatting bootstrap output for cardinality k rows", "topics": [ "oscar.bs.k" ] }, { "page": "oscar.bs.plot", "title": "Bootstrap heatmap plot for oscar models", "topics": [ "oscar.bs.plot" ] }, { "page": "oscar.bs.visu", "title": "Visualize bootstrapping of a fit oscar object", "topics": [ "oscar.bs.visu" ] }, { "page": "oscar.control", "title": "Control OSCAR optimizer parameters", "topics": [ "oscar.control" ] }, { "page": "oscar.cost.after", "title": "Return total cost of model fits if the cost is not included in the oscar object", "topics": [ "oscar.cost.after" ] }, { "page": "oscar.cv", "title": "Cross-validation for oscar-fitted model objects over k-range", "topics": [ "oscar.cv" ] }, { "page": "oscar.cv.visu", "title": "Visualize cross-validation as a function of k", "topics": [ "oscar.cv.visu" ] }, { "page": "oscar.pareto", "title": "Retrieve a set of pareto-optimal points for an oscar-model based on model goodness-of-fit or cross-validation", "topics": [ "oscar.pareto" ] }, { "page": "oscar.pareto.visu", "title": "Visualize oscar model pareto front", "topics": [ "oscar.pareto.visu" ] }, { "page": "oscar.sparsify", "title": "Create a sparse matrix representation of betas as a function of k", "topics": [ "oscar.sparsify" ] }, { "page": "oscar.visu", "title": "Target function value and total kit cost as a function of number of kits included", "topics": [ "oscar.visu" ] }, { "page": "generics", "title": "Showing oscar-objects", "topics": [ "show,oscar-method" ] } ], "_readme": "https://github.com/syksy/oscar/raw/HEAD/README.md", "_rundeps": [ "hamlet", "lattice", "Matrix", "pROC", "Rcpp", "survival" ], "_sysdeps": [ { "shlib": "libgfortran", "package": "libgfortran5", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "fortran", "homepage": "http://gcc.gnu.org/", "description": "Runtime library for GNU Fortran applications" } ], "_vignettes": [ { "source": "example.Rmd", "filename": "example.html", "title": "Example use of the OSCAR package", "author": "Teemu Daniel Laajala", "engine": "knitr::rmarkdown", "headings": [ "OSCAR modelling", "Cox regression (simulated TYKS real-world PCa data)", "Goodness of fit vs. model coefficient cost", "Cross-validation and bootstrapping", "Further useful commands", "Other model families", "Gaussian regression (swiss-data)", "References", "Session info" ], "created": "2020-11-04 20:29:29", "modified": "2023-08-28 21:09:04", "commits": 10 } ], "_score": 4.342422680822207, "_indexed": true, "_nocasepkg": "oscar", "_universes": [ "syksy" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.1", "date": "2026-05-28T15:03:29.000Z", "distro": "noble", "arch": "aarch64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "8581f8adb64dbb3198e2017b4c8cd6c42df41d692e3a90b855cdd9bedbc9e0cd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.7.0", "os": "linux", "version": "1.2.1", "date": "2026-05-28T15:06:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "9964062ac8d7d9320eefffed0d3992e08d7d2bb8a5abd2749c3a6c07d04c6fd1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.6.0", "os": "linux", "version": "1.2.1", "date": "2026-05-28T15:03:24.000Z", "distro": "noble", "arch": "aarch64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "2bd62933e8786c87a267109b3371c24388c1738a8ddfe10667316ec3cd2426b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.6.0", "os": "linux", "version": "1.2.1", "date": "2026-05-28T15:07:33.000Z", "distro": "noble", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "f183f19bc1db0886a0bf5d072bccfe7ba32f2f8d7ddd15883840fce70d436f38", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.5.3", "os": "mac", "version": "1.2.1", "date": "2026-05-28T15:49:09.000Z", "arch": "aarch64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "5307b15b31f7fd8ef687b3cd938c957a558d3ae47f6865feb6a99dc7e608ce75", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.5.3", "os": "mac", "version": "1.2.1", "date": "2026-05-28T15:51:07.000Z", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "54d381fb73506f61777eb6759f6fcfa79d5d9b274475fc49914460cf53827a77", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.6.0", "os": "mac", "version": "1.2.1", "date": "2026-05-28T15:51:30.000Z", "arch": "aarch64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "4cef6d92b5688567bb9a14598761632b47bcd757bcaf6a30e1a0cc98cc998528", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.6.0", "os": "mac", "version": "1.2.1", "date": "2026-05-28T15:50:49.000Z", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "60d691ddf741a1d62e42a3203976235df601a26ca76aeb7c1668f142855d487e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.1", "date": "2026-05-28T15:07:35.000Z", "arch": "emscripten", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "d1ab0c3ac08030c67904adf4f532be9c56e3ef8a506ada2750dbf172f9c1406b", "status": "success", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.7.0", "os": "win", "version": "1.2.1", "date": "2026-05-28T15:05:01.000Z", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "ecdf541c575f059a46fcc412dd349e3759444588fc338cdbd1046d3172099fad", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.5.3", "os": "win", "version": "1.2.1", "date": "2026-05-28T15:05:40.000Z", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "58e0e8183e494fd0e7c46783717b9dfdae0542444a3cb48fc6fd053663f6d987", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" }, { "r": "4.6.0", "os": "win", "version": "1.2.1", "date": "2026-05-28T15:04:48.000Z", "arch": "x86_64", "commit": "7b4f61bcc8c52c74f3332735f0a0850e52400cf8", "fileid": "7ec8c63ab3de1cd7ad61aa59ad7b6c13b201c8ddb871c62916a3dbbbda85ab30", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/syksy/actions/runs/26582412310" } ] }