{
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  "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) <doi:10.1137/16M1115733>) and LMBM ('Limited Memory\nBundle Method for large-scale nonsmooth optimization' as in\nHaarala et al. (2004) <doi:10.1080/10556780410001689225>). The\nOSCAR models are comprehensively exemplified in Halkola et al.\n(2023) <doi:10.1371/journal.pcbi.1010333>). 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",
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  "Author": "Teemu Daniel Laajala [aut, cre]\n(<https://orcid.org/0000-0002-7016-7354>), Kaisa Joki [aut],\nAnni Halkola [aut]",
  "Maintainer": "Teemu Daniel Laajala <teelaa@utu.fi>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2023-10-02 15:31:15 UTC",
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  "_published": "2026-10-07T13:10:23.436Z",
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    "description": "Finn with a knack for bioinformatics (mostly cancer), artificial intelligence, machine learning, game jams, and all that jazz.",
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    "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"
  ],
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    {
      "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"
      ]
    }
  ],
  "_rundeps": [
    "hamlet",
    "lattice",
    "Matrix",
    "pROC",
    "Rcpp",
    "survival"
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      "package": "libgfortran5",
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      "homepage": "http://gcc.gnu.org/",
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      "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": "2022-05-20 17:20:01",
      "modified": "2023-08-29 02:57:29",
      "commits": 4
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