{
  "_id": "6a4fd7e8c30f0868bbf1f07e",
  "Package": "GPTCM",
  "Title": "Generalized Promotion Time Cure Model with Bayesian Shrinkage\nPriors",
  "Version": "2.1.0",
  "Description": "Generalized promotion time cure model (GPTCM) via Bayesian\nhierarchical modeling for multiscale data integration (Zhao et\nal. (2025) <doi:10.48550/arXiv.2509.01001>). The Bayesian\nGPTCMs are applicable for both low- and high-dimensional data.",
  "Authors@R": "c(person(\"Zhi\", \"Zhao\", role=c(\"aut\",\"cre\"), email = \"zhi.zhao@medisin.uio.no\"))",
  "Maintainer": "Zhi Zhao <zhi.zhao@medisin.uio.no>",
  "Copyright": "The code in src/arms.cpp is slightly modified based on the\nresearch paper implementation written by Wally Gilks.",
  "URL": "https://github.com/ocbe-uio/GPTCM",
  "BugReports": "https://github.com/ocbe-uio/GPTCM/issues",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "NeedsCompilation": "yes",
  "SystemRequirements": "C++17",
  "Config/roxygen2/version": "8.0.0",
  "Packaged": {
    "Date": "2026-07-09 17:06:51 UTC",
    "User": "root"
  },
  "Author": "Zhi Zhao [aut, cre]",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://ocbe-uio.r-universe.dev",
  "Date/Publication": "2026-07-09 11:35:52 UTC",
  "RemoteUrl": "https://github.com/ocbe-uio/GPTCM",
  "RemoteRef": "HEAD",
  "RemoteSha": "a9539da35941e3d6d1d942eda2281d2d08db7980",
  "_user": "ocbe-uio",
  "_type": "src",
  "_file": "GPTCM_2.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/dd1ee428e2d00f25215b47ad8a0f2ef0a36cab868fc4ea4b66c1be5f79001e92",
  "_filesize": 863807,
  "_sha256": "dd1ee428e2d00f25215b47ad8a0f2ef0a36cab868fc4ea4b66c1be5f79001e92",
  "_expires": "2026-10-17T17:18:30.000Z",
  "_created": "2026-07-09T17:06:51.000Z",
  "_published": "2026-07-09T17:18:32.831Z",
  "_jobs": [
    {
      "job": 86180732683,
      "time": 317,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8206006251"
    },
    {
      "job": 86180732578,
      "time": 339,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8206013450"
    },
    {
      "job": 86180732669,
      "time": 305,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8206001341"
    },
    {
      "job": 86180732656,
      "time": 345,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8206016222"
    },
    {
      "job": 86180732645,
      "time": 183,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8205949941"
    },
    {
      "job": 86180732611,
      "time": 434,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8206052268"
    },
    {
      "job": 86180732636,
      "time": 202,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8205958757"
    },
    {
      "job": 86180732580,
      "time": 520,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8206086914"
    },
    {
      "job": 86179360115,
      "time": 393,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8205874215"
    },
    {
      "job": 86180732522,
      "time": 207,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8205959679"
    },
    {
      "job": 86180732526,
      "time": 609,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8206125006"
    },
    {
      "job": 86180732588,
      "time": 513,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8206083248"
    },
    {
      "job": 86180732617,
      "time": 515,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8206076695"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915",
  "_status": "success",
  "_upstream": "https://github.com/ocbe-uio/GPTCM",
  "_commit": {
    "id": "a9539da35941e3d6d1d942eda2281d2d08db7980",
    "author": "zhizuio <zhi.zhao@medisin.uio.no>",
    "committer": "zhizuio <zhi.zhao@medisin.uio.no>",
    "message": "add `BVS_Sampler::initializeMrfLookup()`\n",
    "time": 1783596952
  },
  "_maintainer": {
    "name": "Zhi Zhao",
    "email": "zhi.zhao@medisin.uio.no",
    "login": "zhizuio",
    "description": "",
    "uuid": 39630023
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "testthat",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "riskRegression",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggridges",
      "role": "Imports"
    },
    {
      "package": "miCoPTCM",
      "role": "Imports"
    },
    {
      "package": "loo",
      "role": "Imports"
    },
    {
      "package": "mvnfast",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "survminer",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "ocbe-uio",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-35",
      "n": 7
    },
    {
      "week": "2025-36",
      "n": 11
    },
    {
      "week": "2025-37",
      "n": 5
    },
    {
      "week": "2025-38",
      "n": 10
    },
    {
      "week": "2025-39",
      "n": 5
    },
    {
      "week": "2025-40",
      "n": 2
    },
    {
      "week": "2025-42",
      "n": 2
    },
    {
      "week": "2025-43",
      "n": 3
    },
    {
      "week": "2025-44",
      "n": 9
    },
    {
      "week": "2025-47",
      "n": 1
    },
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 3
    },
    {
      "week": "2026-05",
      "n": 11
    },
    {
      "week": "2026-23",
      "n": 10
    },
    {
      "week": "2026-24",
      "n": 7
    },
    {
      "week": "2026-25",
      "n": 16
    },
    {
      "week": "2026-26",
      "n": 9
    },
    {
      "week": "2026-28",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "V1.1.1",
      "date": "2025-09-11"
    },
    {
      "name": "v1.1.2",
      "date": "2025-09-25"
    },
    {
      "name": "v1.2.0",
      "date": "2025-09-29"
    },
    {
      "name": "v1.1.3",
      "date": "2025-10-31"
    },
    {
      "name": "v2.0.0",
      "date": "2026-06-03"
    }
  ],
  "_topics": [
    "bayesian-inference",
    "cell-populations",
    "multiscale-data",
    "omics-data-integration",
    "survival-analysis",
    "tumor-heterogeneity",
    "tumor-microenvironment",
    "variable-selection",
    "openblas",
    "cpp",
    "openmp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zhizuio",
      "count": 118,
      "uuid": 39630023
    }
  ],
  "_userbio": {
    "uuid": 58079878,
    "type": "organization",
    "name": "Oslo Centre for Biostatistics and Epidemiology",
    "followers": 58,
    "description": "This is where we host most of the scientific software we produce at OCBE, a joint center between the University of Oslo and the Oslo University Hospital."
  },
  "_downloads": {
    "count": 467,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GPTCM"
  },
  "_devurl": "https://github.com/ocbe-uio/gptcm",
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GPTCM.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ocbe-uio/gptcm",
  "_realowner": "ocbe-uio",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.1.1",
      "date": "2025-09-16"
    },
    {
      "version": "1.1.2",
      "date": "2025-09-26"
    },
    {
      "version": "1.1.3",
      "date": "2025-11-01"
    },
    {
      "version": "2.0.0",
      "date": "2026-06-03"
    }
  ],
  "_exports": [
    "getEstimator",
    "GPTCM",
    "metropolis_sampler",
    "plotBrier",
    "plotCoeff",
    "plotMCMC",
    "simData",
    "target"
  ],
  "_help": [
    {
      "page": "getEstimator",
      "title": "Extract the posterior estimate of parameters",
      "topics": [
        "getEstimator"
      ]
    },
    {
      "page": "GPTCM",
      "title": "Fit Bayesian GPTCM Models",
      "topics": [
        "GPTCM"
      ]
    },
    {
      "page": "metropolis_sampler",
      "title": "Metropolis sampler for a target density",
      "topics": [
        "metropolis_sampler"
      ]
    },
    {
      "page": "plotBrier",
      "title": "Plot curves of time-dependent Brier score",
      "topics": [
        "plotBrier"
      ]
    },
    {
      "page": "plotCoeff",
      "title": "Plot posterior estimates of regression coefficients",
      "topics": [
        "plotCoeff"
      ]
    },
    {
      "page": "plotMCMC",
      "title": "MCMC trace-plots",
      "topics": [
        "plotMCMC"
      ]
    },
    {
      "page": "predict.GPTCM",
      "title": "Prediction of survival probability",
      "topics": [
        "predict.GPTCM"
      ]
    },
    {
      "page": "run_mcmc",
      "title": "Main function implemented in C++ for the MCMC loop",
      "topics": [
        "run_mcmc"
      ]
    },
    {
      "page": "simData",
      "title": "Simulate data",
      "topics": [
        "simData"
      ]
    },
    {
      "page": "target",
      "title": "Target density",
      "topics": [
        "target"
      ]
    }
  ],
  "_pkglogo": "https://github.com/ocbe-uio/GPTCM/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/ocbe-uio/GPTCM/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "base64enc",
    "BH",
    "brio",
    "bslib",
    "cachem",
    "callr",
    "checkmate",
    "cli",
    "cluster",
    "cmprsk",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "data.table",
    "desc",
    "diagram",
    "diffobj",
    "digest",
    "distr",
    "distributional",
    "doParallel",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "ggridges",
    "glmnet",
    "globals",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "loo",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mets",
    "miCoPTCM",
    "mime",
    "multcomp",
    "mvnfast",
    "mvtnorm",
    "nleqslv",
    "nlme",
    "nnet",
    "numDeriv",
    "otel",
    "parallelly",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "pkgload",
    "plotrix",
    "polspline",
    "posterior",
    "praise",
    "processx",
    "prodlim",
    "progressr",
    "ps",
    "Publish",
    "quantreg",
    "R6",
    "ranger",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "riskRegression",
    "rlang",
    "rmarkdown",
    "rms",
    "rpart",
    "rprojroot",
    "rstudioapi",
    "S7",
    "sandwich",
    "sass",
    "scales",
    "sfsmisc",
    "shape",
    "SparseM",
    "SQUAREM",
    "startupmsg",
    "stringi",
    "stringr",
    "survival",
    "tensorA",
    "testthat",
    "TH.data",
    "tibble",
    "timereg",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "waldo",
    "withr",
    "xfun",
    "yaml",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "GPTCM.Rmd",
      "filename": "GPTCM.html",
      "title": "Introduction",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "A simulation study",
        "References"
      ],
      "created": "2025-09-07 18:11:34",
      "modified": "2026-06-04 22:37:03",
      "commits": 8
    }
  ],
  "_score": 4.954242509439325,
  "_indexed": true,
  "_nocasepkg": "gptcm",
  "_universes": [
    "ocbe-uio",
    "zhizuio"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-07-09T17:11:03.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/a9b459bfdd7353629fa9800fbfbdbed80eab35dc3b468239a9bc43e24ee2b542",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:50.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/4d7bab68a01dcf2cf38c184e6e24811010506adefc55af4d44d8238ed4181b26",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:50.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/4266d1aa2779f88e51a9b27e8aa39faca181dc7cc5ea427d65d790bff229cc67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-07-09T17:11:05.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/c5e704c2749c6f06bafe5c09e6ebddc3e6646140971f9f373b087f2f8c3e4046",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-07-09T17:09:21.000Z",
      "arch": "aarch64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/ff45f901e68551f598c7db3c109f1f56f0e95e4f7c72d8f523199191ffd84120",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:59.000Z",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/2e736c343aa2eb8e882f4b47340db5c09b961fdd8b28ce3c2a482f56181c24b2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-07-09T17:09:30.000Z",
      "arch": "aarch64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/376224a1a947afd29b1338f8f1cb1492bb2f313195eaad9e15bef8f940460680",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-07-09T17:11:54.000Z",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/311d1724e56b8a5843fe0b05d310a428fb5467413606476dbc952b9630eb4ab8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:49.000Z",
      "arch": "emscripten",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/b7a33f7c280bfd4fcf7f2274ea8d566eee1f670e684f3dddfa9efb720b0a50da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:31.000Z",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/a4a328c0d82b21662b04be2e849f870f284f85bd4b8b0b630cb131f0ec95c101",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:22.000Z",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/0be2ca41c170915b366ece3bc2a8ee294712c83461dd560a21b3991e7d772de8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-07-09T17:10:50.000Z",
      "arch": "x86_64",
      "commit": "a9539da35941e3d6d1d942eda2281d2d08db7980",
      "fileid": "https://r2.ropensci.org/27e8eebde8722b12b131866f4a0416514470ee7ddee740039ae6025f42a0c7d1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ocbe-uio/actions/runs/29035524915"
    }
  ]
}