{
  "_id": "6ac95b8ede46216d5edda866",
  "Package": "fdb",
  "Type": "Package",
  "Title": "Frequentist Dynamic Borrowing for Hybrid-Control Survival Trials",
  "Version": "0.2.2",
  "Authors@R": "person(given = \"Yusuke\",\nfamily = \"Yamaguchi\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yamagubed@gmail.com\")",
  "Description": "Implements a class of likelihood-informed frequentist\ndynamic borrowing methods for hybrid-control survival trials\nbased on penalized Cox partial likelihood estimation.\nImplements four likelihood-informed penalty structures\n(precision-weighted L1, smoothed integrated-gate,\ninformation-adaptive minimax concave penalty (MCP), and\nlikelihood-ratio-weighted L1), together with the adaptive lasso\nborrowing approach of Li et al. (2023,\n<doi:10.1002/bimj.202100406>). Provides conditional model-based\nstandard errors and local plug-in sandwich variance\napproximations, with smoothed penalties. Tools for design-stage\nlambda calibration via simulation, including a two-stage\ncoarse-fine grid search, drift-level early stopping, and\nper-method tuning under both inference types, are also\nprovided. A simulation harness for evaluating type I error and\nstatistical power across population drift scenarios is\nincluded.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/yamagubed/fdb",
  "BugReports": "https://github.com/yamagubed/fdb/issues",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.1.0",
  "RoxygenNote": "7.3.3",
  "Repository": "https://yamagubed.r-universe.dev",
  "Date/Publication": "2026-10-09 16:53:10 UTC",
  "RemoteUrl": "https://github.com/yamagubed/fdb",
  "RemoteRef": "HEAD",
  "RemoteSha": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 21:19:36 UTC",
    "User": "root"
  },
  "Author": "Yusuke Yamaguchi [aut, cre]",
  "Maintainer": "Yusuke Yamaguchi <yamagubed@gmail.com>",
  "_user": "yamagubed",
  "_type": "src",
  "_file": "fdb_0.2.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/aae4c19b5d78722ae7457517de35ce7932f8d51c02b247fd303f2a0df5f810f5",
  "_filesize": 311176,
  "_sha256": "aae4c19b5d78722ae7457517de35ce7932f8d51c02b247fd303f2a0df5f810f5",
  "_expires": "2027-01-17T21:24:26.000Z",
  "_created": "2026-10-09T21:19:36.000Z",
  "_published": "2026-10-09T21:24:30.406Z",
  "_buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114031026804,
      "time": 213,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11645289489"
    },
    {
      "job": 114031026791,
      "time": 150,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11645911847"
    },
    {
      "job": 114031026858,
      "time": 125,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11646235765"
    },
    {
      "job": 114031026795,
      "time": 93,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11646270536"
    },
    {
      "job": 114030050099,
      "time": 160,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11645289019"
    },
    {
      "job": 114031026841,
      "time": 96,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11646550025"
    },
    {
      "job": 114031026879,
      "time": 91,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11645294320"
    },
    {
      "job": 114031026903,
      "time": 102,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11645628541"
    },
    {
      "job": 114031026848,
      "time": 71,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11645184886"
    }
  ],
  "_upstream": "https://github.com/yamagubed/fdb",
  "_commit": {
    "id": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
    "author": "yamagubed <113729010+yamagubed@users.noreply.github.com>",
    "committer": "yamagubed <113729010+yamagubed@users.noreply.github.com>",
    "message": "updates\n",
    "time": 1791564790
  },
  "_maintainer": {
    "name": "Yusuke Yamaguchi",
    "email": "yamagubed@gmail.com"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "yamagubed",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-20",
      "n": 1
    },
    {
      "week": "2026-21",
      "n": 1
    },
    {
      "week": "2026-31",
      "n": 1
    },
    {
      "week": "2026-39",
      "n": 7
    },
    {
      "week": "2026-40",
      "n": 2
    },
    {
      "week": "2026-41",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "yamagubed",
      "count": 13,
      "uuid": 113729010
    }
  ],
  "_userbio": {
    "uuid": 113729010,
    "type": "user",
    "name": "yamagubed",
    "followers": 0
  },
  "_downloads": {
    "count": 120,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fdb"
  },
  "_devurl": "https://github.com/yamagubed/fdb",
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fdb.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/yamagubed/fdb",
  "_realowner": "yamagubed",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.0",
      "date": "2026-10-04"
    }
  ],
  "_exports": [
    "add_ess_to_simulation_result",
    "calibrate_all_lambdas",
    "calibrate_censor_rate",
    "calibrate_lambda_grid",
    "calibrate_lambda_grid_two_stage",
    "compute_ess_from_raw",
    "compute_sandwich_se",
    "fit_all_methods",
    "fit_internal_only",
    "fit_li_adaptive_lasso",
    "fit_naive_pooled",
    "fit_one_penalized_method",
    "fit_P1_precision_L1",
    "fit_P2_gated_L1",
    "fit_P3_info_MCP",
    "fit_P4_LRweighted_L1",
    "lambdas_default",
    "make_drift_set",
    "make_drift_set_from_values",
    "method_labels",
    "run_drift_curve",
    "run_fdb_study",
    "run_simulation",
    "scenario_S1",
    "simulate_hybrid_cox"
  ],
  "_help": [
    {
      "page": "fdb-package",
      "title": "fdb: Frequentist Dynamic Borrowing for Hybrid-Control Survival Trials",
      "topics": [
        "fdb-package",
        "fdb"
      ]
    },
    {
      "page": "add_ess_to_simulation_result",
      "title": "Append ESS to a simulation summary",
      "topics": [
        "add_ess_to_simulation_result"
      ]
    },
    {
      "page": "calibrate_all_lambdas",
      "title": "Calibrate lambda for all borrowing methods",
      "topics": [
        "calibrate_all_lambdas"
      ]
    },
    {
      "page": "calibrate_censor_rate",
      "title": "Calculate a fixed exponential censoring rate",
      "topics": [
        "calibrate_censor_rate"
      ]
    },
    {
      "page": "calibrate_lambda_grid",
      "title": "Single-stage lambda calibration for one borrowing method",
      "topics": [
        "calibrate_lambda_grid"
      ]
    },
    {
      "page": "calibrate_lambda_grid_two_stage",
      "title": "Two-stage lambda calibration for one borrowing method",
      "topics": [
        "calibrate_lambda_grid_two_stage"
      ]
    },
    {
      "page": "compute_ess_from_raw",
      "title": "Compute effective sample size from raw simulation output",
      "topics": [
        "compute_ess_from_raw"
      ]
    },
    {
      "page": "compute_sandwich_se",
      "title": "Sandwich standard error for a penalized Cox borrowing estimator",
      "topics": [
        "compute_sandwich_se"
      ]
    },
    {
      "page": "drift_set",
      "title": "Drift set utilities",
      "topics": [
        "drift_set",
        "make_drift_set",
        "make_drift_set_from_values"
      ]
    },
    {
      "page": "fit_all_methods",
      "title": "Fit all borrowing methods on a single dataset",
      "topics": [
        "fit_all_methods"
      ]
    },
    {
      "page": "fit_internal_only",
      "title": "Internal-control-only Cox analysis",
      "topics": [
        "fit_internal_only"
      ]
    },
    {
      "page": "fit_li_adaptive_lasso",
      "title": "Adaptive lasso borrowing of Li et al. (2023)",
      "topics": [
        "fit_li_adaptive_lasso"
      ]
    },
    {
      "page": "fit_naive_pooled",
      "title": "Naive pooled Cox analysis",
      "topics": [
        "fit_naive_pooled"
      ]
    },
    {
      "page": "fit_one_penalized_method",
      "title": "Fit a single penalized borrowing method",
      "topics": [
        "fit_one_penalized_method"
      ]
    },
    {
      "page": "fit_P1_precision_L1",
      "title": "Precision-weighted L1 penalty (P1)",
      "topics": [
        "fit_P1_precision_L1"
      ]
    },
    {
      "page": "fit_P2_gated_L1",
      "title": "Smoothed integrated-gate penalty (P2)",
      "topics": [
        "fit_P2_gated_L1"
      ]
    },
    {
      "page": "fit_P3_info_MCP",
      "title": "Information-adaptive minimax concave penalty (P3)",
      "topics": [
        "fit_P3_info_MCP"
      ]
    },
    {
      "page": "fit_P4_LRweighted_L1",
      "title": "Likelihood-ratio-weighted L1 penalty (P4)",
      "topics": [
        "fit_P4_LRweighted_L1"
      ]
    },
    {
      "page": "lambdas_default",
      "title": "Default tuning parameters",
      "topics": [
        "lambdas_default"
      ]
    },
    {
      "page": "method_labels",
      "title": "Manuscript method labels",
      "topics": [
        "method_labels"
      ]
    },
    {
      "page": "run_drift_curve",
      "title": "Evaluate operating characteristics across a set of drift values",
      "topics": [
        "run_drift_curve"
      ]
    },
    {
      "page": "run_fdb_study",
      "title": "One-stop wrapper: calibrate lambda, then evaluate type I and power",
      "topics": [
        "run_fdb_study"
      ]
    },
    {
      "page": "run_simulation",
      "title": "Run a Monte Carlo simulation under a fixed scenario",
      "topics": [
        "run_simulation"
      ]
    },
    {
      "page": "scenario_S1",
      "title": "Example simulation scenario",
      "topics": [
        "scenario_S1"
      ]
    },
    {
      "page": "simulate_hybrid_cox",
      "title": "Simulate a hybrid-control Cox proportional hazards dataset",
      "topics": [
        "simulate_hybrid_cox"
      ]
    }
  ],
  "_readme": "https://github.com/yamagubed/fdb/raw/HEAD/README.md",
  "_rundeps": [
    "lattice",
    "Matrix",
    "survival"
  ],
  "_vignettes": [
    {
      "source": "fdb-intro.Rmd",
      "filename": "fdb-intro.html",
      "title": "Getting started with fdb",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Fit a hybrid-control trial",
        "Interpret uncertainty",
        "Calibrate a design",
        "Retain replicate estimates",
        "Parallel execution"
      ],
      "created": "2026-05-12 14:52:28",
      "modified": "2026-09-28 20:22:02",
      "commits": 3
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "fdb",
  "_universes": [
    "yamagubed"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.2",
      "date": "2026-10-09T21:22:45.000Z",
      "distro": "resolute",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/f493b89072a1f9f9b8fb7743fba94b95f5e33b2a09044d535a1c4bffa9da15ed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.2.2",
      "date": "2026-10-09T21:21:43.000Z",
      "distro": "resolute",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/b25e5ec2c961db5348d9db57ca0afacd0ab607963d7ae9cf06d987d6afec0538",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.2",
      "date": "2026-10-09T21:23:30.000Z",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/06b7d48849fe86d9ea52a3875fc6b24c5e8e48e468d1ddac16d1c6f69e5a993f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.2.2",
      "date": "2026-10-09T21:22:36.000Z",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/73fa5a5bbc9d158e55d6980a53185d046e0b3034a8b8bdd23e4899ff39e2c290",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.2",
      "date": "2026-10-09T21:21:31.000Z",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/709e9855dc2173d62614d209b976db29ced05b8945b98de755f4a2960f16b24d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.2",
      "date": "2026-10-09T21:20:42.000Z",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/917ca0ce09e07e57e9d8ecc22c8b9b6880d340f931a886afdc16e51fae4ea31c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.2",
      "date": "2026-10-09T21:20:46.000Z",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/a4b48bda055fe4b18d06a0fd61e5475db63992f8e9e08ee5362d74eee2ca20fb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.2.2",
      "date": "2026-10-09T21:20:33.000Z",
      "commit": "dbbb2acd9744b01192beaede971dc8c81dc8d916",
      "fileid": "https://r2.ropensci.org/922d592ce682b7ccf104bb5da078dac653863c277eafcbd0f49b4010cf193c55",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yamagubed/actions/runs/37992482497"
    }
  ]
}