{
  "_id": "6a107d3dacfb0bcc41cae5ef",
  "Package": "seqDesign",
  "Version": "1.3",
  "Date": "2020-08-13",
  "Title": "Simulation and Group-Sequential Monitoring of Randomized\nTreatment Efficacy Trials with Time-to-Event Endpoints",
  "Authors@R": "c(person(\"Michal\", \"Juraska\", email = \"mjuraska@fredhutch.org\", role = c(\"aut\", \"cre\")), person(\"Doug\", \"Grove\", email = \"dgrove@scharp.org\", role = \"aut\"), person(\"Xuesong\", \"Yu\", email = \"xyu@scharp.org\", role = \"ctb\"), person(\"Peter\", \"Gilbert\", email = \"pgilbert@scharp.org\", role = \"ctb\"), person(\"Stephanie\", \"Wu\", email = \"swu18@uw.edu\", role = \"ctb\"))",
  "URL": "https://github.com/mjuraska/seqDesign",
  "Description": "A broad spectrum of both event-driven and fixed follow-up\npreventive vaccine efficacy trial designs, including designs of\nGilbert, Grove et al. (2011, Statistical Communications in\nInfectious Diseases), are implemented, with application\ngenerally to individual-randomized clinical trials with\nmultiple active treatment groups and a shared control group,\nand a study endpoint that is a time-to-event endpoint subject\nto right-censoring. The design accommodates the following\nfeatures: (1) the possibility that the efficacy of the\ntreatment/vaccine groups may take time to accrue while the\nmultiple treatment administrations/vaccinations are given, (2)\nhazard ratio and cumulative incidence-based treatment/vaccine\nefficacy parameters and multiple estimation/hypothesis testing\nprocedures are available, (3) interim/group-sequential\nmonitoring of each treatment group for potential harm,\nnon-efficacy (lack of benefit), efficacy (benefit), and high\nefficacy, (3) arbitrary alpha spending functions for different\nmonitoring outcomes, (4) arbitrary timing of interim looks,\nseparate for each monitoring outcome, in terms of either event\naccrual or calendar time, (5) flexible analysis cohort\ncharacterization (intention-to-treat vs.\nper-protocol/as-treated; counting only events for analysis that\noccur after a specific point in study time), and (6) division\nof the trial into two stages of time periods where each\ntreatment is first evaluated for efficacy in the first stage of\nfollow-up, and, if and only if it shows significant treatment\nefficacy in stage one, it is evaluated for longer-term\ndurability of efficacy in stage two. The package produces plots\nand tables describing operating characteristics of a specified\ndesign including a description of monitoring boundaries on\nmultiple scales for the different outcomes; event accrual since\ntrial initiation; probabilities of stopping early for potential\nharm, non-efficacy, etc.; an unconditional power for\nintention-to-treat and per-protocol analyses; calendar time to\ncrossing a monitoring boundary or reaching the target number of\nendpoints if no boundary is crossed; trial duration;\nunconditional power for comparing treatment efficacies; and the\ndistribution of the number of endpoints within an arbitrary\nstudy time interval (e.g., events occurring after the\ntreatments/vaccinations are given), useful as input parameters\nfor the design of studies of the association of biomarkers with\na clinical outcome (surrogate endpoint problem). The code can\nbe used for a single active treatment versus control design and\nfor a single-stage design.",
  "BugReports": "https://github.com/mjuraska/seqDesign/issues",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyLoad": "yes",
  "VignetteBuilder": "knitr, R.rsp",
  "RoxygenNote": "7.1.1",
  "Repository": "https://mjuraska.r-universe.dev",
  "Date/Publication": "2022-12-08 20:18:27 UTC",
  "RemoteUrl": "https://github.com/mjuraska/seqdesign",
  "RemoteRef": "HEAD",
  "RemoteSha": "23965224e807e5512f3a6c75c008ab02f490e9e5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-06 06:49:10 UTC",
    "User": "root"
  },
  "Author": "Michal Juraska [aut, cre],\nDoug Grove [aut],\nXuesong Yu [ctb],\nPeter Gilbert [ctb],\nStephanie Wu [ctb]",
  "Maintainer": "Michal Juraska <mjuraska@fredhutch.org>",
  "MD5sum": "3515582f70abcca2cbb12fe0db9a7867",
  "_user": "mjuraska",
  "_type": "src",
  "_file": "seqDesign_1.3.tar.gz",
  "_fileid": "29eaff4508b398594e3d61563b938c0130ecea1da74364cfc0d2a78c6a154371",
  "_filesize": 963983,
  "_sha256": "29eaff4508b398594e3d61563b938c0130ecea1da74364cfc0d2a78c6a154371",
  "_created": "2026-05-06T06:49:10.000Z",
  "_published": "2026-05-22T15:58:53.240Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77415977347,
      "time": 125,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "6824302391"
    },
    {
      "job": 77415977489,
      "time": 126,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6824304246"
    },
    {
      "job": 77415977477,
      "time": 80,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "6824291960"
    },
    {
      "job": 77415977549,
      "time": 97,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6824295435"
    },
    {
      "job": 77415977378,
      "time": 164,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6824271425"
    },
    {
      "job": 77415977016,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7164882805"
    },
    {
      "job": 77415977346,
      "time": 96,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "6824295395"
    },
    {
      "job": 77415977508,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "6824293628"
    },
    {
      "job": 77415977927,
      "time": 93,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6824294656"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/mjuraska/seqdesign",
  "_commit": {
    "id": "23965224e807e5512f3a6c75c008ab02f490e9e5",
    "author": "Michal Juraska <mjuraska@fredhutch.org>",
    "committer": "Michal Juraska <mjuraska@fredhutch.org>",
    "message": "Doug's fix for harm monitoring so that it doesn't give an error when turned off\n\n",
    "time": 1670530707
  },
  "_maintainer": {
    "name": "Michal Juraska",
    "email": "mjuraska@fredhutch.org",
    "login": "mjuraska",
    "uuid": 9420213
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.16",
      "role": "Depends"
    },
    {
      "package": "survival",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    }
  ],
  "_owner": "mjuraska",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "mjuraska",
      "count": 49,
      "uuid": 9420213
    },
    {
      "user": "smwu",
      "count": 6,
      "uuid": 33609713
    },
    {
      "user": "briansimpkins",
      "count": 3,
      "uuid": 37308133
    }
  ],
  "_userbio": {
    "uuid": 9420213,
    "type": "user",
    "name": "Michal Juraska",
    "description": "A biostatistician at Fred Hutch"
  },
  "_downloads": {
    "count": 219,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seqDesign"
  },
  "_devurl": "https://github.com/mjuraska/seqdesign",
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/seqDesign.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/mjuraska/seqdesign",
  "_realowner": "mjuraska",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2014-02-25"
    },
    {
      "version": "1.0.1",
      "date": "2014-04-17"
    },
    {
      "version": "1.0.2",
      "date": "2014-10-08"
    },
    {
      "version": "1.1",
      "date": "2015-04-27"
    },
    {
      "version": "1.2",
      "date": "2019-05-23"
    }
  ],
  "_exports": [
    "censTrial",
    "crossBoundCumProb",
    "decisionTimes",
    "estHRbound",
    "getBlockSize",
    "monitorTrial",
    "rankTrial",
    "simTrial",
    "tabEventAccrual",
    "VEpowerPP"
  ],
  "_help": [
    {
      "page": "censTrial",
      "title": "Generation of Pre-Unblinded Follow-Up Data-Sets by Applying the Monitoring Outcomes",
      "topics": [
        "censTrial"
      ]
    },
    {
      "page": "crossBoundCumProb",
      "title": "Estimate cumulative probabilities of crossing an efficacy or non-efficacy boundary in an event-driven 2-arm trial design",
      "topics": [
        "crossBoundCumProb"
      ]
    },
    {
      "page": "decisionTimes",
      "title": "Extract the time since trial start to crossing a stopping boundary or reaching the target number of events if no stopping boundary crossed in an event-driven 2-arm trial design",
      "topics": [
        "decisionTimes"
      ]
    },
    {
      "page": "estHRbound",
      "title": "Estimate hazard ratios at an efficacy or non-efficacy stopping boundary defined using the Wald CI approach in an event-driven 2-arm trial design",
      "topics": [
        "estHRbound"
      ]
    },
    {
      "page": "getBlockSize",
      "title": "Determine block size for use in blocked randomization",
      "topics": [
        "getBlockSize"
      ]
    },
    {
      "page": "monitorTrial",
      "title": "Group Sequential Monitoring of Simulated Efficacy Trials for the Event of Potential Harm, Non-Efficacy, and High Efficacy",
      "topics": [
        "monitorTrial"
      ]
    },
    {
      "page": "rankTrial",
      "title": "Ranking and Selection, and Head-to-Head Comparison of Individual and Pooled Treatment Arms",
      "topics": [
        "rankTrial"
      ]
    },
    {
      "page": "simTrial",
      "title": "Simulation of Multi-Arm Randomized Phase IIb/III Efficacy Trials with Time-to-Event Endpoints",
      "topics": [
        "simTrial"
      ]
    },
    {
      "page": "tabEventAccrual",
      "title": "Tabulate event accrual over time since first enrollment",
      "topics": [
        "tabEventAccrual"
      ]
    },
    {
      "page": "VEpowerPP",
      "title": "Unconditional Power to Detect Positive Treatment Efficacy in a Per-Protocol Cohort",
      "topics": [
        "VEpowerPP"
      ]
    }
  ],
  "_readme": "https://github.com/mjuraska/seqdesign/raw/HEAD/README.md",
  "_rundeps": [
    "lattice",
    "Matrix",
    "survival"
  ],
  "_vignettes": [
    {
      "source": "seqDesignInstructions.Rnw",
      "filename": "seqDesignInstructions.pdf",
      "title": "Instructions for Using seqDesign and Generating the Output PDF Report",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2019-03-20 23:45:54",
      "modified": "2019-05-18 00:30:30",
      "commits": 6
    },
    {
      "source": "seqDesignReportTemplate.pdf.asis",
      "filename": "seqDesignReportTemplate.pdf",
      "title": "seqDesign's Report Template",
      "engine": "R.rsp::asis",
      "headings": [],
      "created": "2019-04-30 19:13:40",
      "modified": "2019-05-17 19:23:31",
      "commits": 4
    }
  ],
  "_score": 4.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "seqdesign",
  "_universes": [
    "mjuraska"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3",
      "date": "2026-05-06T06:51:08.000Z",
      "distro": "noble",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "612382b89f33c80902a38ee58a9d1d29b8fa7d6b244913bca721f734ce8bd4e4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3",
      "date": "2026-05-06T06:51:16.000Z",
      "distro": "noble",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "035fec98e9b9c0a23760232518f0b98a5753dd87b50e1dca87972e3e44821780",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3",
      "date": "2026-05-06T06:50:37.000Z",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "e8ac86efa52ed39bdf893e57d298a03507bf024a43ba0699c6df5b3be23af4fa",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3",
      "date": "2026-05-06T06:50:49.000Z",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "49981f083b69905189247c094737c7569361aba34f2788ef60f018764adc90b7",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3",
      "date": "2026-05-06T06:50:33.000Z",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "bde8959884f9f308347fbdaa8a004836bf0138541430e1d9c0af06ab1bf462e6",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3",
      "date": "2026-05-06T06:50:29.000Z",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "a5f031c51dbff05d19d81061ace74ba21fce647f3d67a9f70515cd89f09af1f6",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3",
      "date": "2026-05-06T06:50:32.000Z",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "0a3435ef08368657e4a7a62f8629789e042db768c3677e099095ede11ed50ba9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3",
      "date": "2026-05-22T15:58:38.000Z",
      "commit": "23965224e807e5512f3a6c75c008ab02f490e9e5",
      "fileid": "3336dd7bac68fdde25896ceb32fdfd4f1bef162b69194373f7079b3500f156ee",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mjuraska/actions/runs/25420642935"
    }
  ]
}