{
  "_id": "6a1ed462b401979e7340e192",
  "Package": "SurrogateRank",
  "Type": "Package",
  "Title": "Rank-Based Test to Evaluate a Surrogate Marker",
  "Version": "3.0",
  "Authors@R": "c(person(\"Layla\", \"Parast\", role = c(\"aut\", \"cre\"), email = \"parast@austin.utexas.edu\"), person(\"Arthur\", \"Hughes\", role = c(\"aut\"), email = \"arthur.hughes@u-bordeaux.fr\"))",
  "Description": "Uses a novel rank-based nonparametric approach to evaluate\na surrogate marker in a small sample size setting. Details are\ndescribed in Parast et al (2024) <doi:10.1093/biomtc/ujad035>,\nin Hughes A et al (2025) <doi:10.1002/sim.70241>, and in Hughes\nA et al (2026) <doi:10.48550/arXiv.2605.03819>. A tutorial for\nthis package can be found at\n<https://www.laylaparast.com/surrogaterank> and a Shiny App\nimplementing the package can be found at\n<https://parastlab.shinyapps.io/SurrogateRankApp/>.",
  "License": "GPL",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://laylaparast.r-universe.dev",
  "Date/Publication": "2026-05-20 17:41:39 UTC",
  "RemoteUrl": "https://github.com/laylaparast/surrogaterank",
  "RemoteRef": "HEAD",
  "RemoteSha": "69bb42c326831322fd1a9348308d75bc6092057b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-20 19:36:52 UTC",
    "User": "root"
  },
  "Author": "Layla Parast [aut, cre],\nArthur Hughes [aut]",
  "Maintainer": "Layla Parast <parast@austin.utexas.edu>",
  "MD5sum": "19a47895d8e8f40fba0829bbf60d2587",
  "_user": "laylaparast",
  "_type": "src",
  "_file": "SurrogateRank_3.0.tar.gz",
  "_fileid": "ba1e5c40099afcb89ee8697b8c8f3eb113cc1160c0602425f1caead3ece678a0",
  "_filesize": 3206445,
  "_sha256": "ba1e5c40099afcb89ee8697b8c8f3eb113cc1160c0602425f1caead3ece678a0",
  "_created": "2026-05-20T19:36:52.000Z",
  "_published": "2026-06-02T13:02:26.339Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79076277922,
      "time": 155,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7119718024"
    },
    {
      "job": 79076278212,
      "time": 153,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7119717362"
    },
    {
      "job": 79076277963,
      "time": 148,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7119716987"
    },
    {
      "job": 79076278058,
      "time": 107,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7119707473"
    },
    {
      "job": 79076276511,
      "time": 164,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7119663891"
    },
    {
      "job": 79076276996,
      "time": 117,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7358360839"
    },
    {
      "job": 79076277675,
      "time": 166,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7119721298"
    },
    {
      "job": 79076278561,
      "time": 101,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7119700086"
    },
    {
      "job": 79076277598,
      "time": 103,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7119700760"
    }
  ],
  "_buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/laylaparast/surrogaterank",
  "_commit": {
    "id": "69bb42c326831322fd1a9348308d75bc6092057b",
    "author": "laylaparast <parast@austin.utexas.edu>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Add files via upload\n\nReplacing with commented out plots so users can run .Rmd while we troubleshoot.",
    "time": 1779298899
  },
  "_maintainer": {
    "name": "Layla Parast",
    "email": "parast@austin.utexas.edu",
    "login": "laylaparast",
    "description": "",
    "uuid": 17624391
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "pbmcapply",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "ComplexUpset",
      "role": "Imports"
    },
    {
      "package": "ggVennDiagram",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    }
  ],
  "_owner": "laylaparast",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-21",
      "n": 10
    },
    {
      "week": "2025-25",
      "n": 3
    },
    {
      "week": "2025-37",
      "n": 5
    },
    {
      "week": "2026-02",
      "n": 5
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-19",
      "n": 1
    },
    {
      "week": "2026-21",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "arthurhughes27",
      "count": 83,
      "uuid": 113607952
    },
    {
      "user": "laylaparast",
      "count": 28,
      "uuid": 17624391
    }
  ],
  "_userbio": {
    "uuid": 17624391,
    "type": "user",
    "name": "laylaparast"
  },
  "_downloads": {
    "count": 246,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SurrogateRank"
  },
  "_devurl": "https://github.com/laylaparast/surrogaterank",
  "_searchresults": 1,
  "_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/SurrogateRank.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/laylaparast/surrogaterank",
  "_realowner": "laylaparast",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2024-04-09"
    },
    {
      "version": "2.0",
      "date": "2025-05-20"
    },
    {
      "version": "2.1",
      "date": "2025-09-11"
    },
    {
      "version": "2.2",
      "date": "2026-01-08"
    }
  ],
  "_exports": [
    "delta.calculate",
    "delta.calculate.extension",
    "delta.reml.meta",
    "est.power",
    "generate.example.data.highdim",
    "generate.example.data.highdim.multistudy",
    "generate.example.data.highdim.multistudy.ipd",
    "rise.evaluate",
    "rise.evaluate.meta",
    "rise.screen",
    "rise.screen.meta",
    "test.surrogate",
    "test.surrogate.extension",
    "test.surrogate.rise"
  ],
  "_datasets": [
    {
      "name": "example.data",
      "title": "Example data",
      "object": "example.data",
      "file": "example.data.highdim.multistudy.ipd.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "example.data.highdim",
      "title": "High‑dimensional surrogate candidate example dataset",
      "object": "example.data.highdim",
      "file": "example.data.highdim.multistudy.ipd.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example.data.highdim.multistudy",
      "title": "High-dimensional, multi-study surrogate candidate example dataset",
      "object": "example.data.highdim.multistudy",
      "file": "example.data.highdim.multistudy.ipd.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example.data.highdim.multistudy.ipd",
      "title": "High‑dimensional multi-study individual participant surrogate candidate example dataset",
      "object": "example.data.highdim.multistudy.ipd",
      "file": "example.data.highdim.multistudy.ipd.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "delta.calculate",
      "title": "Calculates the rank-based test statistic for Y and S and the difference, delta",
      "topics": [
        "delta.calculate"
      ]
    },
    {
      "page": "delta.calculate.extension",
      "title": "Calculate Delta: Difference in Rank-based Statistics for Two Outcomes",
      "topics": [
        "delta.calculate.extension"
      ]
    },
    {
      "page": "delta.reml.meta",
      "title": "Function to perform meta-analysis of summary statistics and hypothesis testing for a single marker",
      "topics": [
        "delta.reml.meta"
      ]
    },
    {
      "page": "est.power",
      "title": "Estimated power to detect a valid surrogate",
      "topics": [
        "est.power"
      ]
    },
    {
      "page": "example.data",
      "title": "Example data",
      "topics": [
        "example.data"
      ]
    },
    {
      "page": "example.data.highdim",
      "title": "High‑dimensional surrogate candidate example dataset",
      "topics": [
        "example.data.highdim"
      ]
    },
    {
      "page": "example.data.highdim.multistudy",
      "title": "High-dimensional, multi-study surrogate candidate example dataset",
      "topics": [
        "example.data.highdim.multistudy"
      ]
    },
    {
      "page": "example.data.highdim.multistudy.ipd",
      "title": "High‑dimensional multi-study individual participant surrogate candidate example dataset",
      "topics": [
        "example.data.highdim.multistudy.ipd"
      ]
    },
    {
      "page": "generate.example.data.highdim",
      "title": "Generate individual participant data for high-dimensional surrogate candidates and response",
      "topics": [
        "generate.example.data.highdim"
      ]
    },
    {
      "page": "generate.example.data.highdim.multistudy",
      "title": "Generate high-dimensional multi-study surrogate marker trial-level effects",
      "topics": [
        "generate.example.data.highdim.multistudy"
      ]
    },
    {
      "page": "generate.example.data.highdim.multistudy.ipd",
      "title": "Generate multi-study individual participant data for high-dimensional surrogate candidates and response",
      "topics": [
        "generate.example.data.highdim.multistudy.ipd"
      ]
    },
    {
      "page": "rise.evaluate",
      "title": "Function to perform the evaluation stage of RISE : Two-Stage Rank-Based Identification of High-Dimensional Surrogate Markers",
      "topics": [
        "rise.evaluate"
      ]
    },
    {
      "page": "rise.evaluate.meta",
      "title": "Function to perform the evaluation stage of RISE-meta : Meta-Analysis of High-Dimensional Surrogate Markers",
      "topics": [
        "rise.evaluate.meta"
      ]
    },
    {
      "page": "rise.screen",
      "title": "Function to perform the screening stage of RISE : Two-Stage Rank-Based Identification of High-Dimensional Surrogate Markers",
      "topics": [
        "rise.screen"
      ]
    },
    {
      "page": "rise.screen.meta",
      "title": "Function to perform the screening stage of RISE-meta : Meta-Analysis of High-Dimensional Surrogate Markers",
      "topics": [
        "rise.screen.meta"
      ]
    },
    {
      "page": "test.surrogate",
      "title": "Tests whether the surrogate is valid",
      "topics": [
        "test.surrogate"
      ]
    },
    {
      "page": "test.surrogate.extension",
      "title": "Function to test for trial-level surrogacy of a single marker extended to the paired, two sided test setting",
      "topics": [
        "test.surrogate.extension"
      ]
    },
    {
      "page": "test.surrogate.rise",
      "title": "Function to perform RISE : Two-Stage Rank-Based Identification of High-Dimensional Surrogate Markers",
      "topics": [
        "test.surrogate.rise"
      ]
    }
  ],
  "_readme": "https://github.com/laylaparast/surrogaterank/raw/HEAD/README.md",
  "_rundeps": [
    "admisc",
    "aplot",
    "cli",
    "colorspace",
    "ComplexUpset",
    "cowplot",
    "cpp11",
    "digest",
    "dplyr",
    "farver",
    "forcats",
    "fs",
    "generics",
    "ggfun",
    "ggplot2",
    "ggplotify",
    "ggVennDiagram",
    "glue",
    "gridGraphics",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "MASS",
    "patchwork",
    "pbmcapply",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "venn",
    "viridisLite",
    "withr",
    "yulab.utils"
  ],
  "_score": 4.431363764158988,
  "_indexed": true,
  "_nocasepkg": "surrogaterank",
  "_universes": [
    "laylaparast"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.0",
      "date": "2026-05-20T19:39:06.000Z",
      "distro": "noble",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "727b8aab8923e551e1bae57b57ae30a681857b168486bf4a1d75765d09a6af8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.0",
      "date": "2026-05-20T19:39:06.000Z",
      "distro": "noble",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "ece765ac52f285912cc00211d9199e0f301523995b47ac2cfcfe7929dfc168e9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.0",
      "date": "2026-05-20T19:39:08.000Z",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "24398535d5c58b3813485429c5debe3c2b81cf383aa3a763b807b9c814f87ee2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.0",
      "date": "2026-05-20T19:38:45.000Z",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "9d9eb5c4d9bca1cb01fd8aa9c74a4a6cf0360bf529e5e8c8e471bab5046cc5b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.0",
      "date": "2026-05-20T19:38:59.000Z",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "db2f71b919f622f169eb9fbeed14a87598ecd4cbd318bafd8d7a654c8c9bd214",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.0",
      "date": "2026-05-20T19:38:08.000Z",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "247436d63fc346124d4e2ee2cc9e61c74044e27bd0efdfbdd15bf1e98fb95857",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "3.0",
      "date": "2026-05-20T19:38:12.000Z",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "90ad771b4d5dd934f2a7343f9794282afc18312cb44998e32e5fef3f11ca8c05",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.0",
      "date": "2026-06-02T13:00:43.000Z",
      "commit": "69bb42c326831322fd1a9348308d75bc6092057b",
      "fileid": "dc2dc1e39fb411453077953f85ddae7637c3142f088b63645e69b043246ca63b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/laylaparast/actions/runs/26185329295"
    }
  ]
}