{
  "_id": "6aaa6c78ea78b3e62eacc594",
  "Package": "gateR",
  "Type": "Package",
  "Title": "Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation",
  "Version": "0.1.16",
  "Date": "2025-08-29",
  "Authors@R": "c(person(given = \"Ian D.\",\nfamily = \"Buller\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"ian.buller@alumni.emory.edu\",\ncomment = c(ORCID = \"0000-0001-9477-8582\")),\nperson(given = \"Elena\",\nfamily = \"Hsieh\",\nrole = \"ctb\",\nemail = \"elena.hsieh@cuanschutz.edu\",\ncomment = c(ORCID = \"0000-0003-3969-6597\")),\nperson(given = \"Debashis\",\nfamily = \"Ghosh\",\nrole = \"ctb\",\nemail = \"debashis.ghosh@cuanschutz.edu\",\ncomment = c(ORCID = \"0000-0001-6618-1316\")),\nperson(given = \"Lance A.\",\nfamily = \"Waller\",\nrole = \"ctb\",\nemail = \"lwaller@emory.edu\",\ncomment = c(ORCID = \"0000-0001-5002-8886\")),\nperson(given = \"NCI\",\nrole = \"cph\"))",
  "Maintainer": "Ian D. Buller <ian.buller@alumni.emory.edu>",
  "Description": "Estimates statistically significant marker combination\nvalues within which one immunologically distinctive group\n(i.e., disease case) is more associated than another group\n(i.e., healthy control), successively, using various\ncombinations (i.e., \"gates\") of markers to examine features of\ncells that may be different between groups. For a two-group\ncomparison, the 'gateR' package uses the spatial relative risk\nfunction estimated using the 'sparr' package. Details about the\n'sparr' package methods can be found in the tutorial: Davies et\nal. (2018) <doi:10.1002/sim.7577>. Details about kernel density\nestimation can be found in J. F. Bithell (1990)\n<doi:10.1002/sim.4780090616>. More information about relative\nrisk functions using kernel density estimation can be found in\nJ. F. Bithell (1991) <doi:10.1002/sim.4780101112>.",
  "License": "Apache License (>= 2.0)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "R.rsp",
  "Language": "en-US",
  "URL": "https://github.com/lance-waller-lab/gateR",
  "BugReports": "https://github.com/lance-waller-lab/gateR/issues",
  "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libproj-dev\nlibsqlite3-dev",
  "Repository": "https://lance-waller-lab.r-universe.dev",
  "Date/Publication": "2025-08-29 04:33:01 UTC",
  "RemoteUrl": "https://github.com/lance-waller-lab/gater",
  "RemoteRef": "HEAD",
  "RemoteSha": "35c062788f917cfadf6e9c1de434d52223376651",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-16 10:05:20 UTC",
    "User": "root"
  },
  "Author": "Ian D. Buller [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-9477-8582>),\nElena Hsieh [ctb] (ORCID: <https://orcid.org/0000-0003-3969-6597>),\nDebashis Ghosh [ctb] (ORCID: <https://orcid.org/0000-0001-6618-1316>),\nLance A. Waller [ctb] (ORCID: <https://orcid.org/0000-0001-5002-8886>),\nNCI [cph]",
  "_user": "lance-waller-lab",
  "_type": "src",
  "_file": "gateR_0.1.16.tar.gz",
  "_fileid": "https://r2.ropensci.org/9e137615a1e998ee992794f3881b30207f04ba32df7aa3aaafe7fd06cfe1792c",
  "_filesize": 1068530,
  "_sha256": "9e137615a1e998ee992794f3881b30207f04ba32df7aa3aaafe7fd06cfe1792c",
  "_expires": "2026-12-25T10:16:22.000Z",
  "_created": "2026-09-16T10:05:20.000Z",
  "_published": "2026-09-16T10:16:24.332Z",
  "_jobs": [
    {
      "job": 104751641187,
      "time": 389,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10441361572"
    },
    {
      "job": 104751641388,
      "time": 413,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10441337735"
    },
    {
      "job": 104751641406,
      "time": 212,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10441571777"
    },
    {
      "job": 104751641282,
      "time": 438,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10441019403"
    },
    {
      "job": 104750166444,
      "time": 284,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10441590284"
    },
    {
      "job": 104751641257,
      "time": 168,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10440883524"
    },
    {
      "job": 104751641303,
      "time": 234,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10440824187"
    },
    {
      "job": 104751641313,
      "time": 208,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10441521298"
    },
    {
      "job": 104751641274,
      "time": 231,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10440814141"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716",
  "_status": "success",
  "_upstream": "https://github.com/lance-waller-lab/gater",
  "_commit": {
    "id": "35c062788f917cfadf6e9c1de434d52223376651",
    "author": "Ian D Buller <ian.d.buller@gmail.com>",
    "committer": "Ian D Buller <ian.d.buller@gmail.com>",
    "message": "Additional preparation for CRAN v0.1.16 release\n\n* Updated vignette with updated package version and dependencies\n* 📝 In 'cran-comments.md': added valid URLs, updated test environments, and OK'd author formatting\n* 📄 Updated LICENSE & CITATION\n* 📛 Updated DOI badge\n* ✅ Added Rhub v2 checks\n",
    "time": 1756441981
  },
  "_maintainer": {
    "name": "Ian D. Buller",
    "email": "ian.buller@alumni.emory.edu",
    "orcid": "0000-0001-9477-8582"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "fields",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "sparr",
      "role": "Imports"
    },
    {
      "package": "SpatialPack",
      "role": "Imports"
    },
    {
      "package": "spatstat.geom",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "terra",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    },
    {
      "package": "utils",
      "role": "Suggests"
    }
  ],
  "_owner": "lance-waller-lab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "cytometry",
    "flow-cytometry",
    "gating",
    "kernel-density-estimation",
    "mass-cytometry",
    "non-euclidean-spaces",
    "spatial-analysis"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "idblr",
      "count": 9,
      "uuid": 10702814
    },
    {
      "user": "rubak",
      "count": 1,
      "uuid": 6704085
    }
  ],
  "_userbio": {
    "uuid": 63425815,
    "type": "organization",
    "name": "lance-waller-lab",
    "followers": 4,
    "description": "Lance Waller's Lab GitHub"
  },
  "_downloads": {
    "count": 361,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gateR"
  },
  "_devurl": "https://github.com/lance-waller-lab/gater",
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gateR.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/lance-waller-lab/gater",
  "_realowner": "lance-waller-lab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.2",
      "date": "2020-11-10"
    },
    {
      "version": "0.1.3",
      "date": "2020-11-17"
    },
    {
      "version": "0.1.4",
      "date": "2020-11-30"
    },
    {
      "version": "0.1.6",
      "date": "2021-01-07"
    },
    {
      "version": "0.1.7",
      "date": "2021-02-04"
    },
    {
      "version": "0.1.8",
      "date": "2021-03-15"
    },
    {
      "version": "0.1.9",
      "date": "2021-06-26"
    },
    {
      "version": "0.1.10",
      "date": "2022-02-05"
    },
    {
      "version": "0.1.11",
      "date": "2022-08-26"
    },
    {
      "version": "0.1.12",
      "date": "2022-12-01"
    },
    {
      "version": "0.1.13",
      "date": "2023-02-02"
    },
    {
      "version": "0.1.15",
      "date": "2024-01-23"
    },
    {
      "version": "0.1.16",
      "date": "2025-08-29"
    }
  ],
  "_exports": [
    "gating",
    "lotrrs",
    "lrr_plot",
    "pval_correct",
    "pval_plot",
    "rrs"
  ],
  "_datasets": [
    {
      "name": "randCyto",
      "title": "Subset of the 'extdata' data in the 'flowWorkspaceData' package",
      "object": "randCyto",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "g1",
        "g2",
        "arcsinh_CD4",
        "arcsinh_CD38",
        "arcsinh_CD8",
        "arcsinh_CD3"
      ],
      "rows": 23526,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "gateR-package",
      "title": "The gateR Package: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation",
      "topics": [
        "gateR-package",
        "gateR"
      ]
    },
    {
      "page": "gating",
      "title": "Gating strategy for mass cytometry data using spatial relative risk functions",
      "topics": [
        "gating"
      ]
    },
    {
      "page": "lotrrs",
      "title": "A single gate for two conditions",
      "topics": [
        "lotrrs"
      ]
    },
    {
      "page": "randCyto",
      "title": "Subset of the 'extdata' data in the 'flowWorkspaceData' package",
      "topics": [
        "randCyto"
      ]
    },
    {
      "page": "rrs",
      "title": "A single gate for a single condition",
      "topics": [
        "rrs"
      ]
    }
  ],
  "_readme": "https://github.com/lance-waller-lab/gater/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "cli",
    "codetools",
    "deldir",
    "doParallel",
    "dotCall64",
    "fastmatrix",
    "fields",
    "foreach",
    "glue",
    "goftest",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "Matrix",
    "mgcv",
    "misc3d",
    "nlme",
    "pillar",
    "pkgconfig",
    "polyclip",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rpart",
    "spam",
    "sparr",
    "SpatialPack",
    "spatstat",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.linnet",
    "spatstat.model",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "tensor",
    "terra",
    "tibble",
    "utf8",
    "vctrs",
    "viridisLite"
  ],
  "_vignettes": [
    {
      "source": "vignette.html.asis",
      "filename": "vignette.html",
      "title": "gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation",
      "engine": "R.rsp::asis",
      "headings": [
        "gateR: Flow/Mass Cytometry Gating via\nSpatial Kernel Density Estimation"
      ],
      "created": "2020-10-27 16:26:25",
      "modified": "2020-11-05 14:27:08",
      "commits": 3
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "gater",
  "_universes": [
    "lance-waller-lab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.16",
      "date": "2026-09-16T10:08:31.000Z",
      "distro": "resolute",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/d4dde4d8f5c2ec20d95247b940ffd3d189bc3010757f89ff6e483a8dc7b9d2d1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.16",
      "date": "2026-09-16T10:08:36.000Z",
      "distro": "resolute",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/d9bcb4029c4c08863092b74d0657af8d32acb2f9af52df8908054c65cbb83724",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.16",
      "date": "2026-09-16T10:11:07.000Z",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/10df7b1255184449fafe7cbd6351bed9a80fe460032b8cfa49d9c0fb642e859e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.16",
      "date": "2026-09-16T10:13:21.000Z",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/e0f6740861e9ea1bb96c573e78c6413c876c2375e185b20aada86b53eb767aa4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.16",
      "date": "2026-09-16T10:08:49.000Z",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/707905fca52263fe8442aa7cfe094552eaa3930f80e3bc2ce5a03c5dab7fa0c6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.16",
      "date": "2026-09-16T10:07:19.000Z",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/cc9ea12eb77161d5ff0704ae2fd45aeca88f3d6adf3b8ca43dd7c5c4e9e5a70d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.16",
      "date": "2026-09-16T10:07:08.000Z",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/bb4b7ac6bbc3ba93802cd43ac57ccbec16a97dfacfda9917221bc903c7f95be2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.16",
      "date": "2026-09-16T10:07:17.000Z",
      "commit": "35c062788f917cfadf6e9c1de434d52223376651",
      "fileid": "https://r2.ropensci.org/94150100069e69e0a7aa280413cfef592b969d1b215171842968c54855bb2ca1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lance-waller-lab/actions/runs/35082659716"
    }
  ]
}