{
  "_id": "6a275c7a24555f66ed531b0a",
  "Package": "bravo",
  "Type": "Package",
  "Title": "Bayesian Screening and Variable Selection",
  "Version": "4.0.0",
  "Author": "Dongjin Li [aut, cre], Debarshi Chakraborty [aut], Somak Dutta\n[aut], Vivekananda Roy [ctb]",
  "Authors@R": "c(person(\"Dongjin\", \"Li\", email = \"liyangxiaobei@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Debarshi\", \"Chakraborty\", role = \"aut\"),\nperson(\"Somak\", \"Dutta\", role = \"aut\"),\nperson(\"Vivekananda\", \"Roy\", role = \"ctb\"))",
  "Maintainer": "Dongjin Li <liyangxiaobei@gmail.com>",
  "Description": "Performs Bayesian variable screening and selection for\nultra-high dimensional linear regression models.Also contains\nan user friendly web application to perform multi trait GWAS.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "NeedsCompilation": "yes",
  "RoxygenNote": "7.3.3",
  "Packaged": {
    "Date": "2026-06-09 00:13:51 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev",
  "Repository": "https://dongjli.r-universe.dev",
  "Date/Publication": "2026-06-08 23:51:14 UTC",
  "RemoteUrl": "https://github.com/dongjli/bravo",
  "RemoteRef": "HEAD",
  "RemoteSha": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
  "MD5sum": "5a0659360b48ae35b1d1f4f3222e04fb",
  "_user": "dongjli",
  "_type": "src",
  "_file": "bravo_4.0.0.tar.gz",
  "_fileid": "99db5d1966f6d41e76d0e3da3087276ea84bf39f54e26c6fbd9b9c1e498858a1",
  "_filesize": 243907,
  "_sha256": "99db5d1966f6d41e76d0e3da3087276ea84bf39f54e26c6fbd9b9c1e498858a1",
  "_created": "2026-06-09T00:13:51.000Z",
  "_published": "2026-06-09T00:21:14.668Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80222923984,
      "time": 173,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7495551906"
    },
    {
      "job": 80222924005,
      "time": 202,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7495557199"
    },
    {
      "job": 80222923974,
      "time": 148,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7495547208"
    },
    {
      "job": 80222923980,
      "time": 207,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7495558235"
    },
    {
      "job": 80222923985,
      "time": 174,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7495546441"
    },
    {
      "job": 80222923986,
      "time": 296,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7495572384"
    },
    {
      "job": 80222924011,
      "time": 154,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7495543055"
    },
    {
      "job": 80222924031,
      "time": 395,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7495587625"
    },
    {
      "job": 80222578073,
      "time": 182,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7495513828"
    },
    {
      "job": 80222924004,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7495539604"
    },
    {
      "job": 80222923990,
      "time": 179,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7495552636"
    },
    {
      "job": 80222924023,
      "time": 111,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": ""
    },
    {
      "job": 80222923993,
      "time": 124,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7495541762"
    }
  ],
  "_buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/dongjli/bravo",
  "_commit": {
    "id": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
    "author": "Somak Dutta <somakd@gmail.com>",
    "committer": "Somak Dutta <somakd@gmail.com>",
    "message": "Rebuild documents and update arguments to dense2sparse\n",
    "time": 1780962674
  },
  "_maintainer": {
    "name": "Dongjin Li",
    "email": "liyangxiaobei@gmail.com",
    "login": "dongjli",
    "description": "",
    "uuid": 26632028
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.2",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.2",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "version": ">= 1.2-17",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "bslib",
      "role": "Imports"
    },
    {
      "package": "memuse",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    }
  ],
  "_owner": "dongjli",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-22",
      "n": 10
    },
    {
      "week": "2026-24",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "dongjli",
      "count": 70,
      "uuid": 26632028
    },
    {
      "user": "somakd",
      "count": 50,
      "uuid": 8738603
    },
    {
      "user": "debarshi-statsforever",
      "count": 8,
      "uuid": 80968315
    },
    {
      "user": "vroys",
      "count": 8,
      "uuid": 5176503
    }
  ],
  "_userbio": {
    "uuid": 26632028,
    "type": "user",
    "name": "dongjli"
  },
  "_downloads": {
    "count": 793,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bravo"
  },
  "_devurl": "https://github.com/dongjli/bravo",
  "_searchresults": 4,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/bravo.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/dongjli/bravo",
  "_realowner": "dongjli",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.3",
      "date": "2020-09-22"
    },
    {
      "version": "1.0.5",
      "date": "2021-06-23"
    },
    {
      "version": "2.0.0",
      "date": "2021-07-20"
    },
    {
      "version": "2.0.1",
      "date": "2021-09-22"
    },
    {
      "version": "2.1.1",
      "date": "2021-10-26"
    },
    {
      "version": "2.1.2",
      "date": "2021-11-12"
    },
    {
      "version": "2.2.1",
      "date": "2023-04-25"
    },
    {
      "version": "2.3.1",
      "date": "2023-08-27"
    },
    {
      "version": "3.2.1",
      "date": "2024-05-13"
    },
    {
      "version": "3.2.2",
      "date": "2024-10-29"
    },
    {
      "version": "4.0.0",
      "date": "2026-05-27"
    }
  ],
  "_exports": [
    "bits",
    "calc.runtime",
    "dense_to_sparse_converter",
    "dense2sparse",
    "mip.sven",
    "parameter_selection",
    "predict.sven",
    "sven",
    "svenetics",
    "svenetics_pipeline"
  ],
  "_help": [
    {
      "page": "basic.sven.model",
      "title": "Run SVEN with Optimal Parameters",
      "topics": [
        "basic.sven.model"
      ]
    },
    {
      "page": "bits",
      "title": "Bayesian Iterated Screening (ultra-high, high or low dimensional).",
      "topics": [
        "bits"
      ]
    },
    {
      "page": "bwas",
      "title": "BWAS: Bayesian GWAS for a Single Trait",
      "topics": [
        "bwas"
      ]
    },
    {
      "page": "calc.runtime",
      "title": "Estimate SVEN Runtime",
      "topics": [
        "calc.runtime"
      ]
    },
    {
      "page": "clean",
      "title": "Clean SNP Matrix",
      "topics": [
        "clean"
      ]
    },
    {
      "page": "create_param_mat",
      "title": "Create Parameter Grid",
      "topics": [
        "create_param_mat"
      ]
    },
    {
      "page": "dense_to_sparse_converter",
      "title": "Launch the Sparse Converter Shiny App",
      "topics": [
        "dense_to_sparse_converter"
      ]
    },
    {
      "page": "dense2sparse",
      "title": "Convert numeric matrix to sparse matrix",
      "topics": [
        "dense2sparse"
      ]
    },
    {
      "page": "FDR_corrected",
      "title": "FDR using correlation threshold",
      "topics": [
        "FDR_corrected"
      ]
    },
    {
      "page": "FDR_WS",
      "title": "FDR using window size",
      "topics": [
        "FDR_WS"
      ]
    },
    {
      "page": "FPR_corrected",
      "title": "FPR using correlation threshold",
      "topics": [
        "FPR_corrected"
      ]
    },
    {
      "page": "FPR_WS",
      "title": "FPR using window size",
      "topics": [
        "FPR_WS"
      ]
    },
    {
      "page": "jcidx",
      "title": "Jaccard Index",
      "topics": [
        "jcidx"
      ]
    },
    {
      "page": "mip.sven",
      "title": "Compute marginal inclusion probabilities from a fitted \"sven\" object.",
      "topics": [
        "mip.sven"
      ]
    },
    {
      "page": "parameter_selection",
      "title": "Select Optimal Tuning Parameters",
      "topics": [
        "parameter_selection"
      ]
    },
    {
      "page": "pipeline_single_trait",
      "title": "Run GWAS for a Single Trait",
      "topics": [
        "pipeline_single_trait"
      ]
    },
    {
      "page": "predict.sven",
      "title": "Make predictions from a fitted \"sven\" object.",
      "topics": [
        "predict.sven"
      ]
    },
    {
      "page": "run_all_params",
      "title": "Run SVEN Across Parameter Grid",
      "topics": [
        "run_all_params"
      ]
    },
    {
      "page": "sven",
      "title": "Selection of variables with embedded screening using Bayesian methods (SVEN) in Gaussian linear models (ultra-high, high or low dimensional).",
      "topics": [
        "sven"
      ]
    },
    {
      "page": "svenetics",
      "title": "Launch the SVENETICS Shiny App",
      "topics": [
        "svenetics"
      ]
    },
    {
      "page": "svenetics_pipeline",
      "title": "Full Multi-Trait GWAS Pipeline",
      "topics": [
        "svenetics_pipeline"
      ]
    },
    {
      "page": "TPR_corrected",
      "title": "TPR using correlation threshold",
      "topics": [
        "TPR_corrected"
      ]
    },
    {
      "page": "TPR_WS",
      "title": "TPR using window size",
      "topics": [
        "TPR_WS"
      ]
    },
    {
      "page": "tune.sven",
      "title": "Tune SVEN Parameters",
      "topics": [
        "tune.sven"
      ]
    },
    {
      "page": "tune.sven.all",
      "title": "Tune SVEN for All Hit Sizes",
      "topics": [
        "tune.sven.all"
      ]
    },
    {
      "page": "unite.sven",
      "title": "UNITE: Post-process SVEN Model",
      "topics": [
        "unite.sven"
      ]
    }
  ],
  "_readme": "https://github.com/dongjli/bravo/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "codetools",
    "commonmark",
    "digest",
    "doParallel",
    "dplyr",
    "fastmap",
    "fontawesome",
    "foreach",
    "fs",
    "generics",
    "glue",
    "htmltools",
    "httpuv",
    "iterators",
    "jquerylib",
    "jsonlite",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "memuse",
    "mime",
    "otel",
    "pillar",
    "pkgconfig",
    "promises",
    "R6",
    "rappdirs",
    "Rcpp",
    "rlang",
    "sass",
    "shiny",
    "shinyjs",
    "sourcetools",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "xtable"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": true,
  "_nocasepkg": "bravo",
  "_universes": [
    "dongjli"
  ],
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "win",
      "version": "4.0.0",
      "date": "2026-05-26T18:03:52.000Z",
      "arch": "x86_64",
      "commit": "30745b0c4ad2278538624d0318ce47e2b1cbaf10",
      "fileid": "03f08b1d77caceb5f8bb33f2146faeb2ba2b9df8aa03d59628c9005b9b4ba622",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/26465826606"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.0.0",
      "date": "2026-06-09T00:16:31.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "9c8947effdcdf38568dd9ffe75d138d36ee50d3bf66ea87c86de46a154ebca63",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.0.0",
      "date": "2026-06-09T00:16:53.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "8d1dd896eec2c9c35d5f84751b13696ac13220a5b3a5b317f953a9a4e5999be4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "4.0.0",
      "date": "2026-06-09T00:16:11.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "44bdef4c84cb1c4b15183babf2fa08416e822ca81c1ff83dc62885d5cfea9d42",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "4.0.0",
      "date": "2026-06-09T00:16:54.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "652ba8c1899477e33402dbef0a9d7dc5b50196a08018188a22824301619a9ba2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.0.0",
      "date": "2026-06-09T00:16:09.000Z",
      "arch": "aarch64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "5f0de73c9d769d028ef0bb6e69683e461fcf65c6b4ed0b06c8b118ecd8901ecf",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.0.0",
      "date": "2026-06-09T00:17:34.000Z",
      "arch": "x86_64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "9edbee3de7685065bc4aeae83f7e267082a7b5e8fb91d9f5997a4fd368165c7d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "4.0.0",
      "date": "2026-06-09T00:15:54.000Z",
      "arch": "aarch64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "e93348e83448e6c4bed75a0ec1be76590a3d9ba1840afc0dde6a8b35548acfe0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "4.0.0",
      "date": "2026-06-09T00:18:46.000Z",
      "arch": "x86_64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "947f78844110d10e05a05ef09f5972247df9eebbe0b711ec41d0367d4a095e0a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "4.0.0",
      "date": "2026-06-09T00:16:06.000Z",
      "arch": "emscripten",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "fd87ae45774829304b2ea929c9314b4c7b95c248f52d883fd17e0d6b70e92fe7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "4.0.0",
      "date": "2026-06-09T00:15:40.000Z",
      "arch": "x86_64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "ff6f815fdf72e852bbe4e76e634e13fdd3401b21807f70a3331ba6f617c06229",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "4.0.0",
      "date": "2026-06-09T00:15:13.000Z",
      "arch": "x86_64",
      "commit": "a3e57ff7a2c83a77d262af18795fbccdf03580b0",
      "fileid": "54da22f93567ad05943a90a99c87edc6d4da7009f9588068f67b51c4c206ca2f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/dongjli/actions/runs/27175210742"
    }
  ]
}