{
  "_id": "6ac10938552a13804ac7eb75",
  "Package": "PhysioML",
  "Title": "Leakage-Aware Machine Learning for Physiological Time Series",
  "Version": "0.4.2",
  "Authors@R": "person(given = \"Yusuke\",\nfamily = \"Matsui\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mail.to.matsui@gmail.com\")",
  "Description": "Provides leakage-aware, reproducible feature transforms\nand reference deep-learning workflows for physiological time\nseries stored in PhysioExperiment objects. Canonical catch22\ncharacteristics are computed through the official R backend,\nwhile ROCKET and MiniRocket transforms use guarded optional\nPython backends. Guarded optional torch and luz backends\nprovide case-aware datasets, compact neural architectures,\ntraining, and prediction. Explicit contracts preserve case,\nchannel, feature, normalization, backend, and model provenance\nwithout claiming clinical validation. Named transfer-learning\npolicies, leakage-safe CORAL alignment, and immutable\nhash-verified foundation-model caches provide bounded reuse\nacross domains.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Collate": "'PhysioML-package.R' 'feature-input.R' 'features-catch22.R'\n'features-rocket.R' 'reduced-features.R' 'torch-input.R'\n'torch-dataset.R' 'torch-models.R' 'torch-train.R'\n'torch-predict.R' 'onnx-contract.R' 'onnx-export.R'\n'onnx-import.R' 'onnx-predict.R' 'transfer.R' 'domain-adapt.R'\n'foundation-cache.R' 'foundation.R' 'zzz.R'",
  "URL": "https://github.com/x-biosignal/PhysioML,\nhttps://x-biosignal.r-universe.dev/PhysioML,\nhttps://x-biosignal.github.io/PhysioML/",
  "BugReports": "https://github.com/x-biosignal/PhysioML/issues",
  "Config/roxygen2/version": "8.0.0",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://x-biosignal.r-universe.dev",
  "Date/Publication": "2026-10-03 13:11:43 UTC",
  "RemoteUrl": "https://github.com/x-biosignal/PhysioML",
  "RemoteRef": "HEAD",
  "RemoteSha": "9d10f45581685a9592b0846fe7d16ff93741ad30",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-03 13:41:58 UTC",
    "User": "root"
  },
  "Author": "Yusuke Matsui [aut, cre]",
  "Maintainer": "Yusuke Matsui <mail.to.matsui@gmail.com>",
  "_user": "x-biosignal",
  "_type": "src",
  "_file": "PhysioML_0.4.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/aac69bc05cc3b46bc3e83980ea6df44b75a0b90935650f7afb278e97333fb08a",
  "_filesize": 402118,
  "_sha256": "aac69bc05cc3b46bc3e83980ea6df44b75a0b90935650f7afb278e97333fb08a",
  "_expires": "2027-01-11T13:55:02.000Z",
  "_created": "2026-10-03T13:41:58.000Z",
  "_published": "2026-10-03T13:55:04.408Z",
  "_jobs": [
    {
      "job": 111214493692,
      "time": 245,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11275342475"
    },
    {
      "job": 111214493678,
      "time": 236,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11275713153"
    },
    {
      "job": 111214493683,
      "time": 189,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11275144685"
    },
    {
      "job": 111214493638,
      "time": 210,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11274703591"
    },
    {
      "job": 111213893347,
      "time": 207,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11274932623"
    },
    {
      "job": 111214493617,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11275388599"
    },
    {
      "job": 111214493640,
      "time": 278,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11275673383"
    },
    {
      "job": 111214493628,
      "time": 172,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11275124049"
    },
    {
      "job": 111214493642,
      "time": 262,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11275293872"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887",
  "_status": "success",
  "_upstream": "https://github.com/x-biosignal/PhysioML",
  "_commit": {
    "id": "9d10f45581685a9592b0846fe7d16ff93741ad30",
    "author": "Yusuke Matsui <mail.to.matsui@gmail.com>",
    "committer": "Yusuke Matsui <mail.to.matsui@gmail.com>",
    "message": "Release snapshot\n",
    "time": 1791033103
  },
  "_maintainer": {
    "name": "Yusuke Matsui",
    "email": "mail.to.matsui@gmail.com",
    "login": "ymatts",
    "description": "Data scientist",
    "uuid": 5744286
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2",
      "role": "Depends"
    },
    {
      "package": "PhysioExperiment",
      "version": ">= 2.0.0",
      "role": "Depends"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "PhysioCore",
      "role": "Suggests"
    },
    {
      "package": "Rcatch22",
      "role": "Suggests"
    },
    {
      "package": "reticulate",
      "role": "Suggests"
    },
    {
      "package": "torch",
      "role": "Suggests"
    },
    {
      "package": "luz",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.2.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "x-biosignal",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-40",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ymatts",
      "count": 1,
      "uuid": 5744286
    }
  ],
  "_userbio": {
    "uuid": 268545536,
    "type": "organization",
    "name": "x-biosignal",
    "followers": 1,
    "description": "Open-source R packages for biosignal analysis, biomechanics, clinical research, and rehabilitation."
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PhysioML"
  },
  "_devurl": "https://github.com/x-biosignal/physioml",
  "_pkgdown": "https://x-biosignal.github.io/PhysioML/",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PhysioML.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "cacheFoundationModel",
    "catch22",
    "domainAdapt",
    "exportONNX",
    "fineTune",
    "foundationCacheInfo",
    "foundationEmbed",
    "freezeLayers",
    "importONNX",
    "minirocket",
    "onnxPredict",
    "peDataset",
    "peModel",
    "peReducedFeatures",
    "predictModel",
    "rocket",
    "trainModel",
    "validateSubjectSplit",
    "withCaseData"
  ],
  "_help": [
    {
      "page": "cacheFoundationModel",
      "title": "Cache an immutable physiological foundation model",
      "topics": [
        "cacheFoundationModel"
      ]
    },
    {
      "page": "catch22",
      "title": "Calculate canonical catch22 features",
      "topics": [
        "catch22"
      ]
    },
    {
      "page": "domainAdapt",
      "title": "Align source embeddings to an unlabeled target domain with CORAL",
      "topics": [
        "domainAdapt"
      ]
    },
    {
      "page": "exportONNX",
      "title": "Export a fitted PhysioML torch model to ONNX",
      "topics": [
        "exportONNX"
      ]
    },
    {
      "page": "fineTune",
      "title": "Fine-tune a fitted torch model",
      "topics": [
        "fineTune"
      ]
    },
    {
      "page": "foundationCacheInfo",
      "title": "Inspect immutable foundation-model cache entries",
      "topics": [
        "foundationCacheInfo"
      ]
    },
    {
      "page": "foundationEmbed",
      "title": "Obtain governed foundation-model embeddings",
      "topics": [
        "foundationEmbed"
      ]
    },
    {
      "page": "freezeLayers",
      "title": "Freeze named parts of a fitted torch model",
      "topics": [
        "freezeLayers"
      ]
    },
    {
      "page": "importONNX",
      "title": "Import a governed PhysioML ONNX graph",
      "topics": [
        "importONNX"
      ]
    },
    {
      "page": "minirocket",
      "title": "Fit or apply the MiniRocket transform",
      "topics": [
        "minirocket"
      ]
    },
    {
      "page": "onnxPredict",
      "title": "Predict through ONNX Runtime on CPU",
      "topics": [
        "onnxPredict"
      ]
    },
    {
      "page": "peDataset",
      "title": "Create a case-aware torch Dataset",
      "topics": [
        "peDataset"
      ]
    },
    {
      "page": "peModel",
      "title": "Construct a reference torch model",
      "topics": [
        "peModel"
      ]
    },
    {
      "page": "peReducedFeatures",
      "title": "Create a case-by-feature design matrix",
      "topics": [
        "peReducedFeatures"
      ]
    },
    {
      "page": "predictModel",
      "title": "Predict with a trained deep-learning model",
      "topics": [
        "predictModel"
      ]
    },
    {
      "page": "rocket",
      "title": "Fit or apply the ROCKET transform",
      "topics": [
        "rocket"
      ]
    },
    {
      "page": "trainModel",
      "title": "Train a reference torch model through luz",
      "topics": [
        "trainModel"
      ]
    },
    {
      "page": "validateSubjectSplit",
      "title": "Validate a split intended to generalize to unseen subjects",
      "topics": [
        "validateSubjectSplit"
      ]
    },
    {
      "page": "withCaseData",
      "title": "Attach explicit subject identity to signal cases or feature rows",
      "topics": [
        "withCaseData"
      ]
    }
  ],
  "_readme": "https://github.com/x-biosignal/PhysioML/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "DelayedArray",
    "digest",
    "generics",
    "GenomicRanges",
    "IRanges",
    "jsonlite",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "PhysioExperiment",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "leakage-aware-ml.Rmd",
      "filename": "leakage-aware-ml.html",
      "title": "Leakage-aware features and subject-safe splits",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A small experiment",
        "Attach subject identity, then split on subjects",
        "Feature extraction",
        "Aligning two domains with CORAL",
        "Backend-gated workflows"
      ],
      "created": "2026-10-03 13:11:43",
      "modified": "2026-10-03 13:11:43",
      "commits": 1
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "physioml",
  "_universes": [
    "x-biosignal",
    "ymatts"
  ],
  "_previous": "0.4.1",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.4.2",
      "date": "2026-10-03T13:44:22.000Z",
      "distro": "resolute",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/ec72c6d923cf3cbe64062c388087b88205f0a00bf82065fb2716db13780455e2",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.4.2",
      "date": "2026-10-03T13:44:18.000Z",
      "distro": "resolute",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/8a6874987018a16bf2d433692c4847e30e176fe124088a930c14dd2b23fa97e3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.4.2",
      "date": "2026-10-03T13:52:54.000Z",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/1bb611db4d58cc729c689a5238d5928004812b5bec237281a15fb1db7d34b555",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.4.2",
      "date": "2026-10-03T13:51:53.000Z",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/8f145303d603bef51ed26ae60b8a5eb80630171146dd58f4e791106676a12720",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.4.2",
      "date": "2026-10-03T13:44:09.000Z",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/985b9dd74760f2f0881fe7d46bdeb1f233880e4ac87e58645295df1a806fc1be",
      "status": "success",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.4.2",
      "date": "2026-10-03T13:43:55.000Z",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/a85887aceb0367283d14f4545cd5775dd69495a19cda3d31ad962f96abfc1356",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.4.2",
      "date": "2026-10-03T13:43:14.000Z",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/4915cf26a258a866f906e905586493a3fcb9d1ecc9f6938cc8ce17a181dc50a0",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.4.2",
      "date": "2026-10-03T13:43:34.000Z",
      "commit": "9d10f45581685a9592b0846fe7d16ff93741ad30",
      "fileid": "https://r2.ropensci.org/563b8c88d36792968762bf6d7658aa4bbed7b5a705acec74710b73e223ffa1d8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126868887"
    }
  ]
}