{
  "_id": "6a548404ff0138dec5d648f4",
  "Package": "zeitzeiger",
  "Type": "Package",
  "Title": "Regularized Supervised Learning for Data from Rhythmic Systems",
  "Version": "2.1.3",
  "Authors@R": "person('Jake', 'Hughey', , 'jakejhughey@gmail.com', c('aut', 'cre'))",
  "Description": "Method for predicting the value of a periodic variable\nfrom a high-dimensional observation. See Hughey et al. (2016)\n<doi:10.1093/nar/gkw030> and Hughey (2017)\n<doi:10.1186/s13073-017-0406-4>.",
  "URL": "https://zeitzeiger.hugheylab.org,\nhttps://github.com/hugheylab/zeitzeiger",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.2",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://hugheylab.r-universe.dev",
  "Date/Publication": "2022-12-01 21:18:13 UTC",
  "RemoteUrl": "https://github.com/hugheylab/zeitzeiger",
  "RemoteRef": "HEAD",
  "RemoteSha": "2b8619997583e58d7733090f34c76ef8fd47afb2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-13 06:18:42 UTC",
    "User": "root"
  },
  "Author": "Jake Hughey [aut, cre]",
  "Maintainer": "Jake Hughey <jakejhughey@gmail.com>",
  "_user": "hugheylab",
  "_type": "src",
  "_file": "zeitzeiger_2.1.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/ddfa5106eda4c83e310bd083aa665d6111a2fb9bb4f31354df7e0476640222d5",
  "_filesize": 607756,
  "_sha256": "ddfa5106eda4c83e310bd083aa665d6111a2fb9bb4f31354df7e0476640222d5",
  "_expires": "2026-10-21T06:21:54.000Z",
  "_created": "2026-07-13T06:18:42.000Z",
  "_published": "2026-07-13T06:21:56.287Z",
  "_jobs": [
    {
      "job": 86747869273,
      "time": 160,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8270712046"
    },
    {
      "job": 86747869323,
      "time": 152,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8270709720"
    },
    {
      "job": 86747869318,
      "time": 95,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8270694191"
    },
    {
      "job": 86747869292,
      "time": 140,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8270706312"
    },
    {
      "job": 86747243965,
      "time": 259,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270667087"
    },
    {
      "job": 86747869334,
      "time": 150,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8270709068"
    },
    {
      "job": 86747869295,
      "time": 85,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8270691222"
    },
    {
      "job": 86747869297,
      "time": 129,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8270703225"
    },
    {
      "job": 86747869337,
      "time": 94,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8270693995"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245",
  "_status": "success",
  "_upstream": "https://github.com/hugheylab/zeitzeiger",
  "_commit": {
    "id": "2b8619997583e58d7733090f34c76ef8fd47afb2",
    "author": "Jake Hughey <jakejhughey@gmail.com>",
    "committer": "Jake Hughey <jakejhughey@gmail.com>",
    "message": "updated actions.\n",
    "time": 1669929493
  },
  "_maintainer": {
    "name": "Jake Hughey",
    "email": "jakejhughey@gmail.com",
    "login": "jakejh",
    "description": "",
    "uuid": 2295314
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2",
      "role": "Depends"
    },
    {
      "package": "abind",
      "version": ">= 1.4-3",
      "role": "Imports"
    },
    {
      "package": "bbmle",
      "version": ">= 1.0.17",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.14.2",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "version": ">= 1.4.3",
      "role": "Imports"
    },
    {
      "package": "limma",
      "version": ">= 3.38.2",
      "role": "Imports"
    },
    {
      "package": "PMA",
      "version": ">= 1.0.9",
      "role": "Imports"
    },
    {
      "package": "statmod",
      "version": ">= 1.4.30",
      "role": "Imports"
    },
    {
      "package": "sva",
      "version": ">= 3.18.0",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "version": ">= 1.0.10",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.1.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.20",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 1.10",
      "role": "Suggests"
    }
  ],
  "_owner": "hugheylab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 12,
  "_contributors": [
    {
      "user": "jakejh",
      "count": 79,
      "uuid": 2295314
    },
    {
      "user": "jschoenbachler",
      "count": 77,
      "uuid": 15148457
    }
  ],
  "_userbio": {
    "uuid": 32131222,
    "type": "organization",
    "name": "Hughey Lab",
    "followers": 3
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/zeitzeiger"
  },
  "_devurl": "https://github.com/hugheylab/zeitzeiger",
  "_pkgdown": "https://zeitzeiger.hugheylab.org",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/zeitzeiger.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "getCircDiff",
    "predictIntensity",
    "zeitzeiger",
    "zeitzeigerBatch",
    "zeitzeigerEnsembleLikelihood",
    "zeitzeigerEnsembleMean",
    "zeitzeigerFit",
    "zeitzeigerFitCv",
    "zeitzeigerPredict",
    "zeitzeigerPredictCv",
    "zeitzeigerPredictGroup",
    "zeitzeigerPredictGroupCv",
    "zeitzeigerSpc",
    "zeitzeigerSpcCv"
  ],
  "_help": [
    {
      "page": "getCircDiff",
      "title": "Calculate circular difference",
      "topics": [
        "getCircDiff"
      ]
    },
    {
      "page": "predictIntensity",
      "title": "Calculate time-dependent mean",
      "topics": [
        "predictIntensity"
      ]
    },
    {
      "page": "zeitzeiger",
      "title": "Train and test a ZeitZeiger predictor",
      "topics": [
        "zeitzeiger"
      ]
    },
    {
      "page": "zeitzeigerBatch",
      "title": "Train and test a ZeitZeiger predictor, accounting for batch effects",
      "topics": [
        "zeitzeigerBatch"
      ]
    },
    {
      "page": "zeitzeigerEnsembleLikelihood",
      "title": "Combine predictions into an ensemble using the log-likelihood",
      "topics": [
        "zeitzeigerEnsembleLikelihood"
      ]
    },
    {
      "page": "zeitzeigerEnsembleMean",
      "title": "Combine predictions into an ensemble using the circular mean",
      "topics": [
        "zeitzeigerEnsembleMean"
      ]
    },
    {
      "page": "zeitzeigerFit",
      "title": "Fit a periodic spline for each feature",
      "topics": [
        "zeitzeigerFit"
      ]
    },
    {
      "page": "zeitzeigerFitCv",
      "title": "Fit a periodic spline for each feature on cross-validation",
      "topics": [
        "zeitzeigerFitCv"
      ]
    },
    {
      "page": "zeitzeigerPredict",
      "title": "Predict corresponding time for test observations",
      "topics": [
        "zeitzeigerPredict"
      ]
    },
    {
      "page": "zeitzeigerPredictCv",
      "title": "Predict corresponding time for observations on cross-validation",
      "topics": [
        "zeitzeigerPredictCv"
      ]
    },
    {
      "page": "zeitzeigerPredictGroup",
      "title": "Predict corresponding time for groups of test observations",
      "topics": [
        "zeitzeigerPredictGroup"
      ]
    },
    {
      "page": "zeitzeigerPredictGroupCv",
      "title": "Predict corresponding time for groups of observations on cross-validation",
      "topics": [
        "zeitzeigerPredictGroupCv"
      ]
    },
    {
      "page": "zeitzeigerSpc",
      "title": "Calculate sparse principal components of time-dependent variation",
      "topics": [
        "zeitzeigerSpc"
      ]
    },
    {
      "page": "zeitzeigerSpcCv",
      "title": "Calculate sparse principal components of time-dependent variation on cross-validation",
      "topics": [
        "zeitzeigerSpcCv"
      ]
    }
  ],
  "_readme": "https://github.com/hugheylab/zeitzeiger/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "bbmle",
    "bdsmatrix",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "edgeR",
    "fastmap",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "glue",
    "httr",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "openssl",
    "pkgconfig",
    "PMA",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "statmod",
    "survival",
    "sva",
    "sys",
    "vctrs",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to ZeitZeiger",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load the necessary packages",
        "Generate example data",
        "Create training and testing observations",
        "Train and test a ZeitZeiger predictor",
        "Plot the periodic spline fits",
        "Plot prediction error on the test set",
        "Plot a test observation's time-dependent likelihood",
        "Run cross-validation",
        "Plot the error for each set of parameter values",
        "Train a model on the full dataset",
        "Plot the behavior of the SPCs over time",
        "Plot the coefficients of the features for the SPCs"
      ],
      "created": "2015-11-21 05:14:13",
      "modified": "2022-04-12 16:01:59",
      "commits": 12
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": true,
  "_nocasepkg": "zeitzeiger",
  "_universes": [
    "hugheylab",
    "jakejh"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.3",
      "date": "2026-07-13T06:21:20.000Z",
      "distro": "resolute",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/a7513fb3d266d1029b2a91abf380881fc82a14e3b5293fecc053ed282390d8ab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1.3",
      "date": "2026-07-13T06:21:14.000Z",
      "distro": "resolute",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/e684f3aebbd379d065e3d76772ebd8dfb14177c11a4bfa864414c500403042b2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.3",
      "date": "2026-07-13T06:20:20.000Z",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/f5b6f1c892bc6ded5ef730e3534fbf263d78f156aca341af1c855924262634c5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.1.3",
      "date": "2026-07-13T06:20:54.000Z",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/9fbf3ace622dc52f83eaa6f8a16b99b707589282aa4fc8b398063ad21d3400f1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.3",
      "date": "2026-07-13T06:21:26.000Z",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/e0e40cc19784bfe8b8bf59a9fc7ea8b9f1c7202e929e82325ea657f99818be52",
      "status": "success",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.3",
      "date": "2026-07-13T06:20:04.000Z",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/d0646cacf0a4457a3d990c0a593415b388284d6a08e0ed947830d89ab7bdaf62",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.3",
      "date": "2026-07-13T06:20:34.000Z",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/08846979924d1749cf5370cb86ee81a5b1ca32eb731905f8ae79669e1b205621",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.1.3",
      "date": "2026-07-13T06:20:13.000Z",
      "commit": "2b8619997583e58d7733090f34c76ef8fd47afb2",
      "fileid": "https://r2.ropensci.org/abf62546509aaad203f67ad352ddc16bc7cfb90409dc327e0c5317d0a7e9511e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29228388245"
    }
  ]
}