{
  "_id": "6a5c8b649baadeef8ab515ea",
  "Package": "simphony",
  "Type": "Package",
  "Title": "Simulating Large-Scale, Rhythmic Data",
  "Version": "1.0.3",
  "Authors@R": "c(person('Jake', 'Hughey', , 'jakejhughey@gmail.com', c('aut', 'cre')),\nperson('Jordan', 'Singer', , 'jordan.m.singer@gmail.com', 'aut'),\nperson('Darwin', 'Fu', , 'darwinyfu@gmail.com', 'ctb'))",
  "Description": "A tool for simulating rhythmic data: transcriptome data\nusing Gaussian or negative binomial distributions, and\nbehavioral activity data using Bernoulli or Poisson\ndistributions. See Singer et al. (2019)\n<doi:10.7717/peerj.6985>.",
  "URL": "https://simphony.hugheylab.org,\nhttps://github.com/hugheylab/simphony",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.1",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Repository": "https://hugheylab.r-universe.dev",
  "Date/Publication": "2022-12-01 21:38:55 UTC",
  "RemoteUrl": "https://github.com/hugheylab/simphony",
  "RemoteRef": "HEAD",
  "RemoteSha": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-19 08:28:34 UTC",
    "User": "root"
  },
  "Author": "Jake Hughey [aut, cre],\nJordan Singer [aut],\nDarwin Fu [ctb]",
  "Maintainer": "Jake Hughey <jakejhughey@gmail.com>",
  "_user": "hugheylab",
  "_type": "src",
  "_file": "simphony_1.0.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/77d79fa3c852eac625991b2b5261216e183158facdda12583940b3a2b1fe21c2",
  "_filesize": 980976,
  "_sha256": "77d79fa3c852eac625991b2b5261216e183158facdda12583940b3a2b1fe21c2",
  "_expires": "2026-10-27T08:31:30.000Z",
  "_created": "2026-07-19T08:28:34.000Z",
  "_published": "2026-07-19T08:31:32.490Z",
  "_jobs": [
    {
      "job": 88174019856,
      "time": 142,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8440222803"
    },
    {
      "job": 88174019816,
      "time": 132,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8440221169"
    },
    {
      "job": 88174019827,
      "time": 85,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8440213887"
    },
    {
      "job": 88174019846,
      "time": 73,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8440212300"
    },
    {
      "job": 88173763596,
      "time": 198,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8440201558"
    },
    {
      "job": 88174019832,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8440218177"
    },
    {
      "job": 88174019844,
      "time": 81,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8440213512"
    },
    {
      "job": 88174019864,
      "time": 110,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8440217972"
    },
    {
      "job": 88174019892,
      "time": 87,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8440214818"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427",
  "_status": "success",
  "_upstream": "https://github.com/hugheylab/simphony",
  "_commit": {
    "id": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
    "author": "Jake Hughey <jakejhughey@gmail.com>",
    "committer": "Jake Hughey <jakejhughey@gmail.com>",
    "message": "updated linting.\n",
    "time": 1669930735
  },
  "_maintainer": {
    "name": "Jake Hughey",
    "email": "jakejhughey@gmail.com",
    "login": "jakejh",
    "description": "",
    "uuid": 2295314
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "version": ">= 1.11.4",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "version": ">= 1.4.4",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "version": ">= 0.9.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.20",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "version": ">= 3.34.9",
      "role": "Suggests"
    },
    {
      "package": "precrec",
      "version": ">= 0.9.1",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 1.9",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "hugheylab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "rhythmic-data",
    "simphony"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "jakejh",
      "count": 121,
      "uuid": 2295314
    },
    {
      "user": "jschoenbachler",
      "count": 33,
      "uuid": 15148457
    },
    {
      "user": "darwinyfu",
      "count": 12,
      "uuid": 4266515
    }
  ],
  "_userbio": {
    "uuid": 32131222,
    "type": "organization",
    "name": "Hughey Lab",
    "followers": 3
  },
  "_downloads": {
    "count": 243,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/simphony"
  },
  "_devurl": "https://github.com/hugheylab/simphony",
  "_pkgdown": "https://simphony.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/simphony.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hugheylab/simphony",
  "_realowner": "hugheylab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-02-09"
    },
    {
      "version": "1.0.3",
      "date": "2022-08-09"
    }
  ],
  "_exports": [
    "getExpectedAbund",
    "getSampledAbund",
    "mergeSimData",
    "simphony",
    "splitDiffFeatureGroups"
  ],
  "_datasets": [
    {
      "name": "defaultDispFunc",
      "title": "Default function for mapping expected counts to dispersion.",
      "object": "defaultDispFunc",
      "class": [
        "function"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "defaultDispFunc",
      "title": "Default function for mapping expected counts to dispersion.",
      "topics": [
        "defaultDispFunc"
      ]
    },
    {
      "page": "getExpectedAbund",
      "title": "Calculate expected abundance",
      "topics": [
        "getExpectedAbund"
      ]
    },
    {
      "page": "getSampledAbund",
      "title": "Sample abundance values",
      "topics": [
        "getSampledAbund"
      ]
    },
    {
      "page": "mergeSimData",
      "title": "Merge abundance data, feature metadata, and sample metadata",
      "topics": [
        "mergeSimData"
      ]
    },
    {
      "page": "simphony",
      "title": "Simulate feature abundance data",
      "topics": [
        "simphony"
      ]
    },
    {
      "page": "splitDiffFeatureGroups",
      "title": "Split differential featureGroups",
      "topics": [
        "splitDiffFeatureGroups"
      ]
    }
  ],
  "_readme": "https://github.com/hugheylab/simphony/raw/HEAD/README.md",
  "_rundeps": [
    "codetools",
    "data.table",
    "foreach",
    "iterators"
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Using simphony to evaluate rhythm detection",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load the packages we'll use",
        "Simulate the data",
        "Plot the simulated time-course for selected genes",
        "Detect rhythmic genes",
        "Evaluate accuracy of rhythmic gene detection"
      ],
      "created": "2018-10-26 19:07:29",
      "modified": "2022-04-11 20:12:13",
      "commits": 10
    },
    {
      "source": "examples.Rmd",
      "filename": "examples.html",
      "title": "Using simphony's various options",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load required packages",
        "Evenly-spaced timepoints",
        "Custom rhythm function",
        "Specified timepoints",
        "Random timepoints",
        "Time-dependent amplitude and base",
        "Differential rhythmicity between conditions",
        "Controlling negative binomial dispersion and base",
        "Poisson sampling at high resolution"
      ],
      "created": "2019-03-08 18:08:21",
      "modified": "2022-04-11 20:12:13",
      "commits": 6
    }
  ],
  "_score": 4.778151250383644,
  "_indexed": true,
  "_nocasepkg": "simphony",
  "_universes": [
    "hugheylab",
    "jakejh"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-07-19T08:30:54.000Z",
      "distro": "resolute",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/d8c092a448a5361eed02e4db64b9169ccc4d8ba972df7c6379bd19af1509ca57",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-07-19T08:30:47.000Z",
      "distro": "resolute",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/e737c21130b2f73e390a3f8c58f73cb41813ada6647d8bde1dc394778060c23c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-07-19T08:30:02.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/74cf26d94a1aa03a1c7f24e937d799dad3f058b4b2d7d2673c615fa93a572c45",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-07-19T08:29:52.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/fe88b8bdb34685e77109b9d3799835951303f35c29d2a79316f3a2ac3dc4abb5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-07-19T08:30:40.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/0a2bf7b67370ec80d76d0816fd389e8fc2f50ac2c7c7be8d29923f8259b08cd4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-07-19T08:29:50.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/4a61528f49ded567f32df85347471041e36766b5e3e219cd5ef1e2da08f2248b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-07-19T08:30:22.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/1647cf774ff09c5f9de0b5122e130a647433716f51ddc2262b426ec47b07bc0a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-07-19T08:29:59.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "https://r2.ropensci.org/7355ba5c37246cc45fad36ada0e7d746050995ccd15812e83584c1afcc75903e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/29679785427"
    }
  ]
}