{
  "_id": "6a3520723efcd9bda43e3a62",
  "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": "2026-06-19 10:54:10 UTC",
    "User": "root"
  },
  "Author": "Jake Hughey [aut, cre],\nJordan Singer [aut],\nDarwin Fu [ctb]",
  "Maintainer": "Jake Hughey <jakejhughey@gmail.com>",
  "MD5sum": "64db32dcc779a0985b3ed3b434f84b73",
  "_user": "hugheylab",
  "_type": "src",
  "_file": "simphony_1.0.3.tar.gz",
  "_fileid": "42d759dbf53c0c732f0bb633d9de441c9297f08ad668ca763f175003fe7fdcd3",
  "_filesize": 978192,
  "_sha256": "42d759dbf53c0c732f0bb633d9de441c9297f08ad668ca763f175003fe7fdcd3",
  "_created": "2026-06-19T10:54:10.000Z",
  "_published": "2026-06-19T10:56:50.178Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 82335445214,
      "time": 121,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7748002878"
    },
    {
      "job": 82335445195,
      "time": 121,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7748003128"
    },
    {
      "job": 82335445208,
      "time": 82,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7747991432"
    },
    {
      "job": 82335445206,
      "time": 104,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7747998255"
    },
    {
      "job": 82334829851,
      "time": 251,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7747966851"
    },
    {
      "job": 82335445231,
      "time": 124,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7748004084"
    },
    {
      "job": 82335445243,
      "time": 92,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7747994786"
    },
    {
      "job": 82335445221,
      "time": 65,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7747986401"
    },
    {
      "job": 82335445215,
      "time": 69,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7747987787"
    }
  ],
  "_buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_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
  },
  "_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": 242,
    "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": "4.6.0",
  "_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": "2026-06-19T10:56:12.000Z",
      "distro": "noble",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "fb79afa5fbd99d1b5ac03265ceb1594be4126a34facca9ea737484ef81d6fb89",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-06-19T10:56:12.000Z",
      "distro": "noble",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "8460894cafd1bd9a21df910d476a48086bb88133d1043dfd35b4814ef4d2e6f3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-06-19T10:55:34.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "04ed19daa45fb24eca615113e5f9922b640039c83a4e6a72f096f972fa586eab",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-06-19T10:55:54.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "dcc394238bda1f394899d6e2949214c0faf5ed31ead2eb45650fbe0dbd290445",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-06-19T10:56:29.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "50d7ffe66b7fefd151c4dd4fc4171c1809a8720c051860978ca1196f9e90ce25",
      "status": "success",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-06-19T10:55:38.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "f8a5b689731164edd8de42416e8e5866983d9eb4f22db4fdeb2c1ea7d689d0d4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-06-19T10:55:14.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "e6e96eaa86af5d87c6e43abea1ad01d7f6aa735f5501ca4399e2bb07faa9530f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-06-19T10:55:18.000Z",
      "commit": "f5a705e50e644d1e787bf860a658bf2d6b0757e4",
      "fileid": "ffcbf108a4d1ef2dcca772d002c00473fa3fbf44bcad149bd8b0d937fb4e0f24",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/27821286207"
    }
  ]
}