{
  "_id": "6a17ff49acfb0bcc41dab6a2",
  "Package": "clockSim",
  "Title": "Streamlined Simulation of Circadian Gene Networks",
  "Version": "0.1.2",
  "Authors@R": "person(\"Ye\", \"Yuan\", , \"yeyu@umich.edu\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-9641-9102\"))",
  "Description": "A user-friendly workflow for simulating circadian clock\ngene networks. Despite decades of advances in modeling\ncircadian clock dynamics, the lack of accessible tools for\nreproducible simulation workflows hinders the integration of\ncomputational modeling with experimental studies. 'clockSim'\naddresses this gap by providing models and helper functions\nwith step-by-step vignettes. This package opens up system-level\nexploration of the circadian clock to wet-lab experimentalists,\nand future development will include additional clock\narchitectures and other gene circuit models. Currently\nimplemented models are based on Leloup and Goldbeter (1998)\n<doi:10.1177/074873098128999934>.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/yeyuan98/clockSim",
  "BugReports": "https://github.com/yeyuan98/clockSim/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://yeyuan98.r-universe.dev",
  "Date/Publication": "2025-04-22 19:41:54 UTC",
  "RemoteUrl": "https://github.com/yeyuan98/clockSim",
  "RemoteRef": "HEAD",
  "RemoteSha": "1afb7d2e515525f86570369da64d238b10f6419d",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-28 08:35:49 UTC",
    "User": "root"
  },
  "Author": "Ye Yuan [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-9641-9102>)",
  "Maintainer": "Ye Yuan <yeyu@umich.edu>",
  "MD5sum": "d8a6e9aece296398c2ccb2c0a61f3a8d",
  "_user": "yeyuan98",
  "_type": "src",
  "_file": "clockSim_0.1.2.tar.gz",
  "_fileid": "0214e220bdf91d8b0bfa23f9e4623b01caa8c118204c94eee4cf5befd7771f3f",
  "_filesize": 6703698,
  "_sha256": "0214e220bdf91d8b0bfa23f9e4623b01caa8c118204c94eee4cf5befd7771f3f",
  "_created": "2026-05-28T08:35:49.000Z",
  "_published": "2026-05-28T08:39:37.848Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78254119726,
      "time": 135,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7261404995"
    },
    {
      "job": 78254119580,
      "time": 128,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7261402489"
    },
    {
      "job": 78254119663,
      "time": 134,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7261404711"
    },
    {
      "job": 78254119753,
      "time": 144,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7261407834"
    },
    {
      "job": 78254119643,
      "time": 116,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7261398481"
    },
    {
      "job": 78254119754,
      "time": 190,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7261423984"
    },
    {
      "job": 78254119641,
      "time": 127,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7261402026"
    },
    {
      "job": 78254119595,
      "time": 156,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7261412093"
    },
    {
      "job": 78253479355,
      "time": 242,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7261356923"
    },
    {
      "job": 78254119564,
      "time": 139,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7261406276"
    },
    {
      "job": 78254119690,
      "time": 93,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7261390741"
    },
    {
      "job": 78254119678,
      "time": 94,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7261391131"
    },
    {
      "job": 78254119604,
      "time": 99,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7261392877"
    }
  ],
  "_buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/yeyuan98/clockSim",
  "_commit": {
    "id": "1afb7d2e515525f86570369da64d238b10f6419d",
    "author": "Ye Yuan <yeyu@umich.edu>",
    "committer": "Ye Yuan <yeyu@umich.edu>",
    "message": "add: badges for R-Universe\n",
    "time": 1745350914
  },
  "_maintainer": {
    "name": "Ye Yuan",
    "email": "yeyu@umich.edu",
    "login": "yeyuan98",
    "description": "",
    "uuid": 62569917,
    "orcid": "0000-0001-9641-9102"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "bench",
      "role": "Imports"
    },
    {
      "package": "dde",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "lomb",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "odin",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "yeyuan98",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "yeyuan98",
      "count": 11,
      "uuid": 62569917
    }
  ],
  "_userbio": {
    "uuid": 62569917,
    "type": "user",
    "name": "Ye Yuan"
  },
  "_downloads": {
    "count": 86,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clockSim"
  },
  "_devurl": "https://github.com/yeyuan98/clocksim",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/clockSim.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2025-04-07"
    },
    {
      "version": "0.1.2",
      "date": "2025-04-22"
    }
  ],
  "_exports": [
    "compute_cosine",
    "compute_normalize",
    "compute_period",
    "compute_rmse",
    "getOdinGen",
    "grid_scan",
    "plot_phase",
    "plot_timeSeries",
    "run_eta"
  ],
  "_help": [
    {
      "page": "dot-compute_validatePair",
      "title": "Trajectory similarity: validate consistency of result matrix pair",
      "topics": [
        ".compute_validatePair"
      ]
    },
    {
      "page": "clockSim",
      "title": "clockSim: Streamlined Simulation of Circadian Gene Networks",
      "topics": [
        "clockSim"
      ]
    },
    {
      "page": "compute_cosine",
      "title": "Trajectory similarity: Cosine Similarity",
      "topics": [
        "compute_cosine"
      ]
    },
    {
      "page": "compute_normalize",
      "title": "Trajectory similarity: variable normalization",
      "topics": [
        "compute_normalize"
      ]
    },
    {
      "page": "compute_period",
      "title": "Compute periodicity of time series",
      "topics": [
        "compute_period"
      ]
    },
    {
      "page": "compute_rmse",
      "title": "Trajectory similarity: Root Mean Squared Error RMSE",
      "topics": [
        "compute_rmse"
      ]
    },
    {
      "page": "getOdinGen",
      "title": "Get all clock model Odin generator objects",
      "topics": [
        "getOdinGen"
      ]
    },
    {
      "page": "grid_scan",
      "title": "Running model on a grid of parameters/initial states",
      "topics": [
        "grid_scan"
      ]
    },
    {
      "page": "plot_phase",
      "title": "2-D phase potrait plot",
      "topics": [
        "plot_phase"
      ]
    },
    {
      "page": "plot_timeSeries",
      "title": "Time series plot (multifaceted)",
      "topics": [
        "plot_timeSeries"
      ]
    },
    {
      "page": "run_eta",
      "title": "Run time estimate for an Odin model run.",
      "topics": [
        "run_eta"
      ]
    }
  ],
  "_readme": "https://github.com/yeyuan98/clockSim/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "bench",
    "bslib",
    "cachem",
    "cinterpolate",
    "cli",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "dde",
    "deSolve",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "lomb",
    "magrittr",
    "matrixStats",
    "memoise",
    "mime",
    "odin",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "pracma",
    "profmem",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "ring",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "noisy-LG-model.Rmd",
      "filename": "noisy-LG-model.html",
      "title": "Noisy LG model: incorporating noise to the classical LG ODE clock model",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A SDE LG model",
        "When is the model valid?",
        "Noising scaling",
        "Loading the noisy LG model",
        "Example: noise in tim RNA M_T turnover",
        "Phase portrait and periodogram"
      ],
      "created": "2025-03-09 19:49:07",
      "modified": "2025-03-09 19:49:07",
      "commits": 1
    },
    {
      "source": "grid-scan.Rmd",
      "filename": "grid-scan.html",
      "title": "Scanning parameter grid to understand circadian clock model",
      "author": "Ye Yuan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Baseline: a limit cycle oscillator",
        "Initial state grid scan",
        "Grid generation",
        "Running grid_scan()"
      ],
      "created": "2025-02-22 15:33:53",
      "modified": "2025-03-28 21:57:22",
      "commits": 3
    },
    {
      "source": "clock-models.Rmd",
      "filename": "clock-models.html",
      "title": "Models for circadian clock simulation",
      "author": "Ye Yuan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "LG model simulation scheme",
        "Continuous LG model",
        "Discrete LG model",
        "Discrete LG model: how small time step is enough?"
      ],
      "created": "2025-02-22 15:33:53",
      "modified": "2025-03-23 15:09:15",
      "commits": 2
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": true,
  "_nocasepkg": "clocksim",
  "_universes": [
    "yeyuan98"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-28T08:38:05.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "00efe78848377652f9f2d6190f84ccd2d16ebcfe0ecd51c5ff3b77a228638f62",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-28T08:37:56.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "5e594e6792b99267c0e5c63bcfc3ad6a70dfbdc7a273e32d4bf55ebe558e21b2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-28T08:38:06.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "597b338d70b35f98c0e1eae0467bd94a3baf3b70c1e35ce59c9cfe7b980321d2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-28T08:38:10.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "a1420510778fdd42b31ce4b047b1785ae904dd3181c56cf96248c3ca81a5768e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-28T08:37:45.000Z",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "0331664a07a5ca80eb449d6f34760b8001db44943a3b014376b55a0995dc7006",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-28T08:38:49.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "41137ac49bac84da27d14a984d5cb78856b353d00bb7aa559d6266f508559993",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-28T08:37:51.000Z",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "5a75661c98acfc86025c18f769ecfb41ba6ba6c1de6cf4df88a7d957a6c3b8e3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-28T08:38:15.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "ab787a0cc960446cec7789f4b07a8daced7192a47aeb4e727cec72b55f9c6578",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-05-28T08:38:26.000Z",
      "arch": "emscripten",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "22c42ad545f682b1d433627bef182f06d372ed857aee61a4da55d48f1b83f56e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-28T08:37:11.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "29abd3119e6f4ca08c45be958698a2868ab21a60f91686f8ccbf1ee00eeab9f5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-28T08:37:11.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "450a5b4ba33250cc38da17aa7af716c1676e744be74f1f79cde7af914bd0bea8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-28T08:37:19.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "6bd93d2f45fab8cf1947485c6bf2b2a2e05526210405e063fc723aa371793e43",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/26563873987"
    }
  ]
}