{
  "_id": "6a53269c9b92047c28d55ddb",
  "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": "2026-07-12 05:26:39 UTC",
    "User": "root"
  },
  "Author": "Ye Yuan [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-9641-9102>)",
  "Maintainer": "Ye Yuan <yeyu@umich.edu>",
  "_user": "yeyuan98",
  "_type": "src",
  "_file": "clockSim_0.1.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/0cece27ca2c654ba789195677f8beb8a79debcf5ee8db802e184e62351c6cb95",
  "_filesize": 6630056,
  "_sha256": "0cece27ca2c654ba789195677f8beb8a79debcf5ee8db802e184e62351c6cb95",
  "_expires": "2026-10-20T05:31:06.000Z",
  "_created": "2026-07-12T05:26:39.000Z",
  "_published": "2026-07-12T05:31:08.312Z",
  "_jobs": [
    {
      "job": 86618970059,
      "time": 149,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8256461107"
    },
    {
      "job": 86618970088,
      "time": 153,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8256460985"
    },
    {
      "job": 86618970054,
      "time": 152,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8256461465"
    },
    {
      "job": 86618970063,
      "time": 145,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8256460157"
    },
    {
      "job": 86618970011,
      "time": 116,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8256456355"
    },
    {
      "job": 86618970035,
      "time": 220,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8256470372"
    },
    {
      "job": 86618970018,
      "time": 102,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8256454774"
    },
    {
      "job": 86618970037,
      "time": 153,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8256461710"
    },
    {
      "job": 86618654314,
      "time": 271,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8256438920"
    },
    {
      "job": 86618970003,
      "time": 130,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8256457952"
    },
    {
      "job": 86618970010,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8256453204"
    },
    {
      "job": 86618970015,
      "time": 110,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8256455167"
    },
    {
      "job": 86618970042,
      "time": 135,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8256458812"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974",
  "_status": "success",
  "_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"
  },
  "_distro": "resolute",
  "_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",
    "followers": 0
  },
  "_downloads": {
    "count": 67,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clockSim"
  },
  "_devurl": "https://github.com/yeyuan98/clocksim",
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_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": "2026-07-12T05:29:17.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/4f71168b6bf215055d1c3ee4e0b2a77d54960d7562befcd87a85ff9d190a2521",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T05:29:12.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/91e0e9810d5615af45e3cc4f82f0d5a8faeb5c9308fe1ab27a3982c1389070f2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T05:29:19.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/1e439044f140bfb94619d47ebbdb68b2033e674da42e07f039d232c44d60bc8d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-07-12T05:29:03.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/c15ad8b4a0a05eaffeb6fd5cce6e79dd4490ede364d579342143042badefa969",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T05:28:36.000Z",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/cecf4dd20e3254dc26d4822fb0a7f5f52fc7a325cd5d60c8b53a23391a2ce5a7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T05:30:04.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/ea0f2da6095e64ff448ec12adcb8af087fc678d2f342b9c4b465243f2dfb8bea",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T05:28:28.000Z",
      "arch": "aarch64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/28062ad3dd50852184ca870fdd8bf38c9b69cae779e50c6c1da2f67089bab273",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-07-12T05:29:05.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/47ce3b7e870ec384f93dec5db66f5e01a2b7bd538290128cc0473520789db21d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-07-12T05:29:08.000Z",
      "arch": "emscripten",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/b096058b977ff4aaef072cc20c18448b084cfadd25457c62c33ee015bfdadea2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-07-12T05:27:59.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/c185b12433d1d2e96db8dc768718ca0442f52a74bd5d34d601c494b7127f4e5e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-07-12T05:28:15.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/9d536fb6e07f0ebe4e2cea0df8586f6024bd3aa0b5a0a7e13bac18d94d736eff",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-07-12T05:28:33.000Z",
      "arch": "x86_64",
      "commit": "1afb7d2e515525f86570369da64d238b10f6419d",
      "fileid": "https://r2.ropensci.org/e6d66c0429cf510cf264fff3c8f2e2932eefac30c61a699ed21b461576630ca2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/yeyuan98/actions/runs/29181067974"
    }
  ]
}