{
  "_id": "6a1eda8db401979e7340f5e0",
  "Package": "magi",
  "Type": "Package",
  "Title": "MAnifold-Constrained Gaussian Process Inference",
  "Version": "1.2.5",
  "Date": "2025-10-22",
  "Authors@R": "c(person(given = \"Shihao\",\nfamily = \"Yang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"shihao.yang@isye.gatech.edu\",\ncomment = c(ORCID = \"0000-0003-3910-4969\")),\nperson(given = \"Samuel W.K.\",\nfamily = \"Wong\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7325-7267\")),\nperson(given = \"S.C.\",\nfamily = \"Kou\",\nrole = c(\"ctb\", \"cph\"),\ncomment = c(role = \"Contributor of MAGI method development\"))\n)",
  "Encoding": "UTF-8",
  "Description": "Provides fast and accurate inference for the parameter\nestimation problem in Ordinary Differential Equations,\nincluding the case when there are unobserved system components.\nImplements the MAGI method (MAnifold-constrained Gaussian\nprocess Inference) of Yang, Wong, and Kou (2021)\n<doi:10.1073/pnas.2020397118>. A user guide is provided by the\naccompanying software paper Wong, Yang, and Kou (2024)\n<doi:10.18637/jss.v109.i04>.",
  "URL": "https://doi.org/10.18637/jss.v109.i04",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "yes",
  "Maintainer": "Shihao Yang <shihao.yang@isye.gatech.edu>",
  "Packaged": {
    "Date": "2026-05-20 09:01:54 UTC",
    "User": "root"
  },
  "Author": "Shihao Yang [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3910-4969>), Samuel W.K. Wong\n[aut] (ORCID: <https://orcid.org/0000-0002-7325-7267>), S.C.\nKou [ctb, cph] (role: Contributor of MAGI method development)",
  "Repository": "https://shihao-yang.r-universe.dev",
  "Date/Publication": "2025-10-22 17:40:02 UTC",
  "RemoteUrl": "https://github.com/cran/magi",
  "RemoteRef": "HEAD",
  "RemoteSha": "c7529470be556a7027971d87ae7cb238ab80feaf",
  "MD5sum": "5c87f5b93ab1f873d88a9efb35d39006",
  "_user": "shihao-yang",
  "_type": "src",
  "_file": "magi_1.2.5.tar.gz",
  "_fileid": "e6cd1cdb7ba155bc72ea2b7836533c1cb5ef58f8f6502fce38b309f64decc872",
  "_filesize": 487995,
  "_sha256": "e6cd1cdb7ba155bc72ea2b7836533c1cb5ef58f8f6502fce38b309f64decc872",
  "_created": "2026-05-20T09:01:54.000Z",
  "_published": "2026-06-02T13:28:45.893Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79081460380,
      "time": 585,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7105930496"
    },
    {
      "job": 79081460076,
      "time": 290,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7105820133"
    },
    {
      "job": 79081460128,
      "time": 589,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105931900"
    },
    {
      "job": 79081460240,
      "time": 261,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105809514"
    },
    {
      "job": 79081460468,
      "time": 234,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7105791984"
    },
    {
      "job": 79081460413,
      "time": 424,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7105861379"
    },
    {
      "job": 79081460602,
      "time": 266,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105798449"
    },
    {
      "job": 79081460261,
      "time": 605,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105928336"
    },
    {
      "job": 79081459265,
      "time": 404,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105713857"
    },
    {
      "job": 79081459131,
      "time": 212,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 79081459999,
      "time": 354,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7105845293"
    },
    {
      "job": 79081460341,
      "time": 341,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7105838442"
    },
    {
      "job": 79081460035,
      "time": 342,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7105840179"
    }
  ],
  "_buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/magi",
  "_commit": {
    "id": "c7529470be556a7027971d87ae7cb238ab80feaf",
    "author": "Shihao Yang <shihao.yang@isye.gatech.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.2.5\n",
    "time": 1761154802
  },
  "_maintainer": {
    "name": "Shihao Yang",
    "email": "shihao.yang@isye.gatech.edu",
    "login": "shihao-yang",
    "description": "",
    "uuid": 6549963,
    "orcid": "0000-0003-3910-4969"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "roptim",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.6",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "gridBase",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "mvtnorm",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.2.5",
      "date": "2025-10-22"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "shihao-yang",
      "count": 9,
      "uuid": 6549963
    }
  ],
  "_userbio": {
    "uuid": 6549963,
    "type": "user",
    "name": "Shihao Yang"
  },
  "_downloads": {
    "count": 219,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/magi"
  },
  "_searchresults": 55,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/magi.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "shihao-yang",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2021-07-27"
    },
    {
      "version": "1.1.3",
      "date": "2022-01-11"
    },
    {
      "version": "1.1.5",
      "date": "2022-01-14"
    },
    {
      "version": "1.2.0",
      "date": "2022-08-29"
    },
    {
      "version": "1.2.1",
      "date": "2022-12-19"
    },
    {
      "version": "1.2.2",
      "date": "2023-04-26"
    },
    {
      "version": "1.2.3",
      "date": "2024-05-05"
    },
    {
      "version": "1.2.4",
      "date": "2024-06-23"
    },
    {
      "version": "1.2.5",
      "date": "2025-10-22"
    }
  ],
  "_exports": [
    "calCov",
    "fnmodelDtheta",
    "fnmodelDx",
    "fnmodelODE",
    "gpcov",
    "gpmean",
    "gpsmoothing",
    "gpsmoothllik",
    "hes1logmodelDtheta",
    "hes1logmodelDx",
    "hes1logmodelODE",
    "hes1modelDtheta",
    "hes1modelDx",
    "hes1modelODE",
    "is.magioutput",
    "magioutput",
    "MagiPosterior",
    "MagiSolver",
    "ptransmodelDtheta",
    "ptransmodelDx",
    "ptransmodelODE",
    "setDiscretization",
    "testDynamicalModel"
  ],
  "_datasets": [
    {
      "name": "FNdat",
      "title": "Dataset of noisy observations from the FitzHugh-Nagumo (FN) equations",
      "object": "FNdat",
      "file": "FNdat.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "time",
        "V",
        "R"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calCov",
      "title": "Calculate stationary Gaussian process kernel",
      "topics": [
        "calCov"
      ]
    },
    {
      "page": "FNdat",
      "title": "Dataset of noisy observations from the FitzHugh-Nagumo (FN) equations",
      "topics": [
        "FNdat"
      ]
    },
    {
      "page": "fnmodelODE",
      "title": "The FitzHugh-Nagumo (FN) equations",
      "topics": [
        "fnmodelDtheta",
        "fnmodelDx",
        "fnmodelODE"
      ]
    },
    {
      "page": "gpcov",
      "title": "Conditional covariance of Gaussian process given observations",
      "topics": [
        "gpcov"
      ]
    },
    {
      "page": "gpmean",
      "title": "Conditional mean of Gaussian process given observations",
      "topics": [
        "gpmean"
      ]
    },
    {
      "page": "gpsmoothing",
      "title": "Gaussian process smoothing",
      "topics": [
        "gpsmoothing"
      ]
    },
    {
      "page": "gpsmoothllik",
      "title": "Marginal log-likelihood for Gaussian process smoothing",
      "topics": [
        "gpsmoothllik"
      ]
    },
    {
      "page": "hes1modelODE",
      "title": "Hes1 equations: oscillation of mRNA and protein levels",
      "topics": [
        "hes1logmodelDtheta",
        "hes1logmodelDx",
        "hes1logmodelODE",
        "hes1modelDtheta",
        "hes1modelDx",
        "hes1modelODE"
      ]
    },
    {
      "page": "is.magioutput",
      "title": "MagiSolver output ('magioutput') object",
      "topics": [
        "is.magioutput",
        "magioutput"
      ]
    },
    {
      "page": "magi",
      "title": "'magi': MAnifold-Constrained Gaussian Process Inference",
      "topics": [
        "magi"
      ]
    },
    {
      "page": "MagiPosterior",
      "title": "MAGI posterior density",
      "topics": [
        "MagiPosterior"
      ]
    },
    {
      "page": "MagiSolver",
      "title": "MAnifold-constrained Gaussian process Inference (MAGI)",
      "topics": [
        "MagiSolver"
      ]
    },
    {
      "page": "plot.magioutput",
      "title": "Generate plots from 'magioutput' object",
      "topics": [
        "plot.magioutput"
      ]
    },
    {
      "page": "ptransmodelODE",
      "title": "Protein transduction model",
      "topics": [
        "ptransmodelDtheta",
        "ptransmodelDx",
        "ptransmodelODE"
      ]
    },
    {
      "page": "setDiscretization",
      "title": "Set discretization level",
      "topics": [
        "setDiscretization"
      ]
    },
    {
      "page": "summary.magioutput",
      "title": "Summary of parameter estimates from 'magioutput' object",
      "topics": [
        "summary.magioutput"
      ]
    },
    {
      "page": "testDynamicalModel",
      "title": "Test dynamic system model specification",
      "topics": [
        "testDynamicalModel"
      ]
    }
  ],
  "_readme": "https://github.com/cran/magi/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "cli",
    "deSolve",
    "glue",
    "gridBase",
    "gridExtra",
    "gtable",
    "lifecycle",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "roptim"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "magi-vignette.Rmd",
      "filename": "magi-vignette.html",
      "title": "magi-vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Basic usage example: Fitzhugh-Nagumo equations",
        "Example with an unobserved component and asynchronous observations: Hes1 system",
        "Example with time-dependency in ODE: HIV model with oscillating infection rate"
      ],
      "created": "2021-07-27 07:30:05",
      "modified": "2024-05-06 02:39:25",
      "commits": 3
    }
  ],
  "_score": 3.439332693830263,
  "_indexed": true,
  "_nocasepkg": "magi",
  "_universes": [
    "shihao-yang"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.5",
      "date": "2026-05-20T09:06:08.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "9553d3d86b55ebe4a5a6240032a7f77c144814758687f608a45098a64044a0e5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.5",
      "date": "2026-05-20T09:06:08.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "46e27bab6998d966006abe46a8a16245d70acd621538225da2f57b6971af0b3c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.5",
      "date": "2026-05-20T09:06:18.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "16386d14bb81c1962d9d1dd15dac5799018389af49bcdfc1da2a94f0636df65a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.5",
      "date": "2026-05-20T09:06:06.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "10e0117593d36aef5f61bf401b3d28f0feec28eb46c2d5983aafd1d71e654c98",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.5",
      "date": "2026-05-20T09:06:04.000Z",
      "arch": "aarch64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "3dce93047d83f431f542bc935bb906c292e4e69792c59bc93417991075db9e76",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.5",
      "date": "2026-05-20T09:07:32.000Z",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "5416331e0b5f544cd658780dc770dd038fd618801f57dc47dd86700834442679",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.5",
      "date": "2026-05-20T09:06:05.000Z",
      "arch": "aarch64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "90f4b31f9a4415622487ab673da9e9afa2cba65be48042d116f72ae04e4a384b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.5",
      "date": "2026-05-20T09:07:31.000Z",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "a4a4cb08688e12144422714f07c51b77b156f1c3a6012ce9be2d07e19c478152",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.5",
      "date": "2026-05-20T09:05:39.000Z",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "c17ddae5b3835c6955861c20468d4e27ad113b71b9b0c72caeaa5bb6f8bfc5bb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.5",
      "date": "2026-05-20T09:05:21.000Z",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "bd23fdde5cf8ce4fa9ace0758ba4c8421f778f54edae27ea1e9142288c2b2402",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2.5",
      "date": "2026-05-20T09:05:16.000Z",
      "arch": "x86_64",
      "commit": "c7529470be556a7027971d87ae7cb238ab80feaf",
      "fileid": "5d410afcb776fd694e2782ca2ec056433386d1dfe0f93d75d0b102152c12fd48",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/shihao-yang/actions/runs/26152249032"
    }
  ]
}