{
  "_id": "6a2543874b233be19839a493",
  "Package": "simode",
  "Type": "Package",
  "Title": "Statistical Inference for Systems of Ordinary Differential\nEquations using Separable Integral-Matching",
  "Version": "1.2.0",
  "Authors@R": "c(\nperson(\"Itai\", \"Dattner\", email = \"idattner@stat.haifa.ac.il\", role = \"aut\"),\nperson(\"Rami\", \"Yaari\", email = \"ramiyaari@gmail.com\", role = c(\"aut\", \"cre\")))",
  "Description": "Implements statistical inference for systems of ordinary\ndifferential equations, that uses the integral-matching\ncriterion and takes advantage of the separability of\nparameters, in order to obtain initial parameter estimates for\nnonlinear least squares optimization. Dattner & Yaari (2018)\n<arXiv:1807.04202>. Dattner et al. (2017)\n<doi:10.1098/rsif.2016.0525>. Dattner & Klaassen (2015)\n<doi:10.1214/15-EJS1053>.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "R.rsp",
  "Repository": "https://ramiyaari.r-universe.dev",
  "Date/Publication": "2020-05-14 13:44:31 UTC",
  "RemoteUrl": "https://github.com/ramiyaari/simode",
  "RemoteRef": "HEAD",
  "RemoteSha": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-07 10:06:43 UTC",
    "User": "root"
  },
  "Author": "Itai Dattner [aut],\nRami Yaari [aut, cre]",
  "Maintainer": "Rami Yaari <ramiyaari@gmail.com>",
  "MD5sum": "c5b55ae1f4b79b0c212808a2e0b3137a",
  "_user": "ramiyaari",
  "_type": "src",
  "_file": "simode_1.2.0.tar.gz",
  "_fileid": "74cf5d74852e83d2484c07d28a30492bfca02c39f89e13e2f08a490ad1425065",
  "_filesize": 773201,
  "_sha256": "74cf5d74852e83d2484c07d28a30492bfca02c39f89e13e2f08a490ad1425065",
  "_created": "2026-06-07T10:06:43.000Z",
  "_published": "2026-06-07T10:10:15.552Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79950212358,
      "time": 179,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7463117068"
    },
    {
      "job": 79950212364,
      "time": 144,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7463112530"
    },
    {
      "job": 79950212359,
      "time": 182,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7463113602"
    },
    {
      "job": 79950212365,
      "time": 167,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7463112687"
    },
    {
      "job": 79950031741,
      "time": 165,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7463094917"
    },
    {
      "job": 79950212351,
      "time": 86,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7463105559"
    },
    {
      "job": 79950212373,
      "time": 158,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7463114290"
    },
    {
      "job": 79950212379,
      "time": 169,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7463115714"
    },
    {
      "job": 79950212378,
      "time": 150,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7463113243"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ramiyaari/simode",
  "_commit": {
    "id": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
    "author": "ramiyaari <41739638+ramiyaari@users.noreply.github.com>",
    "committer": "ramiyaari <41739638+ramiyaari@users.noreply.github.com>",
    "message": "updated version to 1.2.0\n",
    "time": 1589463871
  },
  "_maintainer": {
    "name": "Rami Yaari",
    "email": "ramiyaari@gmail.com",
    "login": "ramiyaari",
    "description": "",
    "uuid": 41739638
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "quadprog",
      "role": "Imports"
    },
    {
      "package": "pracma",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "Rcgmin",
      "role": "Suggests"
    },
    {
      "package": "Rvmmin",
      "role": "Suggests"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "ramiyaari",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "ramiyaari",
      "count": 61,
      "uuid": 41739638
    },
    {
      "user": "mjsottile",
      "count": 1,
      "uuid": 131691
    }
  ],
  "_userbio": {
    "uuid": 41739638,
    "type": "user",
    "name": "ramiyaari"
  },
  "_downloads": {
    "count": 150,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/simode"
  },
  "_devurl": "https://github.com/ramiyaari/simode",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/simode.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ramiyaari/simode",
  "_realowner": "ramiyaari",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2018-08-02"
    },
    {
      "version": "1.0.2",
      "date": "2018-08-06"
    },
    {
      "version": "1.1.0",
      "date": "2018-10-04"
    },
    {
      "version": "1.1.1",
      "date": "2018-10-05"
    },
    {
      "version": "1.1.2",
      "date": "2019-01-21"
    },
    {
      "version": "1.1.4",
      "date": "2019-04-26"
    },
    {
      "version": "1.1.5",
      "date": "2019-09-29"
    },
    {
      "version": "1.1.6",
      "date": "2019-10-01"
    },
    {
      "version": "1.1.8",
      "date": "2019-12-01"
    },
    {
      "version": "1.1.9",
      "date": "2020-05-14"
    },
    {
      "version": "1.2.0",
      "date": "2020-05-14"
    },
    {
      "version": "1.2.2",
      "date": "2024-02-16"
    }
  ],
  "_exports": [
    "plot_trace",
    "simode",
    "simode.control",
    "solve_ode",
    "solve_ode2"
  ],
  "_datasets": [
    {
      "name": "sir_example",
      "title": "Example dataset for a multi-group SIR model",
      "object": "sir_example",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "confint.profile.simode",
      "title": "Calculates confidence intervals for the model parameters",
      "topics": [
        "confint.profile.simode"
      ]
    },
    {
      "page": "plot_trace",
      "title": "Plot optimization trace of a call to 'simode'",
      "topics": [
        "plot_trace"
      ]
    },
    {
      "page": "plot.confint.simode",
      "title": "Plot confidence intervals for the model parameters",
      "topics": [
        "plot.confint.simode"
      ]
    },
    {
      "page": "plot.list.simode",
      "title": "Plot the fit/estimates of a 'list.simode' object",
      "topics": [
        "plot.list.simode"
      ]
    },
    {
      "page": "plot.profile.simode",
      "title": "Plot the likelihood profiles for the model parameters",
      "topics": [
        "plot.profile.simode"
      ]
    },
    {
      "page": "plot.simode",
      "title": "Plot the fit/estimates of a 'simode' object",
      "topics": [
        "plot.simode"
      ]
    },
    {
      "page": "print.confint.simode",
      "title": "Print method for 'confint.simode' objects",
      "topics": [
        "print.confint.simode"
      ]
    },
    {
      "page": "print.profile.simode",
      "title": "Print method for 'profile.simode' objects",
      "topics": [
        "print.profile.simode"
      ]
    },
    {
      "page": "print.simode",
      "title": "Print method for 'simode' objects",
      "topics": [
        "print.simode"
      ]
    },
    {
      "page": "print.summary.simode",
      "title": "Print method for 'summary.simode' objects",
      "topics": [
        "print.summary.simode"
      ]
    },
    {
      "page": "profile.simode",
      "title": "Calculate likelihood profiles for the model parameters",
      "topics": [
        "profile.simode"
      ]
    },
    {
      "page": "simode",
      "title": "Statistical inference of ordinary differential equations using separable integral-matching",
      "topics": [
        "simode"
      ]
    },
    {
      "page": "simode.control",
      "title": "Class containing control parameters for a call to 'simode'",
      "topics": [
        "simode.control"
      ]
    },
    {
      "page": "sir_example",
      "title": "Example dataset for a multi-group SIR model",
      "topics": [
        "sir_example"
      ]
    },
    {
      "page": "solve_ode",
      "title": "Ordinary differential equations solver",
      "topics": [
        "solve_ode"
      ]
    },
    {
      "page": "solve_ode2",
      "title": "Ordinary differential equations solver using a 'simode' object",
      "topics": [
        "solve_ode2"
      ]
    },
    {
      "page": "summary.list.simode",
      "title": "Summary method for 'list.simode' objects",
      "topics": [
        "summary.list.simode"
      ]
    },
    {
      "page": "summary.simode",
      "title": "Summary method for 'simode' objects",
      "topics": [
        "summary.simode"
      ]
    }
  ],
  "_readme": "https://github.com/ramiyaari/simode/raw/HEAD/README.md",
  "_rundeps": [
    "deSolve",
    "pracma",
    "quadprog"
  ],
  "_vignettes": [
    {
      "source": "R_package_simode.pdf.asis",
      "filename": "R_package_simode.pdf",
      "title": "simode: Statistical inference of ODEs using separable integral-matching",
      "engine": "R.rsp::asis",
      "headings": [],
      "created": "2019-01-21 10:52:18",
      "modified": "2019-01-21 10:52:18",
      "commits": 1
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "simode",
  "_universes": [
    "ramiyaari"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:44.000Z",
      "distro": "noble",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "1aca522ecc063a4769f90b0a313b7b14869e96108a2c0f36e56211da8e45ef7d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:25.000Z",
      "distro": "noble",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "ccc6b21c49ba23e3da6cd59a4f45219e34596c5b187414ad80c82a24e278225d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:45.000Z",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "ac9f14d6791f58e0495a9379475ad8ee0ae0ce2ef0548eb06d60632d030c7d3f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:38.000Z",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "da6fd87d270041090afc899ff71b088be1cd4d1675a1fefd6f1bf7caa8093b6a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:26.000Z",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "e25f1bf1089e5f782dfcf72f669772f2922f2cb998b6a6deff27bf8be889a3e0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:00.000Z",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "fc2fc44552f3224128bce7990cc949c3df0d74cbf3c787fe4dbd70661be80766",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-06-07T10:08:25.000Z",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "69060fb50f32b15a726d65847a0e522937a344fbfa84c8fd64afc8f6a47c5cb2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-06-07T10:07:52.000Z",
      "commit": "a8ac4343abe4cf6b1c6df5e720a92a061d7bfddd",
      "fileid": "b41377902955b3b745e0c7f8198c29ebe83f4cb4fa2acc3d769e8a53543be91b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ramiyaari/actions/runs/27089397830"
    }
  ]
}