{
  "_id": "6a181cdbacfb0bcc41db1623",
  "Package": "LoopDetectR",
  "Type": "Package",
  "Title": "Comprehensive Feedback Loop Detection in ODE Models",
  "Version": "0.1.2",
  "Authors@R": "c(person(\"Katharina\", \"Baum\", email = \"katharina.baum@hpi.de\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7256-0566\")),\nperson(\"Sandra\", \"Krüger\", role = c(\"ctb\")))",
  "Description": "Detect feedback loops (cycles, circuits) between species\n(nodes) in ordinary differential equation (ODE) models.\nFeedback loops are paths from a node to itself without visiting\nany other node twice, and they have important regulatory\nfunctions. Loops are reported with their order of participating\nnodes and their length, and whether the loop is a positive or a\nnegative feedback loop. An upper limit of the number of\nfeedback loops limits runtime (which scales with feedback loop\ncount). Model parametrizations and values of the modelled\nvariables are accounted for. Computation uses the\ncharacteristics of the Jacobian matrix as described e.g. in\nThomas and Kaufman (2002) <doi:10.1016/s1631-0691(02)01452-x>.\nInput can be the Jacobian matrix of the ODE model or the ODE\nfunction definition; in the latter case, the Jacobian matrix is\ndetermined using 'numDeriv'. Graph-based algorithms from\n'igraph' are employed for path detection.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 10:42:04 UTC",
    "User": "root"
  },
  "Author": "Katharina Baum [aut, cre]\n(<https://orcid.org/0000-0001-7256-0566>), Sandra Krüger [ctb]",
  "Maintainer": "Katharina Baum <katharina.baum@hpi.de>",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://kathbaum.r-universe.dev",
  "Date/Publication": "2020-07-20 08:20:12 UTC",
  "RemoteUrl": "https://github.com/cran/LoopDetectR",
  "RemoteRef": "HEAD",
  "RemoteSha": "6018976168428d0d68cfe1755206b64d6b51cdf3",
  "MD5sum": "8db7731ba7a3ba7b28140da0a0128b03",
  "_user": "kathbaum",
  "_type": "src",
  "_file": "LoopDetectR_0.1.2.tar.gz",
  "_fileid": "f1a2a3045eae4b8f73d44ca88ac83ec07cf281cba8d4f883e54eaa40b6a254df",
  "_filesize": 392556,
  "_sha256": "f1a2a3045eae4b8f73d44ca88ac83ec07cf281cba8d4f883e54eaa40b6a254df",
  "_created": "2026-05-28T10:42:04.000Z",
  "_published": "2026-05-28T10:45:47.430Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78273955903,
      "time": 116,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7263836707"
    },
    {
      "job": 78273955835,
      "time": 116,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263836768"
    },
    {
      "job": 78273955871,
      "time": 186,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7263845590"
    },
    {
      "job": 78273955845,
      "time": 172,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263842961"
    },
    {
      "job": 78273484463,
      "time": 184,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263799169"
    },
    {
      "job": 78273955803,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263834152"
    },
    {
      "job": 78273955915,
      "time": 89,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7263828309"
    },
    {
      "job": 78273955872,
      "time": 71,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7263822706"
    },
    {
      "job": 78273955842,
      "time": 75,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263823862"
    }
  ],
  "_buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/LoopDetectR",
  "_commit": {
    "id": "6018976168428d0d68cfe1755206b64d6b51cdf3",
    "author": "Katharina Baum <katharina.baum@hpi.de>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.2\n",
    "time": 1595233212
  },
  "_maintainer": {
    "name": "Katharina Baum",
    "email": "katharina.baum@hpi.de",
    "login": "kathbaum",
    "description": "",
    "uuid": 84584704,
    "orcid": "0000-0001-7256-0566"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "numDeriv",
      "role": "Imports"
    },
    {
      "package": "deSolve",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "remotes",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "utils",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "kathbaum",
      "count": 1,
      "uuid": 84584704
    }
  ],
  "_userbio": {
    "uuid": 84584704,
    "type": "user",
    "name": "kathbaum"
  },
  "_downloads": {
    "count": 167,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/LoopDetectR"
  },
  "_searchresults": 1,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/LoopDetectR.html",
    "manual.pdf"
  ],
  "_realowner": "kathbaum",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.2",
      "date": "2020-07-20"
    }
  ],
  "_exports": [
    "compare_loop_list",
    "find_edge",
    "find_loops",
    "find_loops_noscc",
    "find_loops_vset",
    "loop_summary",
    "sort_loop_index"
  ],
  "_datasets": [
    {
      "name": "func_li08",
      "title": "Example ODE function: bacterial cell cycle.",
      "object": "func_li08",
      "class": [
        "function"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "func_POSm4",
      "title": "Example ODE function: chain model with positive regulation.",
      "object": "func_POSm4",
      "class": [
        "function"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "li08_solution",
      "title": "Solution for the cell cycle model related to func_li08",
      "object": "li08_solution",
      "class": [
        "data.frame"
      ],
      "fields": [
        "time",
        "y1",
        "y2",
        "y3",
        "y4",
        "y5",
        "y6",
        "y7",
        "y8",
        "y9",
        "y10",
        "y11",
        "y12",
        "y13",
        "y14",
        "y15",
        "y16",
        "y17",
        "y18"
      ],
      "rows": 634,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "compare_loop_list",
      "title": "Compare two loop lists",
      "topics": [
        "compare_loop_list"
      ]
    },
    {
      "page": "find_edge",
      "title": "Detecting loops with a certain edge",
      "topics": [
        "find_edge"
      ]
    },
    {
      "page": "find_loops",
      "title": "Loop detection in a matrix",
      "topics": [
        "find_loops"
      ]
    },
    {
      "page": "find_loops_noscc",
      "title": "Loop detection in a matrix",
      "topics": [
        "find_loops_noscc"
      ]
    },
    {
      "page": "find_loops_vset",
      "title": "Loop detection for an ODE model at multiple sets of variables",
      "topics": [
        "find_loops_vset"
      ]
    },
    {
      "page": "func_li08",
      "title": "Example ODE function: bacterial cell cycle.",
      "topics": [
        "func_li08"
      ]
    },
    {
      "page": "func_POSm4",
      "title": "Example ODE function: chain model with positive regulation.",
      "topics": [
        "func_POSm4"
      ]
    },
    {
      "page": "li08_solution",
      "title": "Solution for the cell cycle model related to func_li08",
      "topics": [
        "li08_solution"
      ]
    },
    {
      "page": "loop_summary",
      "title": "Summary of a loop list",
      "topics": [
        "loop_summary"
      ]
    },
    {
      "page": "sort_loop_index",
      "title": "Sort loop indices",
      "topics": [
        "sort_loop_index"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "glue",
    "igraph",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "numDeriv",
    "pkgconfig",
    "rlang",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "workflow_LoopDetectR.Rmd",
      "filename": "workflow_LoopDetectR.html",
      "title": "LoopDetectR: Comprehensive Feedback Loop Detection in ODE models",
      "author": "Katharina Baum",
      "engine": "knitr::knitr",
      "headings": [
        "Installation",
        "In brief and quick start",
        "Introduction",
        "Solving the ODE model to generate variable values of interest",
        "Calculating the Jacobian matrix",
        "Computing all feedback loops and useful functions for loop search",
        "Computing feedback loops over multiple sets of variable values of interest",
        "Comparing two loop lists",
        "References"
      ],
      "created": "2020-07-20 08:20:12",
      "modified": "2020-07-20 08:20:12",
      "commits": 1
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "loopdetectr",
  "_universes": [
    "kathbaum"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-28T10:44:06.000Z",
      "distro": "noble",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "b8c1ee566f607ef0ea76d0dcf9e2ff5b0080b01f46fc19be50ad8dba568ce5be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.2",
      "date": "2026-05-28T10:44:09.000Z",
      "distro": "noble",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "2e820c2c995d6381d5a9fb4ca11639c6a5bf25694f2078953f69ebf64cd36607",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-28T10:44:38.000Z",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "dcb1b25b1fc21cfb774ed983c5d5d6de52114dcaf82876c085086b5f9e1a7f15",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.2",
      "date": "2026-05-28T10:44:27.000Z",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "4ca93e62a5680b15e2138d44b704a64d15c1d23492f33828546651e004c05fe4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2",
      "date": "2026-05-28T10:44:12.000Z",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "5afcb04940369b197cccec53c5428eb51e57813697c95c2bca9276ef40722844",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-28T10:43:30.000Z",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "ec20b4c769c08d7798b9c88201fb1ee3ff76835f434497b5a4f3d8b6ca3de6c7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-28T10:43:19.000Z",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "26904b457141cfb791205bfa9e6dc5d6fd18488c05da1839eaa4579d16b398da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.2",
      "date": "2026-05-28T10:43:24.000Z",
      "commit": "6018976168428d0d68cfe1755206b64d6b51cdf3",
      "fileid": "ff551d2a17353643ba5a7c34e41527cd3df3c59a195acd2ab48638bc1bfb9981",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kathbaum/actions/runs/26569708394"
    }
  ]
}