{
  "_id": "6aed8440818c9e3ef6dc38a1",
  "Package": "r2sbml",
  "Type": "Package",
  "Title": "Read 'SBML' Models and Convert Them to Simulation Code",
  "Version": "0.1.1",
  "Authors@R": "c(\nperson(given = \"Satyaprakash\", family = \"Nayak\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"satyaprakash.nayak@gmail.com\"),\nperson(given = \"Sarah M.\", family = \"Keating\", role = \"ctb\",\ncomment = \"Author of 'libSBML' and of the example code adapted in src/convertReactions.cpp and src/getMath.cpp\"),\nperson(given = \"Frank T.\", family = \"Bergmann\", role = \"ctb\",\ncomment = \"Author of 'libSBML' and of the example code adapted in src/convertReactions.cpp and src/getMath.cpp\"),\nperson(given = \"Lucian P.\", family = \"Smith\", role = \"ctb\",\ncomment = \"Author of 'libSBML'\"),\nperson(given = \"Brett G.\", family = \"Olivier\", role = \"ctb\",\ncomment = \"Author of 'libSBML'\"),\nperson(given = \"Akiya\", family = \"Jouraku\", role = \"ctb\",\ncomment = \"Author of 'libSBML'\"),\nperson(given = \"Michael\", family = \"Hucka\", role = \"ctb\",\ncomment = \"Author of 'libSBML'\"),\nperson(given = \"Ben\", family = \"Bornstein\", role = \"ctb\",\ncomment = \"Author of 'libSBML'\"),\nperson(given = \"Jeroen\", family = \"Ooms\", role = \"ctb\",\ncomment = \"Windows build support\"),\nperson(given = \"California Institute of Technology\", role = \"cph\",\ncomment = \"Copyright holder of 'libSBML', 2002-2020\"),\nperson(given = \"EMBL European Bioinformatics Institute\", role = \"cph\",\ncomment = \"Copyright holder of 'libSBML', 2009-2018\"),\nperson(given = \"University of Heidelberg\", role = \"cph\",\ncomment = \"Copyright holder of 'libSBML', 2013-2020\"),\nperson(given = \"University College London\", role = \"cph\",\ncomment = \"Copyright holder of 'libSBML', 2020\"),\nperson(given = \"Japan Science and Technology Agency\", role = \"cph\",\ncomment = \"Copyright holder of 'libSBML', 2002-2005\"),\nperson(given = \"Gilles\", family = \"Vollant\", role = \"cph\",\ncomment = \"Author of MiniZip, bundled with 'libSBML'\"),\nperson(given = \"Mathias\", family = \"Svensson\", role = \"cph\",\ncomment = \"Contributor to MiniZip, bundled with 'libSBML'\"),\nperson(given = \"Even\", family = \"Rouault\", role = \"cph\",\ncomment = \"Contributor to MiniZip, bundled with 'libSBML'\"),\nperson(given = \"Nathan\", family = \"Moinvaziri\", role = \"cph\",\ncomment = \"Contributor to MiniZip, bundled with 'libSBML'\"),\nperson(given = \"Terry\", family = \"Thorsen\", role = \"cph\",\ncomment = \"Contributor to MiniZip, bundled with 'libSBML'\"),\nperson(given = \"Info-ZIP\", role = \"cph\",\ncomment = \"Copyright holder of encryption code in MiniZip, bundled with 'libSBML'\"),\nperson(given = \"Ludwig\", family = \"Schwardt\", role = \"cph\",\ncomment = \"Author of the zlib iostream wrappers bundled with 'libSBML'\"),\nperson(given = \"Kevin\", family = \"Ruland\", role = \"cph\",\ncomment = \"Author of the zlib iostream wrappers bundled with 'libSBML'\"),\nperson(given = \"M. Petra\", family = \"Baranski\", role = \"cph\",\ncomment = \"Author of 'maddy', bundled with 'libSBML'\"),\nperson(given = \"Tim\", family = \"Gromeyer\", role = \"cph\",\ncomment = \"Author of 'html2md', bundled with 'libSBML'\"))",
  "Description": "Reads models in the Systems Biology Markup Language\n('SBML') (Hucka et al. (2003)\n<doi:10.1093/bioinformatics/btg015>) through the bundled\n'libSBML' library (Bornstein et al. (2008)\n<doi:10.1093/bioinformatics/btn051>). Lists a model's species,\nparameters, compartments, reactions, rules, events and function\ndefinitions, and converts the model into ready-to-run\nsimulation code for 'deSolve', 'mrgsolve', 'rxode2', 'MATLAB',\n'Julia' or 'ubiquity'. Models are read, not modified.",
  "URL": "https://sn248.github.io/r2sbml/, https://github.com/sn248/r2sbml",
  "BugReports": "https://github.com/sn248/r2sbml/issues",
  "Encoding": "UTF-8",
  "Language": "en-GB",
  "License": "GPL (>=2)",
  "Copyright": "See file inst/COPYRIGHTS",
  "VignetteBuilder": "knitr",
  "Biarch": "TRUE",
  "SystemRequirements": "cmake, libxml2, libbz2",
  "Roxygen": "list(markdown = TRUE)",
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  "Config/pak/sysreqs": "cmake libbz2-dev libxml2-dev",
  "Repository": "https://sn248.r-universe.dev",
  "Date/Publication": "2026-11-06 03:49:38 UTC",
  "RemoteUrl": "https://github.com/sn248/r2sbml",
  "RemoteRef": "HEAD",
  "RemoteSha": "66a9f6cd208b14b4c28782dea2c76bfdcb912901",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-11-06 07:20:32 UTC",
    "User": "root"
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  "Author": "Satyaprakash Nayak [aut, cre, cph],\nSarah M. Keating [ctb] (Author of 'libSBML' and of the example code\nadapted in src/convertReactions.cpp and src/getMath.cpp),\nFrank T. Bergmann [ctb] (Author of 'libSBML' and of the example code\nadapted in src/convertReactions.cpp and src/getMath.cpp),\nLucian P. Smith [ctb] (Author of 'libSBML'),\nBrett G. Olivier [ctb] (Author of 'libSBML'),\nAkiya Jouraku [ctb] (Author of 'libSBML'),\nMichael Hucka [ctb] (Author of 'libSBML'),\nBen Bornstein [ctb] (Author of 'libSBML'),\nJeroen Ooms [ctb] (Windows build support),\nCalifornia Institute of Technology [cph] (Copyright holder of\n'libSBML', 2002-2020),\nEMBL European Bioinformatics Institute [cph] (Copyright holder of\n'libSBML', 2009-2018),\nUniversity of Heidelberg [cph] (Copyright holder of 'libSBML',\n2013-2020),\nUniversity College London [cph] (Copyright holder of 'libSBML', 2020),\nJapan Science and Technology Agency [cph] (Copyright holder of\n'libSBML', 2002-2005),\nGilles Vollant [cph] (Author of MiniZip, bundled with 'libSBML'),\nMathias Svensson [cph] (Contributor to MiniZip, bundled with 'libSBML'),\nEven Rouault [cph] (Contributor to MiniZip, bundled with 'libSBML'),\nNathan Moinvaziri [cph] (Contributor to MiniZip, bundled with\n'libSBML'),\nTerry Thorsen [cph] (Contributor to MiniZip, bundled with 'libSBML'),\nInfo-ZIP [cph] (Copyright holder of encryption code in MiniZip, bundled\nwith 'libSBML'),\nLudwig Schwardt [cph] (Author of the zlib iostream wrappers bundled\nwith 'libSBML'),\nKevin Ruland [cph] (Author of the zlib iostream wrappers bundled with\n'libSBML'),\nM. Petra Baranski [cph] (Author of 'maddy', bundled with 'libSBML'),\nTim Gromeyer [cph] (Author of 'html2md', bundled with 'libSBML')",
  "Maintainer": "Satyaprakash Nayak <satyaprakash.nayak@gmail.com>",
  "_user": "sn248",
  "_type": "src",
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  "_created": "2026-11-06T07:20:32.000Z",
  "_published": "2026-11-06T07:39:44.307Z",
  "_upstream": "https://github.com/sn248/r2sbml",
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    "extra/NEWS.html",
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  "_exports": [
    "convertReactions",
    "echoSBML",
    "getCmtNames",
    "getCmtSizes",
    "getEventMath",
    "getFunctionDefinition",
    "getModel",
    "getNumSpecies",
    "getParameterTable",
    "getReactionMath",
    "getReactionTable",
    "getRuleMath",
    "getSpeciesIC",
    "getSpeciesNames",
    "getSpeciesTable",
    "printSBML"
  ],
  "_help": [
    {
      "page": "convertReactions",
      "title": "Convert an SBML model to simulation code",
      "topics": [
        "convertReactions"
      ]
    },
    {
      "page": "echoSBML",
      "title": "Check an SBML file for errors",
      "topics": [
        "echoSBML"
      ]
    },
    {
      "page": "getCmtNames",
      "title": "Names of the compartments in a model",
      "topics": [
        "getCmtNames"
      ]
    },
    {
      "page": "getCmtSizes",
      "title": "Sizes of the compartments in a model",
      "topics": [
        "getCmtSizes"
      ]
    },
    {
      "page": "getEventMath",
      "title": "Print the events of a model",
      "topics": [
        "getEventMath"
      ]
    },
    {
      "page": "getFunctionDefinition",
      "title": "Print the function definitions of a model",
      "topics": [
        "getFunctionDefinition"
      ]
    },
    {
      "page": "getModel",
      "title": "Read an SBML model",
      "topics": [
        "getModel"
      ]
    },
    {
      "page": "getNumSpecies",
      "title": "Number of species in a model",
      "topics": [
        "getNumSpecies"
      ]
    },
    {
      "page": "getParameterTable",
      "title": "Table of the parameters in a model",
      "topics": [
        "getParameterTable"
      ]
    },
    {
      "page": "getReactionMath",
      "title": "Print the rate laws of a model",
      "topics": [
        "getReactionMath"
      ]
    },
    {
      "page": "getReactionTable",
      "title": "Table of the reactions in a model",
      "topics": [
        "getReactionTable"
      ]
    },
    {
      "page": "getRuleMath",
      "title": "Print the rules of a model",
      "topics": [
        "getRuleMath"
      ]
    },
    {
      "page": "getSpeciesIC",
      "title": "Initial values of the species in a model",
      "topics": [
        "getSpeciesIC"
      ]
    },
    {
      "page": "getSpeciesNames",
      "title": "Names of the species in a model",
      "topics": [
        "getSpeciesNames"
      ]
    },
    {
      "page": "getSpeciesTable",
      "title": "Table of the species in a model",
      "topics": [
        "getSpeciesTable"
      ]
    },
    {
      "page": "printSBML",
      "title": "Summarise an SBML file",
      "topics": [
        "printSBML"
      ]
    }
  ],
  "_pkglogo": "https://github.com/sn248/r2sbml/raw/HEAD/man/figures/logo.svg",
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      "title": "Getting started with r2sbml",
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      "headings": [
        "Reading a model",
        "Functions that return data",
        "Functions that print",
        "Absent components are an error, not an empty result",
        "Exporting mass balances",
        "What happens before anything is written",
        "The deSolve output",
        "The other five targets",
        "Model features that change the shape of the output",
        "Assignment rules",
        "Algebraic rules make the model a DAE",
        "Changing compartment volumes",
        "Practical notes",
        "Where to go next"
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      "created": "2026-08-02 14:48:50",
      "modified": "2026-10-18 14:41:35",
      "commits": 5
    },
    {
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      "filename": "limitations.html",
      "title": "Limitations and unimplemented behaviour",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "How far the output has been checked",
        "Scope: reading and exporting only",
        "Per-target capability matrix",
        "Algebraic rules",
        "Rules linear in one unknown become assignments",
        "Coupled or nonlinear rules become a DAE where the target can solve one",
        "The DAE path has three further limits",
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        "Values and names",
        "Values the model leaves undefined",
        "Ids the target reserves",
        "No validation is performed",
        "Quirks of the query functions",
        "Initial values are reported as the file states them",
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        "Where these are tracked"
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      "modified": "2026-10-18 15:45:09",
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