{
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  "Package": "scaRabee",
  "Type": "Package",
  "Title": "Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models",
  "Version": "1.1-5",
  "Date": "2026-01-25",
  "Authors@R": "person(\"Sebastien\",\"Bihorel\",role=c(\"aut\",\"cre\"),email=\"sb.pmlab@gmail.com\")",
  "Description": "A port of the Scarabee toolkit originally written as a\nMatlab-based application. scaRabee provides a framework for\nsimulation and optimization of pharmacokinetic-pharmacodynamic\nmodels at the individual and population level. It is built on\ntop of the neldermead package, which provides the direct search\nalgorithm proposed by Nelder and Mead for model optimization.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
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  "Packaged": {
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    "User": "root"
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  "Author": "Sebastien Bihorel [aut, cre]",
  "Maintainer": "Sebastien Bihorel <sb.pmlab@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-01-25 22:50:03 UTC",
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    "convert.infusion",
    "create.intervals",
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    "dde.syst",
    "de.output",
    "derived.parms",
    "estimation.plot",
    "explicit.model",
    "finalize.grid.report",
    "finalize.report",
    "fitmle",
    "fitmle.cov",
    "get.cov.matrix",
    "get.events",
    "get.layout",
    "get.parms.data",
    "get.secondary",
    "init.cond",
    "init.update",
    "initialize.report",
    "input.scaling",
    "make.dosing",
    "ode.model",
    "ode.syst",
    "order.parms.list",
    "pder",
    "problem.eval",
    "residual.report",
    "scarabee.analysis",
    "scarabee.check.model",
    "scarabee.check.reserved",
    "scarabee.clean",
    "scarabee.directory",
    "scarabee.gridsearch",
    "scarabee.new",
    "scarabee.read.data",
    "scarabee.read.model",
    "scarabee.read.parms",
    "simulation.plot",
    "simulation.report",
    "weighting"
  ],
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      "title": "Datasets for scaRabee demo.",
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        "TIME",
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        "RATE",
        "CMT",
        "EVID",
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        "DVID",
        "MDV",
        "DOSE"
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Datasets for scaRabee demo.",
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      "title": "Datasets for scaRabee demo.",
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    },
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      "title": "Datasets for scaRabee demo.",
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      "title": "Datasets for scaRabee demo.",
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  ],
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      "title": "scaRabee toolkit",
      "topics": [
        "scaRabee-package",
        "scaRabee"
      ]
    },
    {
      "page": "bound.parameters",
      "title": "Forces parameter estimates between defined boundaries.",
      "topics": [
        "bound.parameters"
      ]
    },
    {
      "page": "compute.secondary",
      "title": "Computes secondary parameter values",
      "topics": [
        "compute.secondary"
      ]
    },
    {
      "page": "convert.infusion",
      "title": "Process Infusion Information",
      "topics": [
        "convert.infusion"
      ]
    },
    {
      "page": "dde.model",
      "title": "Delay Differential Equations",
      "topics": [
        "dde.model"
      ]
    },
    {
      "page": "dde.utils",
      "title": "Utility Functions for Delay Differential Equation Systems",
      "topics": [
        "dde.lags",
        "dde.syst"
      ]
    },
    {
      "page": "estimation.plot",
      "title": "Create Summary Estimation Plots",
      "topics": [
        "estimation.plot"
      ]
    },
    {
      "page": "examples.data",
      "title": "Datasets for scaRabee demo.",
      "topics": [
        "example1.data",
        "example1.initials",
        "example2.data",
        "example2.initials",
        "example3.data",
        "example3.initials",
        "example4.data",
        "example4.initials",
        "example6.data",
        "example6.initials",
        "example8.data",
        "example8.initials"
      ]
    },
    {
      "page": "explicit.model",
      "title": "Explicit Equations",
      "topics": [
        "explicit.model"
      ]
    },
    {
      "page": "finalize.grid.report",
      "title": "Finalize Direct Grid Search Report",
      "topics": [
        "finalize.grid.report"
      ]
    },
    {
      "page": "finalize.report",
      "title": "Finalize Estimation Report",
      "topics": [
        "finalize.report"
      ]
    },
    {
      "page": "fitmle",
      "title": "Maximum Likelihood Estimator",
      "topics": [
        "fitmle"
      ]
    },
    {
      "page": "fitmle.cov",
      "title": "Computation of the Covariance Matrix",
      "topics": [
        "fitmle.cov"
      ]
    },
    {
      "page": "get.cov.matrix",
      "title": "Computation of the Covariance Matrix",
      "topics": [
        "get.cov.matrix"
      ]
    },
    {
      "page": "get.events",
      "title": "Create events from bolus dosing records.",
      "topics": [
        "get.events"
      ]
    },
    {
      "page": "get.layout",
      "title": "Layout for Lattice Functions",
      "topics": [
        "get.layout"
      ]
    },
    {
      "page": "get.parms.data",
      "title": "Extract data from scaRabee parameter table",
      "topics": [
        "get.parms.data"
      ]
    },
    {
      "page": "get.secondary",
      "title": "Computation of Secondary Parameter Estimates",
      "topics": [
        "get.secondary"
      ]
    },
    {
      "page": "initialize.report",
      "title": "Initialize Report Files",
      "topics": [
        "initialize.report"
      ]
    },
    {
      "page": "ode.model",
      "title": "Ordinary Differential Equations",
      "topics": [
        "ode.model"
      ]
    },
    {
      "page": "ode.utils",
      "title": "Utility Functions for Ordinary Differential Equation Systems",
      "topics": [
        "create.intervals",
        "de.output",
        "derived.parms",
        "init.cond",
        "init.update",
        "input.scaling",
        "make.dosing",
        "ode.syst"
      ]
    },
    {
      "page": "order.parms.list",
      "title": "Sort a scaRabee parameter table",
      "topics": [
        "order.parms.list"
      ]
    },
    {
      "page": "pder",
      "title": "Compute Matrix of Partial Derivatives",
      "topics": [
        "pder"
      ]
    },
    {
      "page": "problem.eval",
      "title": "Evaluation of structural and residual variability models",
      "topics": [
        "problem.eval"
      ]
    },
    {
      "page": "residual.report",
      "title": "Creation of Prediction & Residual Report",
      "topics": [
        "residual.report"
      ]
    },
    {
      "page": "scarabee.analysis",
      "title": "Run a scaRabee Analysis",
      "topics": [
        "scarabee.analysis"
      ]
    },
    {
      "page": "scarabee.check.model",
      "title": "Check scaRabee Models",
      "topics": [
        "scarabee.check.model"
      ]
    },
    {
      "page": "scarabee.check.reserved",
      "title": "Check for Reserved Variable Names",
      "topics": [
        "scarabee.check.reserved"
      ]
    },
    {
      "page": "scarabee.clean",
      "title": "Cleaning of the Run Directory",
      "topics": [
        "scarabee.clean"
      ]
    },
    {
      "page": "scarabee.directory",
      "title": "Creation of the Run Directory",
      "topics": [
        "scarabee.directory"
      ]
    },
    {
      "page": "scarabee.gridsearch",
      "title": "Direct Grid Search Utility",
      "topics": [
        "scarabee.gridsearch"
      ]
    },
    {
      "page": "scarabee.new",
      "title": "Create a scaRabee Analysis Folder",
      "topics": [
        "scarabee.new"
      ]
    },
    {
      "page": "scarabee.read.data",
      "title": "Read scaRabee Data File",
      "topics": [
        "scarabee.read.data"
      ]
    },
    {
      "page": "scarabee.read.model",
      "title": "Read scaRabee Model File",
      "topics": [
        "scarabee.read.model"
      ]
    },
    {
      "page": "scarabee.read.parms",
      "title": "Read scaRabee Parameter File",
      "topics": [
        "scarabee.read.parms"
      ]
    },
    {
      "page": "simulation.plot",
      "title": "Create Simulation Plots",
      "topics": [
        "simulation.plot"
      ]
    },
    {
      "page": "simulation.report",
      "title": "Simulations",
      "topics": [
        "simulation.report"
      ]
    },
    {
      "page": "weighting",
      "title": "Residual Variability",
      "topics": [
        "weighting"
      ]
    }
  ],
  "_readme": "https://github.com/cran/scaRabee/raw/HEAD/README.md",
  "_rundeps": [
    "deSolve",
    "lattice",
    "Matrix",
    "neldermead",
    "optimbase",
    "optimsimplex"
  ],
  "_vignettes": [
    {
      "source": "manual.Rmd",
      "filename": "manual.html",
      "title": "scaRabee: An R-based Tool for Model Simulation and Optimization in Pharmacometrics",
      "author": "Sebastien Bihorel",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Preliminary notice",
        "What's new?",
        "How to obtain scaRabee",
        "Installation and dependencies",
        "Credits",
        "Reporting bugs",
        "Analysis types",
        "Simulation",
        "Estimation",
        "Direct grid search",
        "Getting started",
        "Creation of a new analysis folder",
        "Creation of new models in an on-going analysis",
        "Editing of the data file",
        "Editing of the parameter file",
        "Editing of the model file",
        "$ANALYSIS",
        "$DERIVED",
        "$IC",
        "$SCALE",
        "$LAGS",
        "$ODE",
        "$DDE",
        "$OUTPUT",
        "$VARIANCE",
        "$SECONDARY",
        "Editing of the master scaRabee script",
        "Execution of the master scaRabee script",
        "Scope of analysis",
        "Design information",
        "Solvers of differential equations",
        "Implementation of dosing history for model defined with differential equations",
        "Implementation of dosing history for model defined with algebraic equations",
        "Analysis examples",
        "Example 1: Simulation of a model defined with algebraic equations at the population level",
        "Example 2: Simulation of inputs into a model defined with ordinary differential equations",
        "Example 3: Simulation of a model defined with ordinary differential equations at the population level",
        "Example 4: Simulation of a model defined with delay differential equations at the population level",
        "Example 5: Estimation of a model defined with algebraic equations at the",
        "Example 6: Simulation of a model defined with ordinary differential equations at the subject level",
        "Example 7: Estimation of a model defined with algebraic equations at the subject level",
        "Example 8: Direct grid search for a model defined with delay differential equations",
        "Network of scaRabee functions",
        "References"
      ],
      "created": "2022-02-04 12:00:02",
      "modified": "2026-01-25 22:50:03",
      "commits": 2
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "scarabee",
  "_universes": [
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      "version": "1.1-5",
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