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  "Title": "Dynamic Modeling and Parameter Estimation in ODE Models",
  "Version": "2026.06.9000",
  "Date": "2026-06-06",
  "Author": "Daniel Kaschek",
  "Maintainer": "Daniel Kaschek <daniel.kaschek@gmail.com>",
  "Description": "The framework provides functions to generate ODEs of\nreaction networks, parameter transformations, observation\nfunctions, residual functions, etc. The framework follows the\nparadigm that derivative information should be used for\noptimization whenever possible. Therefore, all major functions\nproduce and can handle expressions for symbolic derivatives.",
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    "controls<-",
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    "covariates",
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    "getSteps",
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    "insert",
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    "is.parframe",
    "lbind",
    "load.parlist",
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    "mname",
    "modelname",
    "modelname<-",
    "msParframe",
    "mstrust",
    "mutatedMod.frame",
    "nll",
    "normL2",
    "nullZ",
    "objframe",
    "objlist",
    "obsfn",
    "odemodel",
    "P",
    "parfn",
    "parframe",
    "parlist",
    "parvec",
    "Pexpl",
    "Pimpl",
    "plotCombined",
    "plotData",
    "plotFluxes",
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    "plotPaths",
    "plotPrediction",
    "plotProfile",
    "plotResiduals",
    "plotValues",
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    "prdlist",
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    "profile",
    "progressBar",
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    "scale_fill_dMod",
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    "wide2long.list",
    "wide2long.matrix",
    "write.eqnlist",
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    "Xf",
    "Xs",
    "Xt",
    "Y"
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        "sigma",
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      "table": true,
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      "title": "Concatenation of functions",
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        "prodfn"
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    {
      "page": "grapes-.-times-grapes",
      "title": "Multiplication of objective functions with scalars",
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    {
      "page": "plus-.fn",
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        "sumfn"
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    {
      "page": "plus-.objfn",
      "title": "Direct sum of objective functions",
      "topics": [
        "+.objfn",
        "sumobjfn"
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    },
    {
      "page": "plus-.objlist",
      "title": "Add two lists element by element",
      "topics": [
        "+.objlist",
        "sumobjlist"
      ]
    },
    {
      "page": "addReaction",
      "title": "Add reaction to reaction table",
      "topics": [
        "addReaction"
      ]
    },
    {
      "page": "appendObj",
      "title": "Append an objective function to a basic dMod.frame",
      "topics": [
        "appendObj"
      ]
    },
    {
      "page": "appendParframes",
      "title": "Make a column \"parframes\" out of \"fits\"",
      "topics": [
        "appendParframes"
      ]
    },
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      "page": "as.data.frame.dMod",
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        "as.data.frame.prdlist"
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    },
    {
      "page": "as.data.frame.eqnlist",
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      "topics": [
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    },
    {
      "page": "as.eqnvec",
      "title": "Coerce to an equation vector",
      "topics": [
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        "as.eqnvec.character",
        "as.eqnvec.eqnlist"
      ]
    },
    {
      "page": "as.eventlist",
      "title": "Coerce to eventlist",
      "topics": [
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        "as.eventlist.data.frame",
        "as.eventlist.list"
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    },
    {
      "page": "as.objlist",
      "title": "Generate objective list from numeric vector",
      "topics": [
        "as.objlist"
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    },
    {
      "page": "as.parframe",
      "title": "Coerce object to a parameter frame",
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        "as.parframe.parlist"
      ]
    },
    {
      "page": "as.parvec.parframe",
      "title": "Select a parameter vector from a parameter frame.",
      "topics": [
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      ]
    },
    {
      "page": "attrs",
      "title": "Select attributes.",
      "topics": [
        "attrs"
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    },
    {
      "page": "BAdata",
      "title": "Time-course data for the Bile Acid model The dataset used in the dMod publication: Kaschek D, Mader W, Fehling-Kaschek M, Rosenblatt M, Timmer J. Dynamic modeling, parameter estimation, and uncertainty analysis in R.  Journal of Statistical Software. 2019 Apr 30;88:1-32.",
      "topics": [
        "BAdata"
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    },
    {
      "page": "blockdiagSymb",
      "title": "Embed two matrices into one blockdiagonal matrix",
      "topics": [
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      ]
    },
    {
      "page": "build_est.grid",
      "title": "Build the est.grid from prd, fixed.grid, conditional and condition.grid",
      "topics": [
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    },
    {
      "page": "check_cond",
      "title": "Do some consistency checks on conditional and condition.grid",
      "topics": [
        "check_cond"
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    },
    {
      "page": "check_grids",
      "title": "Some consistency checks for fixed.grid and est.grid",
      "topics": [
        "check_grids"
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    },
    {
      "page": "checkout_hypothesis",
      "title": "Load one row of a dMod.frame into the .GlobalEnv",
      "topics": [
        "checkout_hypothesis"
      ]
    },
    {
      "page": "combine",
      "title": "Combine several data.frames by rowbind",
      "topics": [
        "combine"
      ]
    },
    {
      "page": "compare",
      "title": "Compare two objects and return differences",
      "topics": [
        "compare",
        "compare.character",
        "compare.data.frame",
        "compare.eqnvec",
        "compare.list"
      ]
    },
    {
      "page": "compile",
      "title": "Compile one or more prdfn, obsfn or parfn objects",
      "topics": [
        "compile"
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    },
    {
      "page": "confint.parframe",
      "title": "Profile uncertainty extraction",
      "topics": [
        "confint.parframe"
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    },
    {
      "page": "conservedQuantities",
      "title": "Determine conserved quantites by finding the kernel of the stoichiometric matrix",
      "topics": [
        "conservedQuantities"
      ]
    },
    {
      "page": "constraintExp2",
      "title": "Compute a differentiable box prior",
      "topics": [
        "constraintExp2"
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    },
    {
      "page": "constraintL2",
      "title": "Soft L2 constraint on parameters",
      "topics": [
        "constraintL2"
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    },
    {
      "page": "controls",
      "title": "List, get and set controls for different functions",
      "topics": [
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        "controls.fn",
        "controls.objfn",
        "controls<-",
        "controls<-.fn",
        "controls<-.objfn"
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    },
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      "page": "coordTransform",
      "title": "Coordinate transformation for data frames",
      "topics": [
        "coordTransform"
      ]
    },
    {
      "page": "covariates",
      "title": "Access the covariates in the data",
      "topics": [
        "covariates",
        "covariates.data.frame",
        "covariates.datalist",
        "covariates.tbl_df"
      ]
    },
    {
      "page": "createExample",
      "title": "Open a unit test template.",
      "topics": [
        "createExample"
      ]
    },
    {
      "page": "datalist",
      "title": "Generate a datalist object",
      "topics": [
        "as.datalist",
        "as.datalist.data.frame",
        "as.datalist.list",
        "c.datalist",
        "datalist",
        "is.datalist",
        "names<-.datalist"
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    },
    {
      "page": "datapointL2",
      "title": "L2 objective function for validation data point",
      "topics": [
        "datapointL2"
      ]
    },
    {
      "page": "define",
      "title": "Define parameter transformations by 'define()', 'branch()' and 'insert()'",
      "topics": [
        "branch",
        "define",
        "insert"
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    },
    {
      "page": "dMod.frame",
      "title": "Generate a dMod.frame",
      "topics": [
        "dMod.frame"
      ]
    },
    {
      "page": "dot",
      "title": "Symbolic time derivative of equation vector given an equation list",
      "topics": [
        "dot"
      ]
    },
    {
      "page": "eqnlist",
      "title": "Generate eqnlist object",
      "topics": [
        "as.eqnlist",
        "as.eqnlist.data.frame",
        "eqnlist",
        "is.eqnlist"
      ]
    },
    {
      "page": "eqnvec",
      "title": "Generate equation vector object",
      "topics": [
        "eqnvec",
        "is.eqnvec"
      ]
    },
    {
      "page": "eventlist",
      "title": "Eventlist",
      "topics": [
        "addEvent",
        "eventlist"
      ]
    },
    {
      "page": "exmpextr",
      "title": "Extract an example from a unit test file.",
      "topics": [
        "exmpextr"
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    },
    {
      "page": "expand.grid.alt",
      "title": "Alternative version of expand.grid",
      "topics": [
        "expand.grid.alt"
      ]
    },
    {
      "page": "extractExamples",
      "title": "Extract example from unit tests.",
      "topics": [
        "extractExamples"
      ]
    },
    {
      "page": "fitErrorModel",
      "title": "Fit an error model",
      "topics": [
        "fitErrorModel"
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    },
    {
      "page": "forcingsSymb",
      "title": "Return some useful forcing functions as strings",
      "topics": [
        "forcingsSymb"
      ]
    },
    {
      "page": "format.eqnvec",
      "title": "Encode equation vector in format with sufficient spaces",
      "topics": [
        "format.eqnvec"
      ]
    },
    {
      "page": "funC0",
      "title": "Evaluation of algebraic expressions defined by characters",
      "topics": [
        "funC0"
      ]
    },
    {
      "page": "getCoefficients",
      "title": "Get coefficients from a character",
      "topics": [
        "getCoefficients"
      ]
    },
    {
      "page": "getConditions",
      "title": "Extract the conditions of an object",
      "topics": [
        "getConditions",
        "getConditions.fn",
        "getConditions.list",
        "getConditions.tbl_df"
      ]
    },
    {
      "page": "getDerivs",
      "title": "Extract the derivatives of an object",
      "topics": [
        "getDerivs",
        "getDerivs.list",
        "getDerivs.objlist",
        "getDerivs.parvec",
        "getDerivs.prdframe",
        "getDerivs.prdlist"
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    },
    {
      "page": "getElements",
      "title": "Get Symbols and Numeric constants from a character",
      "topics": [
        "getElements"
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    },
    {
      "page": "getEquations",
      "title": "Extract the equations of an object",
      "topics": [
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        "getEquations.fn",
        "getEquations.odemodel",
        "getEquations.prdfn"
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    },
    {
      "page": "getFluxes",
      "title": "Generate list of fluxes from equation list",
      "topics": [
        "getFluxes"
      ]
    },
    {
      "page": "getLocalDLLs",
      "title": "Determine loaded DLLs available in working directory",
      "topics": [
        "getLocalDLLs"
      ]
    },
    {
      "page": "getObservables",
      "title": "Extract the observables of an object",
      "topics": [
        "getObservables",
        "getObservables.tbl_df"
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    },
    {
      "page": "getParameters",
      "title": "Extract the parameters of an object",
      "topics": [
        "getParameters",
        "getParameters_dispatch",
        "getParameters_dispatch.eqnlist",
        "getParameters_dispatch.eventlist",
        "getParameters_dispatch.fn",
        "getParameters_dispatch.odemodel",
        "getParameters_dispatch.parvec",
        "getParameters_dispatch.prdframe",
        "getParameters_dispatch.prdlist"
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    {
      "page": "getParameters_est.grid",
      "title": "Extract parameter names from est.grid",
      "topics": [
        "getParameters_est.grid"
      ]
    },
    {
      "page": "getReactions",
      "title": "Generate a table of reactions (data.frame) from an equation list",
      "topics": [
        "getReactions"
      ]
    },
    {
      "page": "getStepIndices",
      "title": "Get the indices of the n largest (not necessarily best) steps of a parframe",
      "topics": [
        "getStepIndices"
      ]
    },
    {
      "page": "getSteps",
      "title": "Get the rows of the n largest steps of a parframe",
      "topics": [
        "getSteps"
      ]
    },
    {
      "page": "ggopen",
      "title": "Open last plot in external pdf viewer",
      "topics": [
        "ggopen"
      ]
    },
    {
      "page": "ginv",
      "title": "Generalized Inverse of a Matrix",
      "concept": [
        "Auxiliary"
      ],
      "topics": [
        "ginv"
      ]
    },
    {
      "page": "Id",
      "title": "An identity function which vanishes upon concatenation of fns",
      "topics": [
        "Id"
      ]
    },
    {
      "page": "init_empty_objlist",
      "title": "Create an objlist with zeros as entries",
      "topics": [
        "init_empty_objlist"
      ]
    },
    {
      "page": "jakstat",
      "title": "Time-course data for the JAK-STAT cell signaling pathway",
      "topics": [
        "jakstat"
      ]
    },
    {
      "page": "lbind",
      "title": "Bind named list of data.frames into one data.frame",
      "topics": [
        "lbind"
      ]
    },
    {
      "page": "load.parlist",
      "title": "Construct fitlist from temporary files.",
      "topics": [
        "load.parlist"
      ]
    },
    {
      "page": "loadDLL",
      "title": "Load shared object for a dMod object",
      "topics": [
        "loadDLL"
      ]
    },
    {
      "page": "long2wide",
      "title": "Translate long to wide format (inverse of wide2long.matrix)",
      "topics": [
        "long2wide"
      ]
    },
    {
      "page": "lsdMod",
      "title": "Print list of dMod objects in .GlobalEnv",
      "topics": [
        "lsdMod"
      ]
    },
    {
      "page": "make_pars",
      "title": "Extract individualized parameters for one ID",
      "topics": [
        "make_pars"
      ]
    },
    {
      "page": "match.fnargs",
      "title": "dMod match function arguments",
      "topics": [
        "match.fnargs"
      ]
    },
    {
      "page": "mname",
      "title": "Get modelname from single object (used internally)",
      "topics": [
        "mname",
        "mname.character",
        "mname.fn",
        "mname.NULL",
        "mname.objfn"
      ]
    },
    {
      "page": "modelname",
      "title": "Get and set modelname",
      "topics": [
        "modelname",
        "modelname<-",
        "modelname<-.fn",
        "modelname<-.objfn"
      ]
    },
    {
      "page": "msParframe",
      "title": "Reproducibly construct \"random\" parframes",
      "topics": [
        "msParframe"
      ]
    },
    {
      "page": "mstrust",
      "title": "Non-Linear Optimization, multi start",
      "topics": [
        "mstrust"
      ]
    },
    {
      "page": "mutatedMod.frame",
      "title": "A version of dplyr::mutate",
      "topics": [
        "mutatedMod.frame"
      ]
    },
    {
      "page": "nll",
      "title": "Compute the negative log-likelihood",
      "topics": [
        "nll"
      ]
    },
    {
      "page": "nll_ALOQ",
      "title": "Non-linear log likelihood for the ALOQ part of the data",
      "topics": [
        "nll_ALOQ"
      ]
    },
    {
      "page": "nll_BLOQ",
      "title": "Non-linear log likelihood for the BLOQ part of the data",
      "topics": [
        "nll_BLOQ"
      ]
    },
    {
      "page": "normL2",
      "title": "L2 norm between data and model prediction",
      "topics": [
        "normIndiv",
        "normL2"
      ]
    },
    {
      "page": "nullZ",
      "title": "Find integer-null space of matrix A",
      "topics": [
        "nullZ"
      ]
    },
    {
      "page": "objframe",
      "title": "Objective frame",
      "topics": [
        "objframe"
      ]
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    {
      "page": "objlist",
      "title": "Generate objective list",
      "topics": [
        "objlist"
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    {
      "page": "obsfn",
      "title": "Observation function",
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        "obsfn"
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      "page": "odemodel",
      "title": "Generate the model objects for use in Xs (models with sensitivities)",
      "topics": [
        "odemodel"
      ]
    },
    {
      "page": "P",
      "title": "Generate a parameter transformation function",
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        "P"
      ]
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    {
      "page": "parfn",
      "title": "Parameter transformation function",
      "topics": [
        "parfn"
      ]
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    {
      "page": "parframe",
      "title": "Generate a parameter frame",
      "topics": [
        "is.parframe",
        "parframe",
        "subset.parframe",
        "[.parframe"
      ]
    },
    {
      "page": "parlist",
      "title": "Parameter list",
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        "as.parlist",
        "c.parlist",
        "parlist",
        "summary.parlist"
      ]
    },
    {
      "page": "parvec",
      "title": "Parameter vector",
      "topics": [
        "as.parvec",
        "as.parvec.numeric",
        "c.parvec",
        "parvec",
        "[.parvec"
      ]
    },
    {
      "page": "Pexpl",
      "title": "Parameter transformation",
      "topics": [
        "Pexpl"
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      "page": "Pimpl",
      "title": "Parameter transformation (implicit)",
      "topics": [
        "Pimpl"
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    {
      "page": "plot.datalist",
      "title": "Plot a list data points",
      "topics": [
        "plot.datalist"
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    {
      "page": "plot.parlist",
      "title": "Plot a parameter list.",
      "topics": [
        "plot.parlist"
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    {
      "page": "plotCombined",
      "title": "Plot a list of model predictions and a list of data points in a combined plot",
      "topics": [
        "plot.prdframe",
        "plot.prdlist",
        "plotCombined",
        "plotCombined.prdlist",
        "plotCombined.tbl_df"
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    {
      "page": "plotData",
      "title": "Plot a list data points",
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        "plotData",
        "plotData.data.frame",
        "plotData.datalist",
        "plotData.tbl_df"
      ]
    },
    {
      "page": "plotFluxes",
      "title": "Plot Fluxes given a list of flux Equations",
      "topics": [
        "plotFluxes"
      ]
    },
    {
      "page": "plotPars",
      "title": "Plot parameter values for a fitlist",
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        "plotPars.parframe",
        "plotPars.tbl_df"
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      "page": "plotPaths",
      "title": "Profile likelihood: plot of the parameter paths.",
      "topics": [
        "plotPaths",
        "plotPaths.list",
        "plotPaths.parframe",
        "plotPaths.tbl_df"
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      "page": "plotPrediction",
      "title": "Plot a list of model predictions",
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        "plotPrediction.prdlist",
        "plotPrediction.tbl_df"
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      "page": "plotProfile",
      "title": "Profile likelihood plot",
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        "plotProfile.list",
        "plotProfile.parframe",
        "plotProfile.tbl_df"
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    {
      "page": "plotResiduals",
      "title": "Plot residuals for a fitlist",
      "topics": [
        "plotResiduals"
      ]
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    {
      "page": "plotValues",
      "title": "Plotting objective values of a collection of fits",
      "topics": [
        "plotValues",
        "plotValues.parframe",
        "plotValues.tbl_df"
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    {
      "page": "prdfn",
      "title": "Prediction function",
      "topics": [
        "prdfn"
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      "page": "prdframe",
      "title": "Prediction frame",
      "topics": [
        "prdframe"
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      "page": "prdlist",
      "title": "Prediction list",
      "topics": [
        "as.prdlist",
        "as.prdlist.list",
        "prdlist"
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      "page": "predict.prdfn",
      "title": "Model Predictions",
      "topics": [
        "predict.prdfn"
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    {
      "page": "print.eqnlist",
      "title": "Print or pander equation list",
      "topics": [
        "print.eqnlist"
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    {
      "page": "print.eqnvec",
      "title": "Print equation vector",
      "topics": [
        "print.eqnvec"
      ]
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    {
      "page": "print.parfn",
      "title": "Pretty printing parameter transformations",
      "topics": [
        "print.parfn"
      ]
    },
    {
      "page": "print.parvec",
      "title": "Pretty printing for a parameter vector",
      "topics": [
        "print.parvec"
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    {
      "page": "print0",
      "title": "Print object and its \"default\" attributes only.",
      "topics": [
        "print0"
      ]
    },
    {
      "page": "priorL2",
      "title": "L2 objective function for prior value",
      "topics": [
        "priorL2"
      ]
    },
    {
      "page": "profile",
      "title": "Profile-likelihood (PL) computation",
      "topics": [
        "profile"
      ]
    },
    {
      "page": "progressBar",
      "title": "Progress bar",
      "topics": [
        "progressBar"
      ]
    },
    {
      "page": "reduceReplicates",
      "title": "Reduce replicated measurements to mean and standard deviation",
      "topics": [
        "reduceReplicates"
      ]
    },
    {
      "page": "rename_objlist",
      "title": "Rename the derivatives of an objective function according to a lookup table",
      "topics": [
        "rename_objlist"
      ]
    },
    {
      "page": "repar",
      "title": "Reparameterization",
      "topics": [
        "repar"
      ]
    },
    {
      "page": "res",
      "title": "Compare data and model prediction by computing residuals",
      "concept": [
        "dMod interface"
      ],
      "topics": [
        "res"
      ]
    },
    {
      "page": "resolveRecurrence",
      "title": "Place top elements into bottom elemens",
      "topics": [
        "resolveRecurrence"
      ]
    },
    {
      "page": "rref",
      "title": "Transform matrix A into reduced row echelon form this function is written along the lines of the rref-matlab function.",
      "topics": [
        "rref"
      ]
    },
    {
      "page": "scale_color_dMod",
      "title": "Standard dMod color palette",
      "topics": [
        "scale_color_dMod"
      ]
    },
    {
      "page": "scale_fill_dMod",
      "title": "Standard dMod color scheme",
      "topics": [
        "scale_fill_dMod"
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    {
      "page": "stat.parlist",
      "title": "Gather statistics of a fitlist",
      "topics": [
        "stat.parlist"
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      "page": "strelide",
      "title": "Elide character vector",
      "topics": [
        "strelide"
      ]
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      "page": "strpad",
      "title": "Pad string to desired width",
      "topics": [
        "strpad"
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    {
      "page": "submatrix",
      "title": "Submatrix of a matrix returning ALWAYS a matrix",
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        "submatrix"
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      "page": "subset.eqnlist",
      "title": "subset of an equation list",
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      "page": "summary.eqnvec",
      "title": "Summary of an equation vector",
      "topics": [
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      "page": "theme_dMod",
      "title": "Standard plotting theme of dMod",
      "topics": [
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      "page": "trust",
      "title": "Non-Linear Optimization",
      "topics": [
        "trust",
        "trustL1"
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    {
      "page": "unique.parframe",
      "title": "Extract those lines of a parameter frame with unique elements in the value column",
      "topics": [
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    },
    {
      "page": "vcov",
      "title": "Get variance-covariance matrix from trust result",
      "topics": [
        "vcov"
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    {
      "page": "wide2long",
      "title": "Translate wide output format (e.g. from ode) into long format",
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        "wide2long"
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      "page": "wide2long.data.frame",
      "title": "Translate wide output format (e.g. from ode) into long format",
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      "page": "wide2long.list",
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      "page": "Xd",
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      "title": "Model prediction function for ODE models.",
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      "page": "Xt",
      "title": "Generate a prediction function that returns times",
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        "Xt"
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      "title": "Observation functions.",
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      "source": "concatenation.Rmd",
      "filename": "concatenation.html",
      "title": "The Operators + and * in dMod",
      "author": "Daniel Kaschek",
      "engine": "knitr::rmarkdown",
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        "Using the * operator",
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        "Less common example"
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      "created": "2018-11-26 21:47:15",
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    {
      "source": "dMod.Rmd",
      "filename": "dMod.html",
      "title": "Dynamic Modeling and Parameter Estimation with dMod",
      "author": "Daniel Kaschek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example 1: The JAK-STAT signaling pathway",
        "Load framework",
        "Prediction and forward simulation",
        "Model definition",
        "Prediction and observation functions",
        "Parameter transformations",
        "Parameter estimation",
        "Preparing the data",
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        "Fitting the data",
        "Exporing the parameter space",
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      "source": "event_estimation.Rmd",
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      "headings": [
        "Required libraries",
        "Setting up the model",
        "Simulation of data",
        "Estimation",
        "Evaluation"
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      "created": "2018-11-14 18:42:20",
      "modified": "2026-06-07 09:57:27",
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    {
      "source": "getFunctions.Rmd",
      "filename": "getFunctions.html",
      "title": "Accessing Information in dMod Objects",
      "author": "Daniel Kaschek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Extract equations with getEquations",
        "Extract derivative information with getDerivs",
        "Extract parameters with getParameters",
        "Changing options of dMod objects",
        "Conclusion"
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      "created": "2018-11-14 22:39:16",
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    {
      "source": "lists.Rmd",
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        "prdlist",
        "Additional lists in dMod",
        "eqnlist",
        "parlist"
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    {
      "source": "solvers.Rmd",
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      "title": "Using different ODE solves with dMod",
      "author": "Daniel Kaschek",
      "engine": "knitr::rmarkdown",
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    {
      "source": "Pimpl_Pexpl.Rmd",
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      "title": "Explicit and Implicit Transformations",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Implicit transformations",
        "Application of implicit transformations",
        "Keeping states",
        "Using additional constraints",
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      "modified": "2026-06-07 09:57:27",
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