{ "_id": "6ae7f2f3818c9e3ef6dbd40f", "Package": "rxode2", "Version": "5.1.8.9000", "Title": "Facilities for Simulating from ODE-Based Models", "Authors@R": "c(\nperson(\"Matthew L.\",\"Fidler\", role = c(\"aut\", \"cre\"), email = \"matthew.fidler@gmail.com\", comment=c(ORCID=\"0000-0001-8538-6691\")),\nperson(\"Wenping\", \"Wang\", role = c(\"aut\"), email = \"wwang8198@gmail.com\"),\nperson(\"Aaron\", \"Collier\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Alan\", \"Hindmarsh\",role=\"ctb\"),\nperson(\"Arun\", \"Srinivasan\", role=\"ctb\", email=\"arunkumar.sriniv@gmail.com\"),\nperson(\"Ashley\", \"Crawford\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Awad H.\", \"Al-Mohy\",role=\"ctb\"),\nperson(\"Bill\", \"Denney\", email=\"wdenney@humanpredictions.com\", role=\"ctb\", comment=c(ORCID=\"0000-0002-5759-428X\")),\nperson(\"Brian\", \"Ripley\", role=\"ctb\"),\nperson(\"Cleve\", \"Moler\", role=\"ctb\"),\nperson(\"Cody J.\", \"Balos\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Dan\", \"Shumaker\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Daniel\", \"Kaschek\", email=\"daniel.kaschek@gmail.com\", role=\"ctb\"),\nperson(\"Daniel R.\", \"Reynolds\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"David\", \"Cooley\", role=\"ctb\"),\nperson(\"David J.\", \"Gardner\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Drew\", \"Schmidt\", role=\"ctb\"),\nperson(\"Ernst\", \"Hairer\", role=\"ctb\"),\nperson(\"Gabriel\", \"Staples\", role=\"ctb\"),\nperson(\"Gerhard\", \"Wanner\", role=\"ctb\"),\nperson(\"Gilbert\", \"Stewart\", role=\"ctb\"),\nperson(\"Goro\", \"Fuji\", role=\"ctb\", email=\"gfuji@cpan.org\"),\nperson(\"Hadley\", \"Wickham\", role=\"ctb\"),\nperson(\"Hidde\", \"van de Beek\", role=\"ctb\", email=\"hiddevdbeek@icloud.com\"),\nperson(\"Igor\", \"Kushnir\", email=\"igorkuo@gmail.com\", role=\"ctb\"),\nperson(\"Imperial College of Science, Technology and Medicine\", role=\"cph\"),\nperson(\"Jack\", \"Dongarra\", role=\"ctb\"),\nperson(\"Jacob\", \"Williams\", role=\"ctb\"),\nperson(\"Jim\", \"Bunch\", role=\"ctb\"),\nperson(\"Karline\", \"Soetaert\", role=\"ctb\"),\nperson(\"Kevin\", \"Ushey\", role=\"ctb\"),\nperson(\"Lawrence Livermore National Security\", role=\"cph\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Linda\", \"Petzold\", role=\"ctb\"),\nperson(\"Mark M.\", \"Baum\", role=\"ctb\"),\nperson(\"Martin\", \"Maechler\", role=\"ctb\"),\nperson(\"Matt\", \"Dowle\", role=\"ctb\", email=\"mattjdowle@gmail.com\"),\nperson(\"Matteo\", \"Fasiolo\", email = \"matteo.fasiolo@gmail.com\", role = \"ctb\"),\nperson(\"Melissa\", \"Hallow\", role = \"aut\", email = \"hallowkm@uga.edu\"),\nperson(\"Michel\", \"Lang\", , \"michellang@gmail.com\", role = \"ctb\"),\nperson(\"Morwenn\",\"\", role=\"ctb\"),\nperson(\"Nicholas J.\", \"Higham\",role=\"ctb\"),\nperson(\"Omar\", \"Elashkar\", email=\"omar.i.elashkar@gmail.com\", role=\"ctb\"),\nperson(\"Peter N.\", \"Brown\", role=\"ctb\"),\nperson(\"Radu\", \"Serban\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Rich\", \"FitzJohn\", role=\"ctb\", email=\"rich.fitzjohn@gmail.com\"),\nperson(\"Richard\", \"Upton\", role = \"ctb\"),\nperson(\"Roger B.\", \"Sidje\", role=\"ctb\"),\nperson(\"Scott D.\", \"Cohen\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Simon\", \"Frost\", role=\"ctb\"),\nperson(\"Slaven\", \"Peles\", role=\"ctb\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Southern Methodist University\", role=\"cph\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Thomas\", \"Petzoldt\", role=\"ctb\"),\nperson(\"University of Maryland Baltimore County\", role=\"cph\", comment=\"SUNDIALS/CVODE\"),\nperson(\"Wes\", \"Hinsley\", role=\"ctb\"),\nperson(\"Woodrow\", \"Setzer\", role=\"ctb\"),\nperson(\"Yu\", \"Feng\", role=\"ctb\"),\nperson(\"Zufar\", \"Mulyukov\", role=\"ctb\", email=\"zufar.mulyukov@novartis.com\"))", "Maintainer": "Matthew L. Fidler ", "Description": "Facilities for running simulations from ordinary\ndifferential equation ('ODE') models, such as pharmacometrics\nand other compartmental models. A compilation manager\ntranslates the ODE model into C, compiles it, and dynamically\nloads the object code into R for improved computational\nefficiency. An event table object facilitates the\nspecification of complex dosing regimens (optional) and\nsampling schedules. NB: The use of this package requires both\nC and Fortran compilers, for details on their use with R please\nsee Section 6.3, Appendix A, and Appendix D in the \"R\nAdministration and Installation\" manual. Also the code is\nmostly released under GPL. The 'VODE' and 'LSODA' are in the\npublic domain. The vendored 'SUNDIALS' 'CVODE' sources and\nheaders are released under the BSD-3-Clause license. The\ninformation is available in the inst/COPYRIGHTS.", "BugReports": "https://github.com/nlmixr2/rxode2/issues/", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "License": "GPL (>= 3)", "URL": "https://nlmixr2.github.io/rxode2/,\nhttps://github.com/nlmixr2/rxode2/", "Biarch": "true", "Encoding": "UTF-8", "LazyData": "true", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake make", "Repository": "https://nlmixr2.r-universe.dev", "Date/Publication": "2026-11-01 23:39:26 UTC", "RemoteUrl": "https://github.com/nlmixr2/rxode2", "RemoteRef": "HEAD", "RemoteSha": "fb71a18d8651fd64a486ea869ca08d8228db9c72", "Packaged": { "Date": "2026-11-02 01:06:02 UTC", "User": "root" }, "Author": "Matthew L. Fidler [aut, cre] (ORCID:\n),\nWenping Wang [aut],\nAaron Collier [ctb] (SUNDIALS/CVODE),\nAlan Hindmarsh [ctb],\nArun Srinivasan [ctb],\nAshley Crawford [ctb] (SUNDIALS/CVODE),\nAwad H. 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"rxSolve", "rxSolveAdjoint", "rxSolveAdjointRk4", "rxSolveChunked", "rxSolveFree", "rxSolveSetup", "rxSplitPlusQ", "rxStack", "rxState", "rxStateOde", "rxStripModelSrc", "rxSumProdModel", "rxSupportedFuns", "rxSuppressMsg", "rxSymInvChol", "rxSymInvCholCreate", "rxSymInvCholN", "rxSyncOptions", "rxt", "rxTempDir", "rxTest", "rxTheme", "rxTick", "rxToIndLin", "rxToSE", "rxTrans", "rxUdfUi", "rxUdfUiControl", "rxUdfUiData", "rxUdfUiEst", "rxUdfUiExpr", "rxUdfUiFlag", "rxUdfUiIniDf", "rxUdfUiIniLhs", "rxUdfUiIsValue", "rxUdfUiLhs", "rxUdfUiMv", "rxUdfUiNum", "rxUdfUiParsing", "rxUdfUiReset", "rxUiCompress", "rxUiDecompress", "rxUiDeparse", "rxUiDevelop", "rxUiEtaDistAnchors", "rxUiEtaDists", "rxUiGet", "rxUiPriors", "rxunif", "rxUnload", "rxUnloadAll", "rxUnlock", "rxUse", "rxValidate", "rxVersion", "rxweibull", "rxWithPreserveSeed", "rxWithSeed", "scale_type", "scale_x_continuous", "scale_x_date", "scale_x_discrete", "scale_y_continuous", "scale_y_date", "scale_y_discrete", "SELU", "setCvodeLinearSolver", "setRxThreads", "softplus", "splitBolus", "splitInfusion", "stat_amt", "stat_cens", "studentTCdf", "studentTCdfDnu", "studentTDen", "studentTInv", "swapMatListWithCube", "Swish", "testCompartmentExists", "testExists", "testIniDf", "testRxLinCmt", "testRxUiEtaDist", "testRxUiNormalPriors", "testRxUiOmegaDf", "testRxUiOmegaNormalPriors", "testRxUiPriors", "testRxUnbounded", "testVariableExists", "toTrialDuration", "uppergamma", "waiver", "warnRxBounded", "write.template.server", "write.template.ui", "xlab", "yeoJohnson", "yeoJohnsonInv", "ylab", "zeroRe" ], "_datasets": [ { "name": "rxReservedKeywords", "title": "A list and description of rxode2 supported reserved keywords", "object": "rxReservedKeywords", "class": [ "data.frame" ], "fields": [ "Reserved Name", "Meaning", "Alias" ], "rows": 31, "table": true, "tojson": true }, { "name": "rxResidualError", "title": "A description of Rode2 supported residual errors", "object": "rxResidualError", "class": [ "data.frame" ], "fields": [ "Error model", "Functional Form", "Transformation", "code", "addProp", "lhs" ], "rows": 183, "table": true, "tojson": true }, { "name": "rxSyntaxFunctions", "title": "A list and description of Rode supported syntax functions", "object": "rxSyntaxFunctions", "class": [ "data.frame" ], "fields": [ "Function", "Description", "Aliases" ], "rows": 119, "table": true, "tojson": true } ], "_help": [ { "page": "dot-cbindOme", "title": "cbind Ome", "concept": [ "Developer API" ], "topics": [ ".cbindOme" ] }, { "page": "dot-collectWarnings", "title": "Collect warnings and just warn once.", "concept": [ "Developer API" ], "topics": [ ".collectWarnings" ] }, { "page": "dot-copyUi", "title": "This copies the rxode2 UI object so it can be modified", "concept": [ "Developer API" ], "topics": [ ".copyUi" ] }, { "page": "dot-handleSingleErrTypeNormOrTFoceiBase", "title": "Handle the single error for normal or t distributions", "concept": [ "Developer API" ], "topics": [ ".handleSingleErrTypeNormOrTFoceiBase" ] }, { "page": "dot-matchesLangTemplate", "title": "Check if a language object matches a template language object", "concept": [ "Developer API" ], "topics": [ ".matchesLangTemplate" ] }, { "page": "dot-modelHandleModelLines", "title": "Handle model lines", "concept": [ "Developer API" ], "topics": [ ".modelHandleModelLines" ] }, { "page": "dot-quoteCallInfoLines", "title": "Returns quoted call information", "concept": [ "Developer API" ], "topics": [ ".quoteCallInfoLines" ] }, { "page": "dot-rxLinCmtGen", "title": "Internal function to generate the model variables for a linCmt() model", "concept": [ "Developer API" ], "topics": [ ".rxLinCmtGen" ] }, { "page": "dot-rxode2ptrs", "title": "Get the rxode2 function pointers", "concept": [ "Developer API" ], "topics": [ ".rxode2ptrs" ] }, { "page": "dot-rxSensStrippable", "title": "Get model properties without compiling it.", "concept": [ "Developer API" ], "topics": [ ".rxSensStrippable" ] }, { "page": "dot-rxWithOptions", "title": "Temporarily set options then restore them while running code", "concept": [ "Developer API" ], "topics": [ ".rxWithOptions" ] }, { "page": "dot-rxWithWd", "title": "Temporarily set options then restore them while running code", "concept": [ "Developer API" ], "topics": [ ".rxWithWd" ] }, { "page": "dot-toClassicEvid", "title": "This converts NONMEM-style EVIDs to classic RxODE events", "concept": [ "Developer API" ], "topics": [ ".toClassicEvid" ] }, { "page": "dot-vecDf", "title": "Convert numeric vector to repeated data.frame", "concept": [ "Developer API" ], "topics": [ ".vecDf" ] }, { "page": "add.dosing", "title": "Add dosing to eventTable", "concept": [ "Event tables" ], "topics": [ "add.dosing" ] }, { "page": "add.sampling", "title": "Add sampling to eventTable", "concept": [ "Event tables" ], "topics": [ "add.sampling" ] }, { "page": "as_tibble.rxEt", "title": "Convert to tbl", "concept": [ "Developer API" ], "topics": [ "as_tibble.rxEt" ] }, { "page": "as.arrow", "title": "Convert an rxSolveOom result to a lazy Arrow Dataset", "concept": [ "Solving" ], "topics": [ "as.arrow", "as.arrow.rxSolveOom" ] }, { "page": "as.data.table.rxEt", "title": "Convert an event table to a data.table", "concept": [ "Developer API" ], "topics": [ "as.data.table.rxEt" ] }, { "page": "as.et", "title": "Coerce object to data.frame", "concept": [ "Event tables" ], "topics": [ "as.et", "as.et.default" ] }, { "page": "as.ini", "title": "Turn into an ini block for initialization", "concept": [ "Model UI and piping" ], "topics": [ "as.ini", "as.ini.call", "as.ini.character", "as.ini.data.frame", "as.ini.default", "as.ini.lotriFix", "as.ini.matrix" ] }, { "page": "as.model", "title": "Turn into a model expression", "concept": [ "Model UI and piping" ], "topics": [ "as.model", "as.model.call", "as.model.character", "as.model.default", "as.model.list" ] }, { "page": "as.rxUi", "title": "As rxode2 ui", "concept": [ "Model UI and piping" ], "topics": [ "as.rxUi", "as.rxUi.default", "as.rxUi.function", "as.rxUi.rxModelVars", "as.rxUi.rxode2", "as.rxUi.rxode2tos", "as.rxUi.rxUi" ] }, { "page": "assertCompartmentExists", "title": "Verify that the compartment exists in a model", "concept": [ "Assertions" ], "topics": [ "assertCompartmentExists", "testCompartmentExists" ] }, { "page": "assertCompartmentName", "title": "Verify that a value is a valid nlmixr2 compartment name", "concept": [ "Assertions" ], "topics": [ "assertCompartmentName", "assertExists", "assertParameterValue", "assertVariableName", "testExists" ] }, { "page": "assertCompartmentNew", "title": "Verify that a compartment would be new to the model", "concept": [ "Assertions" ], "topics": [ "assertCompartmentNew" ] }, { "page": "assertRxUi", "title": "Assert properties of the rxUi models", "concept": [ "Assertions" ], "topics": [ "assertRxUi", "assertRxUiAddProp", "assertRxUiErrType", "assertRxUiEstimatedResiduals", "assertRxUiIovNoCor", "assertRxUiMixedOnly", "assertRxUiMuRefOnly", "assertRxUiNoAutoregressive", "assertRxUiNoFixedOmega", "assertRxUiNoFixedResiduals", "assertRxUiNoMix", "assertRxUiNoOmegaDf", "assertRxUiNoOmegaNormalPriors", "assertRxUiNoPriors", "assertRxUiNormal", "assertRxUiNormalPriors", "assertRxUiPopulationOnly", "assertRxUiPrediction", "assertRxUiRandomOnIdOnly", "assertRxUiSingleEndpoint", "assertRxUiTransform", "assertRxUiTransformNormal", "testRxUiNormalPriors", "testRxUiOmegaDf", "testRxUiOmegaNormalPriors", "testRxUiPriors" ] }, { "page": "assertVariableExists", "title": "Assert a variable exists in the model", "concept": [ "Assertions" ], "topics": [ "assertVariableExists", "testVariableExists" ] }, { "page": "assertVariableNew", "title": "Assert a variable would be new to the model", "concept": [ "Assertions" ], "topics": [ "assertVariableNew" ] }, { "page": "binomProbs", "title": "Calculate expected confidence bands with binomial sampling distribution", "concept": [ "Random variables" ], "topics": [ "binomProbs", "binomProbs.default" ] }, { "page": "bolus", "title": "Administer a bolus dose inside a rxode2 model", "concept": [ "In-model dosing" ], "topics": [ "bolus" ] }, { "page": "boxCox", "title": "boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions", "concept": [ "Special functions" ], "topics": [ "boxCox", "boxCoxInv", "yeoJohnson", "yeoJohnsonInv" ] }, { "page": "coef.rxUi", "title": "Extract the initial coefficients from an rxode2 model (rxUi)", "concept": [ "Model UI and piping" ], "topics": [ "coef.function", "coef.rxUi" ] }, { "page": "confint.rxSolve", "title": "Simulated percentiles, with confidence bands, from a solved rxode2 object", "concept": [ "Variability and uncertainty" ], "topics": [ "confint.rxSolve" ] }, { "page": "cvPost", "title": "Sample a covariance Matrix from the Posterior Inverse Wishart distribution.", "concept": [ "Variability and uncertainty" ], "topics": [ "cvPost" ] }, { "page": "delay", "title": "Delayed state for delay differential equations", "concept": [ "Special functions" ], "topics": [ "delay" ] }, { "page": "dELU", "title": "Derivatives of the Exponential Linear Unit (ELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "d2aELU", "d2ELU", "d2ELUa", "dELU", "dELUa" ] }, { "page": "dfWishart", "title": "This uses simulations to match the rse", "concept": [ "Variability and uncertainty" ], "topics": [ "dfWishart" ] }, { "page": "dGELU", "title": "Derivatives of GELU", "concept": [ "Activation Functions" ], "topics": [ "d2GELU", "d3GELU", "d4GELU", "dGELU" ] }, { "page": "dlReLU", "title": "Derivative of Leaky ReLU activation function", "concept": [ "Activation Functions" ], "topics": [ "dlReLU" ] }, { "page": "dPReLU", "title": "Derivatives Parametric ReLU Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dPReLU", "dPReLUa", "dPReLUa1" ] }, { "page": "dReLU", "title": "Derivative of the Rectified Linear Unit (ReLU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dReLU" ] }, { "page": "dSELU", "title": "Derivative of the Scaled Exponential Linear Unit (SELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dSELU" ] }, { "page": "dsoftplus", "title": "Default Softplus Activation Function", "concept": [ "Activation Functions" ], "topics": [ "d2softplus", "d3softplus", "d4softplus", "dsoftplus" ] }, { "page": "dSwish", "title": "Derivative of the Swish Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dSwish" ] }, { "page": "ELU", "title": "Exponential Linear Unit (ELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "ELU" ] }, { "page": "erf", "title": "Error function", "concept": [ "Special functions" ], "topics": [ "erf" ] }, { "page": "et", "title": "Event Table Function", "concept": [ "Event tables" ], "topics": [ "et", "et.default", "et.function", "et.rxode2", "et.rxParams", "et.rxSolve", "et.rxUi" ] }, { "page": "etExpand", "title": "Expand additional doses", "concept": [ "Event tables" ], "topics": [ "etExpand" ] }, { "page": "etRbind", "title": "Combining event tables", "concept": [ "Event tables" ], "topics": [ "etRbind", "rbind.rxEt" ] }, { "page": "etRep", "title": "Repeat an rxode2 event table", "concept": [ "Event tables" ], "topics": [ "etRep", "rep.rxEt" ] }, { "page": "etSeq", "title": "Sequence of event tables", "concept": [ "Event tables" ], "topics": [ "etSeq", "seq.rxEt" ] }, { "page": "eventTable", "title": "Create an event table object", "concept": [ "Event tables", "Nonlinear regression", "Pharmacodynamics (PD)", "Pharmacokinetics (PK)", "ordinary differential equations" ], "topics": [ "eventTable" ] }, { "page": "evid_", "title": "Push a future dose or observation event from within an rxode2 model", "concept": [ "In-model dosing" ], "topics": [ "evid_" ] }, { "page": "gammap", "title": "Gammap: normalized lower incomplete gamma function", "concept": [ "Special functions" ], "topics": [ "gammap" ] }, { "page": "gammapDer", "title": "gammapDer: derivative of gammap", "concept": [ "Special functions" ], "topics": [ "gammapDer" ] }, { "page": "gammapInv", "title": "gammapInv and gammapInva: Inverses of normalized gammap function", "concept": [ "Special functions" ], "topics": [ "gammapInv", "gammapInva" ] }, { "page": "gammaq", "title": "Gammaq: normalized upper incomplete gamma function", "concept": [ "Special functions" ], "topics": [ "gammaq" ] }, { "page": "gammaqInv", "title": "gammaqInv and gammaqInva: Inverses of normalized gammaq function", "concept": [ "Special functions" ], "topics": [ "gammaqInv", "gammaqInva" ] }, { "page": "GELU", "title": "GELU activation function", "concept": [ "Activation Functions" ], "topics": [ "GELU" ] }, { "page": "genShinyApp.template", "title": "Generate an example (template) of a dosing regimen shiny app", "concept": [ "PK/PD", "Shiny", "pharmacometrics" ], "topics": [ "genShinyApp.template", "write.template.server", "write.template.ui" ] }, { "page": "getRxThreads", "title": "Get/Set the number of threads that rxode2 uses", "concept": [ "Solver options and performance" ], "topics": [ "getRxThreads", "rxCores", "setRxThreads" ] }, { "page": "indLin", "title": "Transition ODEs written in d/dt() format to matrix exponential / inductive linearization format", "concept": [ "Model UI and piping" ], "topics": [ "indLin", "rxOdeToIndLin", "rxToIndLin" ] }, { "page": "infuse", "title": "Administer a infusion (with rate being fixed) inside a rxode2 model", "concept": [ "In-model dosing" ], "topics": [ "infuse" ] }, { "page": "infuseDur", "title": "Administer a infusion (with duration being fixed) inside a rxode2 model", "concept": [ "In-model dosing" ], "topics": [ "infuseDur" ] }, { "page": "ini", "title": "Ini block for rxode2/nlmixr models", "concept": [ "Initial conditions", "Model UI and piping" ], "topics": [ "ini", "ini.default", "ini.rxUi" ] }, { "page": "ini-set", "title": "Assign the ini block in the rxode2 related object", "concept": [ "Model UI and piping" ], "topics": [ "ini<-" ] }, { "page": "is.rxEt", "title": "Check if object is an rxEt event table", "concept": [ "Event tables" ], "topics": [ "is.rxEt" ] }, { "page": "is.rxStackData", "title": "Return if the object can be stacked", "concept": [ "rxode2 plotting" ], "topics": [ "is.rxStackData" ] }, { "page": "linCmtMicro", "title": "Get the micro-constant parameterization of a linCmt() model", "concept": [ "Model UI and piping" ], "topics": [ "linCmtMicro" ] }, { "page": "linMod", "title": "Linear model to replace in rxode2 ui model", "concept": [ "User functions" ], "topics": [ "linMod", "linMod0", "linModA", "linModA0", "linModB", "linModB0", "linModD", "linModD0", "linModM", "linModM0" ] }, { "page": "linToOde", "title": "Convert linCmt rxUi models to ODE rxUi models", "concept": [ "Model UI and piping" ], "topics": [ "linToOde" ] }, { "page": "llikBeta", "title": "Calculate the log likelihood of the binomial function (and its derivatives)", "concept": [ "Log-likelihood functions" ], "topics": [ "llikBeta" ] }, { "page": "llikBinom", "title": "Calculate the log likelihood of the binomial function (and its derivatives)", "concept": [ "Log-likelihood functions" ], "topics": [ "llikBinom" ] }, { "page": "llikCauchy", "title": "log likelihood of Cauchy distribution and it's derivatives (from stan)", "concept": [ "Log-likelihood functions" ], "topics": [ "llikCauchy" ] }, { "page": "llikChisq", "title": "log likelihood and derivatives for chi-squared distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikChisq" ] }, { "page": "llikExp", "title": "log likelihood and derivatives for exponential distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikExp" ] }, { "page": "llikF", "title": "log likelihood and derivatives for F distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikF" ] }, { "page": "llikGamma", "title": "log likelihood and derivatives for Gamma distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikGamma" ] }, { "page": "llikGeom", "title": "log likelihood and derivatives for Geom distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikGeom" ] }, { "page": "llikNbinom", "title": "Calculate the log likelihood of the negative binomial function (and its derivatives)", "concept": [ "Log-likelihood functions" ], "topics": [ "llikNbinom" ] }, { "page": "llikNbinomMu", "title": "Calculate the log likelihood of the negative binomial function (and its derivatives)", "concept": [ "Log-likelihood functions" ], "topics": [ "llikNbinomMu" ] }, { "page": "llikNorm", "title": "Log likelihood for normal distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikNorm" ] }, { "page": "llikPois", "title": "log-likelihood for the Poisson distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikPois" ] }, { "page": "llikT", "title": "Log likelihood of T and it's derivatives (from stan)", "concept": [ "Log-likelihood functions" ], "topics": [ "llikT" ] }, { "page": "llikUnif", "title": "log likelihood and derivatives for Unif distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikUnif" ] }, { "page": "llikWeibull", "title": "log likelihood and derivatives for Weibull distribution", "concept": [ "Log-likelihood functions" ], "topics": [ "llikWeibull" ] }, { "page": "logit", "title": "logit and inverse logit (expit) functions", "concept": [ "Special functions" ], "topics": [ "expit", "logit", "logitNormInfo", "probitNormInfo" ] }, { "page": "lowergamma", "title": "lowergamma: upper incomplete gamma function", "concept": [ "Special functions" ], "topics": [ "lowergamma" ] }, { "page": "lReLU", "title": "Leaky ReLU activation function", "concept": [ "Activation Functions" ], "topics": [ "lReLU" ] }, { "page": "meanProbs", "title": "Calculate expected confidence bands or prediction intreval with normal or t sampling distribution", "concept": [ "Random variables" ], "topics": [ "meanProbs", "meanProbs.default" ] }, { "page": "mexpit", "title": "mexpit - Convert log-scale numbers to probabilities", "concept": [ "Special functions" ], "topics": [ "dmexpit", "mexpit" ] }, { "page": "mix", "title": "Specify a mixture model of variables", "concept": [ "User functions" ], "topics": [ "mix" ] }, { "page": "mlogit", "title": "mlogit - Convert multiple probabilities to log-scale numbers", "concept": [ "Special functions" ], "topics": [ "mlogit" ] }, { "page": "model", "title": "Model block for rxode2/nlmixr models", "concept": [ "Model UI and piping" ], "topics": [ "model", "model.default", "model.function", "model.rxModelVars", "model.rxode2", "model.rxUi" ] }, { "page": "model-set", "title": "Assign the model block in the rxode2 related object", "concept": [ "Model UI and piping" ], "topics": [ "model<-" ] }, { "page": "modelExtract", "title": "Extract model lines from a rxui model", "concept": [ "Model UI and piping" ], "topics": [ "modelExtract", "modelExtract.default", "modelExtract.function", "modelExtract.rxModelVars", "modelExtract.rxode2", "modelExtract.rxUi" ] }, { "page": "multiply", "title": "Multiply dose the rxode2 system in the model", "concept": [ "In-model dosing" ], "topics": [ "multiply" ] }, { "page": "obs", "title": "Add observations to a model", "concept": [ "In-model dosing" ], "topics": [ "obs" ] }, { "page": "odeMethodToInt", "title": "Conversion between character and integer ODE integration methods for rxode2", "concept": [ "Solver options and performance" ], "topics": [ "odeMethodToInt" ] }, { "page": "odeToLin", "title": "Convert ODE-based linear compartment models to analytical linCmt() form", "concept": [ "Model UI and piping" ], "topics": [ "odeToLin" ] }, { "page": "phantom", "title": "Administer a phantom/transit dose inside a rxode2 model", "concept": [ "In-model dosing" ], "topics": [ "phantom" ] }, { "page": "phi", "title": "Cumulative distribution of standard normal", "concept": [ "Special functions" ], "topics": [ "phi" ] }, { "page": "phiU", "title": "Inverse CDFs for declared non-normal random effects", "concept": [ "Special functions" ], "topics": [ "gammapDera", "ibeta", "ibetaDer", "ibetaDera", "ibetaDerb", "ibetaInv", "phiU", "studentTCdf", "studentTCdfDnu", "studentTDen", "studentTInv" ] }, { "page": "plot.rxSolve", "title": "Plot rxode2 objects", "concept": [ "rxode2 plotting" ], "topics": [ "plot.rxSolve", "plot.rxSolveConfint1", "plot.rxSolveConfint2" ] }, { "page": "PReLU", "title": "Parametric ReLU Activation Function", "concept": [ "Activation Functions" ], "topics": [ "PReLU" ] }, { "page": "print.rxModelVars", "title": "Print Values", "concept": [ "Developer API" ], "topics": [ "print.rxModelVars" ] }, { "page": "probit", "title": "probit and inverse probit functions", "concept": [ "Special functions" ], "topics": [ "probit", "probitInv" ] }, { "page": "ReLU", "title": "Rectified Linear Unit (ReLU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "ReLU" ] }, { "page": "replace", "title": "Replace dose the rxode2 system in the model", "concept": [ "In-model dosing" ], "topics": [ "replace" ] }, { "page": "reset", "title": "Reset the rxode2 system in the model", "concept": [ "In-model dosing" ], "topics": [ "reset" ] }, { "page": "rinvchisq", "title": "Scaled Inverse Chi Squared distribution", "concept": [ "Variability and uncertainty" ], "topics": [ "rinvchisq" ] }, { "page": "rxAllowUnload", "title": "Allow unloading of dlls", "concept": [ "Developer API" ], "topics": [ "rxAllowUnload" ] }, { "page": "rxAppendModel", "title": "Append two rxui models together", "concept": [ "Model UI and piping" ], "topics": [ "rxAppendModel" ] }, { "page": "rxAssignControlValue", "title": "Assign Control Variable", "concept": [ "Developer API" ], "topics": [ "rxAssignControlValue" ] }, { "page": "rxAssignPtr", "title": "Assign pointer based on model variables", "concept": [ "Developer API" ], "topics": [ "rxAssignPtr" ] }, { "page": "rxbeta", "title": "Simulate beta variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxbeta" ] }, { "page": "rxbinom", "title": "Simulate Binomial variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxbinom" ] }, { "page": "rxcauchy", "title": "Simulate Cauchy variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxcauchy" ] }, { "page": "rxCbindStudyIndividual", "title": "Bind the study parameters and individual parameters", "concept": [ "Solving" ], "topics": [ "rxCbindStudyIndividual" ] }, { "page": "rxchisq", "title": "Simulate chi-squared variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxchisq" ] }, { "page": "rxClean", "title": "Cleanup anonymous DLLs by unloading them", "concept": [ "Model definition" ], "topics": [ "rxClean" ] }, { "page": "rxCompile", "title": "Compile a model if needed", "concept": [ "Model definition" ], "topics": [ "rxCompile", "rxCompile.character", "rxCompile.rxDll", "rxCompile.rxModelVars", "rxCompile.rxode2" ] }, { "page": "rxControlUpdateSens", "title": "This updates the tolerances based on the sensitivity equations", "concept": [ "Sensitivities" ], "topics": [ "rxControlUpdateSens" ] }, { "page": "rxCreateCache", "title": "This will create the cache directory for rxode2 to save between sessions", "concept": [ "Model definition" ], "topics": [ "rxCreateCache" ] }, { "page": "rxD", "title": "Add to rxode2's derivative tables", "concept": [ "User functions" ], "topics": [ "rxD" ] }, { "page": "rxDelete", "title": "Delete the DLL for the model", "concept": [ "Model definition" ], "topics": [ "rxDelete" ] }, { "page": "rxDerived", "title": "Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.", "concept": [ "Utilities" ], "topics": [ "rxDerived" ] }, { "page": "rxDfdy", "title": "Jacobian and parameter derivatives", "concept": [ "Query model information", "Sensitivities" ], "topics": [ "rxDfdy" ] }, { "page": "rxEtaDistExpand", "title": "Expand declared non-normal random effect distributions into a model", "concept": [ "Variability and uncertainty" ], "topics": [ "rxEtaDistExpand" ] }, { "page": "rxEtaDistMuRef", "title": "Mu-reference the parameters of a declared eta distribution", "concept": [ "Variability and uncertainty" ], "topics": [ "rxEtaDistMuRef" ] }, { "page": "rxEtDispatchSolve", "title": "Dispatch solve to 'rxode2' solve", "concept": [ "Developer API" ], "topics": [ "rxEtDispatchSolve", "rxEtDispatchSolve.default" ] }, { "page": "rxEventListen", "title": "rxode2 event bus", "topics": [ ".rxEventCall", ".rxEventEnter", ".rxEventExit", "rxEventDepth", "rxEventEmit", "rxEventListen", "rxEventListeners", "rxEventScope", "rxEventSeq", "rxEventUnlisten" ] }, { "page": "rxEventTableFile", "title": "Create a file-backed event table reference", "concept": [ "Event tables" ], "topics": [ "rxEventTableFile" ] }, { "page": "rxEvid", "title": "EVID formatting for tibble and other places.", "concept": [ "Developer API" ], "topics": [ "as.character.rxEvid", "as.rxEvid", "c.rxEvid", "c.rxRateDur", "format.rxEvid", "format.rxRateDur", "print.rxEvid", "rxEvid", "units<-.rxEvid", "[.rxEvid", "[[.rxEvid" ] }, { "page": "rxexp", "title": "Simulate exponential variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxexp" ] }, { "page": "rxf", "title": "Simulate F variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxf" ] }, { "page": "rxFixPop", "title": "Apply the fixed population estimated parameters", "concept": [ "Model UI and piping" ], "topics": [ "rxFixPop" ] }, { "page": "rxFixRes", "title": "Literally fix residual parameters", "concept": [ "Model UI and piping" ], "topics": [ "rxFixRes" ] }, { "page": "rxForcedPars", "title": "Forced parameters carried by a model / ui", "concept": [ "Solving" ], "topics": [ "rxForcedPars", "rxForcedPars<-" ] }, { "page": "rxFun", "title": "Add/Create C functions for use in rxode2", "concept": [ "User functions" ], "topics": [ "rxFun", "rxRmFun" ] }, { "page": "rxgamma", "title": "Simulate gamma variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxgamma" ] }, { "page": "rxgeom", "title": "Simulate geometric variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxgeom" ] }, { "page": "rxGetControl", "title": "rxGetControl option from ui", "concept": [ "Model UI and piping" ], "topics": [ "rxGetControl" ] }, { "page": "rxGetDefaultSerialize", "title": "Get the Default Serialization Type", "concept": [ "Utilities" ], "topics": [ "rxGetDefaultSerialize" ] }, { "page": "rxGetLin", "title": "Get the linear compartment model true function", "concept": [ "Developer API" ], "topics": [ "rxGetLin" ] }, { "page": "rxGetrxode2", "title": "Get rxode2 model from object", "concept": [ "Developer API" ], "topics": [ "rxGetrxode2" ] }, { "page": "rxGetSeed", "title": "Get the rxode2 seed", "concept": [ "Random seeds" ], "topics": [ "rxGetSeed" ] }, { "page": "rxHasAr", "title": "Test if a model uses an autoregressive ('ar()') residual", "concept": [ "Assertions" ], "topics": [ "rxHasAr" ] }, { "page": "rxHtml", "title": "Format rxSolve and related objects as html.", "concept": [ "Utilities" ], "topics": [ "rxHtml", "rxHtml.rxSolve" ] }, { "page": "rxIndLinState", "title": "Set the preferred factoring by state", "concept": [ "Solver options and performance" ], "topics": [ "rxIndLinState" ] }, { "page": "rxIndLinStrategy", "title": "This sets the inductive linearization strategy for matrix building", "concept": [ "Solver options and performance" ], "topics": [ "rxIndLinStrategy" ] }, { "page": "rxInjectedPars", "title": "Parameters injected into a solve by a par-loader hook", "concept": [ "Solving" ], "topics": [ "rxInjectedPars" ] }, { "page": "rxIntToBase", "title": "Convert a positive base", "concept": [ "User functions" ], "topics": [ "rxIntToBase" ] }, { "page": "rxIntToLetter", "title": "Convert a positive integer to a letter series", "concept": [ "User functions" ], "topics": [ "rxIntToLetter" ] }, { "page": "rxInv", "title": "Invert matrix using RcppArmadillo.", "concept": [ "Utilities" ], "topics": [ "rxInv" ] }, { "page": "rxIsAutoSwitch", "title": "Check whether an ODE method string is an AutoSwitch composite pair", "concept": [ "Solver options and performance" ], "topics": [ "rxIsAutoSwitch" ] }, { "page": "rxIsCurrent", "title": "Checks if the rxode2 object was built with the current build", "concept": [ "Utilities" ], "topics": [ "rxIsCurrent" ] }, { "page": "rxIsDense", "title": "Check whether an ODE solving method supports dense output", "concept": [ "Solver options and performance" ], "topics": [ "rxIsDense" ] }, { "page": "rxIsImplicit", "title": "Check whether an ODE solving method requires a Jacobian (is implicit)", "concept": [ "Solver options and performance" ], "topics": [ "rxIsImplicit" ] }, { "page": "rxIsNonStiff", "title": "Check whether an ODE solving method is a purely non-stiff solver", "concept": [ "Solver options and performance" ], "topics": [ "rxIsNonStiff" ] }, { "page": "rxIsStiff", "title": "Check whether an ODE solving method is a purely stiff solver", "concept": [ "Solver options and performance" ], "topics": [ "rxIsStiff" ] }, { "page": "rxLastCompile", "title": "Get the last compiled model information as alist", "concept": [ "Model definition" ], "topics": [ "rxLastCompile" ] }, { "page": "rxLhs", "title": "Left handed Variables", "concept": [ "Query model information" ], "topics": [ "rxLhs" ] }, { "page": "rxLock", "title": "Lock/unlocking of rxode2 dll file", "concept": [ "Utilities" ], "topics": [ "rxLock", "rxUnlock" ] }, { "page": "rxMemoryEstimate", "title": "Estimate memory required by rxSolve() for a given dataset and model", "concept": [ "Solver options and performance" ], "topics": [ "rxMemoryEstimate" ] }, { "page": "rxMemSummary", "title": "Create a per-ID event summary for memory estimation", "concept": [ "Solver options and performance" ], "topics": [ "rxMemSummary" ] }, { "page": "rxModelName", "title": "Name a model from the function that created it", "concept": [ "Model names" ], "topics": [ "rxModelName", "rxModelName.default" ] }, { "page": "rxModelNameLhs", "title": "Name a model from the left hand side of an assignment", "concept": [ "Model names" ], "topics": [ "rxModelNameLhs" ] }, { "page": "rxnbinom", "title": "Simulate Binomial variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxnbinom", "rxnbinomMu" ] }, { "page": "rxNorm", "title": "Get the normalized model", "concept": [ "Model definition" ], "topics": [ "rxNorm" ] }, { "page": "rxnormV", "title": "Simulate random normal variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxnorm", "rxnormV" ] }, { "page": "rxNumLoaded", "title": "Get the number of loaded rxode2 DLLs", "concept": [ "Utilities" ], "topics": [ "rxNumLoaded" ] }, { "page": "rxode2", "title": "Create an ODE-based model specification", "concept": [ "Model definition", "Nonlinear regression", "ODE models", "Ordinary differential equations", "Pharmacodynamics (PD)", "Pharmacokinetics (PK)" ], "topics": [ "RxODE", "rxode", "rxode2" ] }, { "page": "rxode2-set", "title": "Set the function body of an rxUi object while retaining other object information (like data)", "concept": [ "Model UI and piping" ], "topics": [ "rxode2<-", "rxode2<-.default", "rxode2<-.function", "RxODE<-", "rxode<-" ] }, { "page": "rxode2parse", "title": "Internal translation to get model variables list", "concept": [ "Developer API" ], "topics": [ "rxode2parse" ] }, { "page": "rxode2parseAssignTranslation", "title": "This assigns the c level linkages for a roxde2 model", "concept": [ "Developer API" ], "topics": [ "rxode2parseAssignTranslation" ] }, { "page": "rxode2parseD", "title": "This gives the derivative table for rxode2", "concept": [ "Developer API" ], "topics": [ "rxode2parseD" ] }, { "page": "rxode2parseAssignPackagesToLoad", "title": "Control the packages that are loaded when a 'rxode2' model dll is loaded", "concept": [ "Developer API" ], "topics": [ "rxode2parseAssignPackagesToLoad", "rxode2parseGetPackagesToLoad" ] }, { "page": "rxode2parseGetPointerAssignment", "title": "This function gets the currently assigned function pointer assignments", "concept": [ "Developer API" ], "topics": [ "rxode2parseGetPointerAssignment" ] }, { "page": "rxode2parseGetTranslation", "title": "This function gets the currently assigned translations", "concept": [ "Developer API" ], "topics": [ "rxode2parseGetTranslation" ] }, { "page": "rxOmegaVarCovDeriv", "title": "Variance-covariance (non-Cholesky) Omega parameterization derivatives", "concept": [ "Utilities" ], "topics": [ "rxOmegaVarCovDeriv" ] }, { "page": "rxOptExpr", "title": "Optimize rxode2 for computer evaluation", "concept": [ "Solver options and performance" ], "topics": [ "rxOptExpr" ] }, { "page": "rxord", "title": "Simulate ordinal value", "concept": [ "Random variables" ], "topics": [ "rxord" ] }, { "page": "rxParams", "title": "Parameters specified by the model", "concept": [ "Query model information" ], "topics": [ "rxParam", "rxParams", "rxParams.function", "rxParams.rxEt", "rxParams.rxode2", "rxParams.rxSolve", "rxParams.rxUi" ] }, { "page": "rxParLoader", "title": "Parameter-loader flag on a model", "concept": [ "Solving" ], "topics": [ "rxParLoader", "rxParLoader<-" ] }, { "page": "rxParseSuppressMsg", "title": "Respect suppress messages", "concept": [ "Developer API" ], "topics": [ "rxParseSuppressMsg" ] }, { "page": "rxPkg", "title": "Creates a package from compiled rxode2 models", "concept": [ "Packaging" ], "topics": [ "rxPkg" ] }, { "page": "rxpois", "title": "Simulate random Poisson variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxpois" ] }, { "page": "rxPp", "title": "Simulate a from a Poisson process", "concept": [ "Variability and uncertainty" ], "topics": [ "rxPp" ] }, { "page": "rxPreferredDistributionName", "title": "Change distribution name to the preferred distribution name term", "concept": [ "Developer API" ], "topics": [ "rxPreferredDistributionName" ] }, { "page": "rxPriorBuildSpec", "title": "Build the C spec 'rxPriorLogDensityEval()' (and the C API) evaluates", "concept": [ "Assertions" ], "topics": [ "rxPriorBuildSpec" ] }, { "page": "rxPriorLogDensity", "title": "Value and gradient of a model's prior log density, on the natural scale", "concept": [ "Assertions" ], "topics": [ "rxPriorLogDensity" ] }, { "page": "rxPriorOmegaToCholOmegaInvGrad", "title": "Chain-rule a natural-scale omega gradient into FOCEI's cholOmegaInv scale", "concept": [ "Assertions" ], "topics": [ "rxPriorOmegaToCholOmegaInvGrad" ] }, { "page": "rxProgress", "title": "rxode2 progress bar functions", "concept": [ "Solver options and performance" ], "topics": [ "rxProgress", "rxProgressAbort", "rxProgressStop", "rxTick" ] }, { "page": "rxRateDur", "title": "Creates a rxRateDur object", "concept": [ "Developer API" ], "topics": [ "as.character.rxRateDur", "as.rxRateDur", "rxRateDur", "[.rxRateDur", "[[.rxRateDur" ] }, { "page": "rxRegisterUiAssembled", "title": "Register or remove a ui assembly hook", "concept": [ "Solving" ], "topics": [ "rxRegisterUiAssembled", "rxRemoveUiAssembled" ] }, { "page": "rxRegisterUiPrep", "title": "Register or remove a solve-time ui preparation hook", "concept": [ "Solving" ], "topics": [ "rxRegisterUiPrep", "rxRemoveUiPrep" ] }, { "page": "rxRemoveControl", "title": "rxRemoveControl options for UI object", "concept": [ "Model UI and piping" ], "topics": [ "rxRemoveControl" ] }, { "page": "rxRename", "title": "Rename items inside of a 'rxode2' ui model", "concept": [ "Model UI and piping" ], "topics": [ ".rxRename", "rename.function", "rename.rxUi", "rxRename", "rxRename.default", "rxRename.function", "rxRename.rxUi" ] }, { "page": "rxReservedKeywords", "title": "A list and description of rxode2 supported reserved keywords", "concept": [ "Model definition" ], "topics": [ "rxReservedKeywords" ] }, { "page": "rxResidualError", "title": "A description of Rode2 supported residual errors", "topics": [ "rxResidualError" ] }, { "page": "rxRmvn", "title": "Simulate from a (truncated) multivariate normal", "concept": [ "Variability and uncertainty" ], "topics": [ "rxRmvn" ] }, { "page": "rxRmvt", "title": "Simulate from a (truncated) multivariate t distribution", "concept": [ "Variability and uncertainty" ], "topics": [ "rxRmvt" ] }, { "page": "rxS", "title": "Load a model into a symengine environment", "concept": [ "Symbolic tools" ], "topics": [ "rxS" ] }, { "page": "rxSensMatExp", "title": "Differentiate and expand a matrix exponential model with forward sensitivities", "concept": [ "Sensitivities" ], "topics": [ "rxSensMatExp" ] }, { "page": "rxSetActiveParLoader", "title": "Activate a registered parameter loader for solves", "concept": [ "Solving" ], "topics": [ "rxClearActiveParLoader", "rxSetActiveParLoader" ] }, { "page": "rxSetControl", "title": "rxSetControl options for UI object", "concept": [ "Model UI and piping" ], "topics": [ "rxSetControl" ] }, { "page": "rxSetCovariateNamesForPiping", "title": "Assign covariates for piping", "concept": [ "Model UI and piping" ], "topics": [ "rxSetCovariateNamesForPiping" ] }, { "page": "rxSetIni0", "title": "Set Initial conditions to time zero instead of the first observed/dosed time", "concept": [ "Solving" ], "topics": [ "rxSetIni0" ] }, { "page": "rxSetPipingAuto", "title": "Set the variables for the model piping automatic covarite selection", "concept": [ "Model UI and piping" ], "topics": [ "rxSetPipingAuto" ] }, { "page": "rxSetProd", "title": "Defunct setting of product", "concept": [ "Solver options and performance" ], "topics": [ "rxSetProd" ] }, { "page": "rxSetProgressBar", "title": "Set timing for progress bar", "concept": [ "Solver options and performance" ], "topics": [ "rxSetProgressBar" ] }, { "page": "rxSetSeed", "title": "Set the parallel seed for rxode2 random number generation", "concept": [ "Random seeds" ], "topics": [ "rxSetSeed" ] }, { "page": "rxSetSum", "title": "Defunct setting of sum", "concept": [ "Solver options and performance" ], "topics": [ "rxSetSum" ] }, { "page": "rxShiny", "title": "Use Shiny to help develop an rxode2 model", "concept": [ "Shiny" ], "topics": [ "rxShiny", "rxShiny.default", "rxShiny.rxSolve" ] }, { "page": "rxSimThetaOmega", "title": "Simulate Parameters from a Theta/Omega specification", "concept": [ "Variability and uncertainty" ], "topics": [ "rxSimThetaOmega" ] }, { "page": "rxSolve", "title": "Options, Solving & Simulation of an ODE/solved system", "concept": [ "Solving" ], "topics": [ "predict.function", "predict.rxEt", "predict.rxode2", "predict.rxParams", "predict.rxSolve", "predict.rxUi", "rxControl", "rxSolve", "rxSolve.default", "rxSolve.function", "rxSolve.nlmixr2FitCore", "rxSolve.nlmixr2FitData", "rxSolve.rxode2tos", "rxSolve.rxSolve", "rxSolve.rxUi", "simulate.rxode2", "simulate.rxParams", "simulate.rxSolve", "solve.function", "solve.rxEt", "solve.rxode2", "solve.rxParams", "solve.rxSolve", "solve.rxUi", "update.rxSolve" ] }, { "page": "rxSolveAdjoint", "title": "Solve a model with adjoint (backward) sensitivities, drop-in for forward sens", "concept": [ "Sensitivities" ], "topics": [ "rxSolveAdjoint" ] }, { "page": "rxSolveAdjointRk4", "title": "Solve a model with an in-engine discrete-adjoint ('s') method", "concept": [ "Sensitivities" ], "topics": [ "rxSolveAdjointRk4" ] }, { "page": "rxSolveChunked", "title": "Solve an ODE model in memory-safe chunks", "concept": [ "Solving" ], "topics": [ "rxSolveChunked" ] }, { "page": "rxStack", "title": "Stack a solved object for things like default ggplot2 plot", "concept": [ "rxode2 plotting" ], "topics": [ "rxStack" ] }, { "page": "rxState", "title": "State variables", "concept": [ "Query model information" ], "topics": [ "rxState" ] }, { "page": "rxStateOde", "title": "Get the ODE states only", "concept": [ "Query model information" ], "topics": [ "rxStateOde" ] }, { "page": "rxSumProdModel", "title": "Recast model in terms of sum/prod", "concept": [ "Solver options and performance" ], "topics": [ "rxSumProdModel" ] }, { "page": "rxSupportedFuns", "title": "Get list of supported functions", "concept": [ "Model definition" ], "topics": [ "rxSupportedFuns" ] }, { "page": "rxSuppressMsg", "title": "Respect suppress messages", "concept": [ "Utilities" ], "topics": [ "rxSuppressMsg" ] }, { "page": "rxSymInvChol", "title": "Get Omega^-1 and derivatives", "concept": [ "Utilities" ], "topics": [ "rxSymInvChol" ] }, { "page": "rxSyncOptions", "title": "Sync options with rxode2 variables", "concept": [ "Developer API" ], "topics": [ "rxSyncOptions" ] }, { "page": "rxSyntaxFunctions", "title": "A list and description of Rode supported syntax functions", "concept": [ "Model definition" ], "topics": [ "rxSyntaxFunctions" ] }, { "page": "rxt", "title": "Simulate student t variable from threefry generator", "concept": [ "Random variables" ], "topics": [ "rxt" ] }, { "page": "rxTempDir", "title": "Get the rxode2 temporary directory", "concept": [ "Utilities" ], "topics": [ "rxTempDir" ] }, { "page": "rxTheme", "title": "rxTheme is the ggplot2 theme for rxode2 plots", "concept": [ "rxode2 plotting" ], "topics": [ "rxTheme" ] }, { "page": "rxToSE", "title": "rxode2 to symengine environment", "concept": [ "Symbolic tools" ], "topics": [ ".rxFromSE", ".rxToSE", "rxFromSE", "rxToSE" ] }, { "page": "rxTrans", "title": "Translate the model to C code if needed", "concept": [ "Developer API" ], "topics": [ "rxTrans", "rxTrans.character", "rxTrans.default" ] }, { "page": "rxUdfUiControl", "title": "Return the control that is being processed or setup control for processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiControl" ] }, { "page": "rxUdfUiData", "title": "Return the data.frame that is being processed or setup data.frame for processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiData" ] }, { "page": "rxUdfUiEst", "title": "Return the current estimation method for the UI processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiEst" ] }, { "page": "rxUdfUiExpr", "title": "Give the expression as a compressed model or expression", "concept": [ "User functions" ], "topics": [ "rxUdfUiExpr" ] }, { "page": "rxUdfUiFlag", "title": "Is the expression actually a flag that can be used in the rxUdfUi functions?", "concept": [ "User functions" ], "topics": [ "rxUdfUiFlag" ] }, { "page": "rxUdfUiIniDf", "title": "Get the rxode2 iniDf of the current UI being processed (or return NULL)", "concept": [ "User functions" ], "topics": [ "rxUdfUiIniDf" ] }, { "page": "rxUdfUiIniLhs", "title": "Return the lhs parsed language expression", "concept": [ "User functions" ], "topics": [ "rxUdfUiIniLhs" ] }, { "page": "rxUdfUiIsValue", "title": "Is the expression actually equal to a value?", "concept": [ "User functions" ], "topics": [ "rxUdfUiIsValue" ] }, { "page": "rxUdfUiLhs.dist", "title": "Declare a non-Gaussian random effect distribution in the model block", "concept": [ "User functions" ], "topics": [ "rxUdfUiLhs.dist" ] }, { "page": "rxUdfUiMv", "title": "Return the model variables that is being processed or setup model variables for processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiMv" ] }, { "page": "rxUdfUiNum", "title": "This gives the current number in the ui of the particular function being called.", "concept": [ "User functions" ], "topics": [ "rxUdfUiNum" ] }, { "page": "rxUdfUiParsing", "title": "Returns if the current ui function is being parsed", "concept": [ "User functions" ], "topics": [ "rxUdfUiParsing" ] }, { "page": "rxUiDecompress", "title": "Compress/Decompress 'rxode2' ui", "concept": [ "Model UI and piping" ], "topics": [ "rxUiCompress", "rxUiDecompress" ] }, { "page": "rxUiDeparse", "title": "This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information", "concept": [ "Developer API" ], "topics": [ "rxUiDeparse", "rxUiDeparse.default", "rxUiDeparse.lotriFix", "rxUiDeparse.rxControl" ] }, { "page": "rxUiDevelop", "title": "rxUiDevelop - Enable/Disable rxUi development. Here all $ completions are given", "concept": [ "Developer API" ], "topics": [ "rxUiDevelop" ] }, { "page": "rxUiEtaDistAnchors", "title": "Where each declared distribution's arguments are computed in the model", "concept": [ "Variability and uncertainty" ], "topics": [ "rxUiEtaDistAnchors" ] }, { "page": "rxUiEtaDists", "title": "The random effects that declare a distribution", "concept": [ "Variability and uncertainty" ], "topics": [ "assertRxUiNoEtaDist", "rxUiEtaDists", "testRxUiEtaDist" ] }, { "page": "rxUiGet", "title": "S3 for getting information from UI model", "concept": [ "Developer API" ], "topics": [ "rxUiGet", "rxUiGet.allCovs", "rxUiGet.cmtLines", "rxUiGet.covLhs", "rxUiGet.default", "rxUiGet.dvidLine", "rxUiGet.etaLhs", "rxUiGet.fun", "rxUiGet.funPartsDigest", "rxUiGet.funPrint", "rxUiGet.funTxt", "rxUiGet.ini", "rxUiGet.iniFun", "rxUiGet.interpLines", "rxUiGet.levelLhs", "rxUiGet.levels", "rxUiGet.lhsCov", "rxUiGet.lhsEta", "rxUiGet.lhsTheta", "rxUiGet.lhsVar", 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"title": "Softplus Activation Function", "concept": [ "Activation Functions" ], "topics": [ "softplus" ] }, { "page": "splitBolus", "title": "Split bolus doses across compartments inside an rxode2 model", "concept": [ "Event tables" ], "topics": [ "splitBolus" ] }, { "page": "splitBolusInfusion-directive", "title": "Split bolus doses into bolus and infusion paths (model directive)", "concept": [ "Event tables" ], "topics": [ "splitBolusInfusion", "splitBolusInfusion()", "splitBolusInfusion-directive" ] }, { "page": "splitInfusion", "title": "Split infusion doses across compartments inside an rxode2 model", "concept": [ "Event tables" ], "topics": [ "splitInfusion" ] }, { "page": "splitInfusionBolus-directive", "title": "Split infusion doses into infusion and bolus paths (model directive)", "concept": [ "Event tables" ], "topics": [ "splitInfusionBolus", "splitInfusionBolus()", "splitInfusionBolus-directive" ] }, { "page": "stat_amt", "title": "Dosing/Amt geom/stat", "concept": [ 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