Man pages for rxode2
Facilities for Simulating from ODE-Based Models

add.dosingAdd dosing to eventTable
add.samplingAdd sampling to eventTable
as.arrowConvert an rxSolveOom result to a lazy Arrow Dataset
as.data.table.rxEtConvert an event table to a data.table
as.etCoerce object to data.frame
as.iniTurn into an ini block for initialization
as.modelTurn into a model expression
as.rxUiAs rxode2 ui
assertCompartmentExistsVerify that the compartment exists in a model
assertCompartmentNameVerify that a value is a valid nlmixr2 compartment name
assertCompartmentNewVerify that a compartment would be new to the model
assertRxUiAssert properties of the rxUi models
assertVariableExistsAssert a variable exists in the model
assertVariableNewAssert a variable would be new to the model
as_tibble.rxEtConvert to tbl
binomProbsCalculate expected confidence bands with binomial sampling...
bolusAdminister a bolus dose inside a rxode2 model
boxCoxboxCox/yeoJohnson and inverse boxCox/yeoJohnson functions
coef.rxode2Return the rxode2 coefficients
coef.rxUiExtract the initial coefficients from an rxode2 model (rxUi)
cvPostSample a covariance Matrix from the Posterior Inverse Wishart...
delayDelayed state for delay differential equations
dELUDerivatives of the Exponential Linear Unit (ELU) Activation...
dfWishartThis uses simulations to match the rse
dGELUDerivatives of GELU
dlReLUDerivative of Leaky ReLU activation function
dot-assertRenameErrorModelLineThis function asserts the requested rename makes sense
dot-cbindOmecbind Ome
dot-clearPipeClear/Set pipeline
dot-collectWarningsCollect warnings and just warn once.
dot-convertIdConvert a factor/char to an id
dot-copyUiThis copies the rxode2 UI object so it can be modified
dot-expandParsExpand parameters
dot-extraCGenerate extraC information for rxode2 models
dot-extraCnowGet the extraCnow for compiling
dot-getErrDistGet defined residual information for parsing elsewhere
dot-getLastIdLvlGet the last 'idLvl'
dot-getWhGet the internal breakdown of an evid
dot-handleSingleErrTypeNormOrTFoceiBaseHandle the single error for normal or t distributions
dot-iniGetAppendArgThis gets the append arg for the ini() piping
dot-iniHandleAppendReorder rows in iniDf
dot-iniHandleLineUpdate the iniDf of a model
dot-matchesLangTemplateCheck if a language object matches a template language object
dot-minfoInternal messaging statements
dot-modelHandleModelLinesHandle model lines
dot-pipeRxAssign in the rxode2 pipeline
dot-quoteCallInfoLinesReturns quoted call information
dot-rstudioCompleteDetermine if Rstudio completion 2025+ is running
dot-rxAdjointAdjoint (backward) sensitivity equations for a model
dot-rxAdjointExpandBuild the adjoint-expansion model text for an in-engine...
dot-rxAdjointGradAdjoint gradient of an objective (single backward sweep)
dot-rxAdjointGradBuildBuild the symbolic part of an adjoint objective gradient...
dot-rxAdjointGradEvalEvaluate a prebuilt adjoint objective gradient at given...
dot-rxAdjointGradEvalCEvaluate a prebuilt adjoint objective gradient in C++
dot-rxAdjointGradPopAdjoint gradient of a POPULATION objective (sum over...
dot-rxAdjointMethodStiffDoes an adjoint ('s') solve method require the stiff analytic...
dot-rxAdjointModelBuild (and cache) the compiled adjoint-expansion model for...
dot-rxAdjointSolveSolve the full-trajectory adjoint sensitivities for a model
dot-rxAdjointSolveBuildBuild the symbolic part of a full-trajectory adjoint solve...
dot-rxAdjointSolveEvalCEvaluate a prebuilt full-trajectory adjoint solve in C++
dot-rxBlankIniGet a blank, theta1, or eta1 initialization block for iniDf
dot-rxCReturn the C code of an internal function
dot-rxDelaySensJumpMapDose-induced breaking-point jump for forward delay...
dot-rxDiscreteAdjointBuildBuild symbolic evaluators for the discrete adjoint (RHS,...
dot-rxDiscreteAdjointGradDiscrete adjoint gradient of a trajectory objective
dot-rxDiscreteForwardSensDiscrete forward sensitivity of a fixed-step RK4 solve
dot-rxDocTablePrint out a table in the documentation
dot-rxFwdSensJacBlockFull-system Jacobian for a first-order forward-sensitivity...
dot-rxGetHiBoundaryPred1AndIniGet the upper boundary condition when the transformation it
dot-rxGetLambdaFromPred1AndIniGet the lambda value based on the pred information
dot-rxGetLowBoundaryPred1AndIniGet the lower boundary condition when the transformation...
dot-rxGetPredictionDVTransformGet the Observation transformation
dot-rxGetPredictionFGet the prediction name
dot-rxGetPredictionFTransformGet the prediction transformation
dot-rxGetSeedGet the random seed for the session
dot-rxGetVarianceForErrorTypeGet Variance for error type
dot-rxInjectMatExpOdesInternal function for calculating the Jacobian
dot-rxIsLinCmtInternal function to tell if the linCmt() is the model...
dot-rxJacobianInternal function for calculating the Jacobian
dot-rxLastCompileSuccessWas the last compilation successful?
dot-rxLinCmtGet the linear compartment model states
dot-rxLinCmtGenInternal function to generate the model variables for a...
dot-rxLinNcmtGet the number of linear compartments
dot-rxMemoisedFnsClear memoise cache for rxode2
dot-rxode2ptrsGet the rxode2 function pointers
dot-rxPastBaseLinesFromEnvBase past(state, tau) <- expr history lines from a symengine...
dot-rxPruneInternal Pruning function
dot-rxSEeqUsrReturn the equivalents symengine user functions from C
dot-rxSensSensitivity for model
dot-rxSensStrippableGet model properties without compiling it.
dot-rxSetSeedSet the random seed for the session
dot-rxTransformrxode2 general transformation function
dot-rxTransInfoGet the information about the rxode2 derived parameter...
dot-rxWithOptionsTemporarily set options then restore them while running code
dot-rxWithSinkWith one sink, then release
dot-rxWithWdTemporarily set options then restore them while running code
dot-s3registerRegister a method for a suggested dependency
dot-solComp2Calculate the lambdas and coefficients of the two compartment...
dot-solComp3Calculate the lambdas and coefficients of the three...
dot-symengineFsReturn symengineFs from user functions
dot-toClassicEvidThis converts NONMEM-style EVIDs to classic RxODE events
dot-udfCallFunArgGet the function name with the current arguments as a string
dot-udfEnvResetLock/Unlock environment for getting R user functions
dot-udfEnvSetSetup the UDF environment (for querying user defined...
dot-udfEnvSetUdfUse the udf model variable information to get the environment...
dot-udfExistsSee if the UI function exists in given environment.
dot-udfMd5InfoGet the udf strings for creating model md5
dot-uiArgHandle arguments for ui functions
dot-useUtfInternal function to figure out if this session supports...
dot-vecDfConvert numeric vector to repeated data.frame
dPReLUDerivatives Parametric ReLU Activation Function
dReLUDerivative of the Rectified Linear Unit (ReLU) Activation...
dSELUDerivative of the Scaled Exponential Linear Unit (SELU)...
dsoftplusDefault Softplus Activation Function
dSwishDerivative of the Swish Activation Function
ELUExponential Linear Unit (ELU) Activation Function
erfError function
etEvent Table Function
etExpandExpand additional doses
etRbindCombining event tables
etRepRepeat an rxode2 event table
etSeqSequence of event tables
etTransEvent translation for rxode2
eventTableCreate an event table object
evid_Push a future dose or observation event from within an rxode2...
findLhsFind the assignments in R expression
fixef.rxUiExtract fixed effects from an rxode2 model (rxUi)
forderForceBaseForce using base order for rxode2 radix sorting
gammapGammap: normalized lower incomplete gamma function
gammapDergammapDer: derivative of gammap
gammapInvgammapInv and gammapInva: Inverses of normalized gammap...
gammaqGammaq: normalized upper incomplete gamma function
gammaqInvgammaqInv and gammaqInva: Inverses of normalized gammaq...
GELUGELU activation function
genShinyApp.templateGenerate an example (template) of a dosing regimen shiny app
getBaseIniSimModelGet the base simulation model for simulation with inis in the...
getBaseSimModelGet the base simulation model for simulation
getBaseSymengineModelGet the symengine for loading into symengine with 'rxS()'
getRxThreadsGet/Set the number of threads that rxode2 uses
guide_noneEmpty Guide
head.rxSolveOomFirst rows of an out-of-memory solved object
indLinTransition ODEs written in d/dt() format to matrix...
infuseAdminister a infusion (with rate being fixed) inside a rxode2...
infuseDurAdminister a infusion (with duration being fixed) inside a...
iniIni block for rxode2/nlmixr models
ini-setAssign the ini block in the rxode2 related object
invWR1dOne correlation sample from the Inverse Wishart distribution
is.rxEtCheck if object is an rxEt event table
is.rxSolveCheck to see if this is an rxSolve object.
is.rxStackDataReturn if the object can be stacked
linModLinear model to replace in rxode2 ui model
linToOdeConvert linCmt rxUi models to ODE rxUi models
llikBetaCalculate the log likelihood of the binomial function (and...
llikBinomCalculate the log likelihood of the binomial function (and...
llikCauchylog likelihood of Cauchy distribution and it's derivatives...
llikChisqlog likelihood and derivatives for chi-squared distribution
llikExplog likelihood and derivatives for exponential distribution
llikFlog likelihood and derivatives for F distribution
llikGammalog likelihood and derivatives for Gamma distribution
llikGeomlog likelihood and derivatives for Geom distribution
llikNbinomCalculate the log likelihood of the negative binomial...
llikNbinomMuCalculate the log likelihood of the negative binomial...
llikNormLog likelihood for normal distribution
llikPoislog-likelihood for the Poisson distribution
llikTLog likelihood of T and it's derivatives (from stan)
llikUniflog likelihood and derivatives for Unif distribution
llikWeibulllog likelihood and derivatives for Weibull distribution
logitlogit and inverse logit (expit) functions
lowergammalowergamma: upper incomplete gamma function
lReLULeaky ReLU activation function
meanProbsCalculate expected confidence bands or prediction intreval...
mexpitmexpit - Convert log-scale numbers to probabilities
mixSpecify a mixture model of variables
mlogitmlogit - Convert multiple probabilities to log-scale numbers
modelModel block for rxode2/nlmixr models
modelExtractExtract model lines from a rxui model
model-setAssign the model block in the rxode2 related object
multiplyMultiply dose the rxode2 system in the model
obsAdd observations to a model
odeMethodToIntConversion between character and integer ODE integration...
odeToLinConvert ODE-based linear compartment models to analytical...
phantomAdminister a phantom/transit dose inside a rxode2 model
phiCumulative distribution of standard normal
plot.rxSolvePlot rxode2 objects
plus-.rxSolveUpdate Solved object with '+'
PReLUParametric ReLU Activation Function
print.rxCoefPrint the rxCoef object
print.rxDllPrint rxDll object
print.rxModelVarsPrint Values
print.rxode2Print information about the rxode2 object.
probitprobit and inverse probit functions
reexportsObjects exported from other packages
ReLURectified Linear Unit (ReLU) Activation Function
replaceReplace dose the rxode2 system in the model
resetReset the rxode2 system in the model
rinvchisqScaled Inverse Chi Squared distribution
rLKJ1One correlation sample from the LKJ distribution
rxAllowUnloadAllow unloading of dlls
rxAppendModelAppend two rxui models together
rxAssignControlValueAssign Control Variable
rxAssignPtrAssign pointer based on model variables
rxbetaSimulate beta variable from threefry generator
rxbinomSimulate Binomial variable from threefry generator
rxBlockZerosCreates a logical matrix for block matrixes.
rxCReturn the C file associated with the rxode2 object
rxCatUse cat when rxode2.verbose is TRUE
rxcauchySimulate Cauchy variable from threefry generator
rxCbindStudyIndividualBind the study parameters and individual parameters
rxChainrxChain Chain or add item to solved system of equations
rxChain2Second command in chaining commands
rxchisqSimulate chi-squared variable from threefry generator
rxCleanCleanup anonymous DLLs by unloading them
rxCombineErrorLinesCombine Error Lines and create rxode2 expression
rxCompileCompile a model if needed
rxConditionCurrent Condition for rxode2 object
rxControlUpdateSensThis updates the tolerances based on the sensitivity...
rxCreateCacheThis will create the cache directory for rxode2 to save...
rxDAdd to rxode2's derivative tables
rxDeleteDelete the DLL for the model
rxDemoteAddErrDemote the error type
rxDerivedCalculate derived parameters for the 1-, 2-, and 3-...
rxDeserializeDeserialize a Raw Vector or String to an R Object
rxDfdyJacobian and parameter derivatives
rxDllReturn the DLL associated with the rxode2 object
rxDynLoadLoad rxode2 object
rxDynUnloadUnload rxode2 object
rxErrTypeCombineCombine transformations and error structures
rxEtDispatchSolveDispatch solve to 'rxode2' solve
rxEventSensDeactivateTurn off the rxode2 event-sensitivity jump injection
rxEventSensLoadModelPoint the rxode2 event-sensitivity globals at a...
rxEventTableFileCreate a file-backed event table reference
rxEvidEVID formatting for tibble and other places.
rxexpSimulate exponential variable from threefry generator
rxExpandFEta_Expand d(f)/d(eta)
rxExpandGridFaster expand.grid
rxExpandGrid_Expand grid internal function
rxExpandIfElseExpand if/else clauses into multiple different types of...
rxExpandSens_Expand sensitivity
rxExpandSens2_Expand second order sensitivity
rxExpandSens3_Expand third order sensitivity
rxfSimulate F variable from threefry generator
rxFixPopApply the fixed population estimated parameters
rxFixResLiterally fix residual parameters
rxForgetClear memoise caches for rxode2
rxFunAdd/Create C functions for use in rxode2
rxFunParseAdd user function to rxode2
rxgammaSimulate gamma variable from threefry generator
rxgeomSimulate geometric variable from threefry generator
rxGetControlrxGetControl option from ui
rxGetDefaultSerializeGet the Default Serialization Type
rxGetDistributionSimulationLinesThis is a S3 method for getting the distribution lines for a...
rxGetLinGet the linear compartment model true function
rxGetModelGet the rxode2 model variables without compiling the model
rxGetrxode2Get rxode2 model from object
rxGetSeedGet the rxode2 seed
rxGetSerialType_Get the serialization type from raw vector
rxHasArTest if a model uses an autoregressive ('ar()') residual
rxHtmlFormat rxSolve and related objects as html.
rxIndLinStateSet the preferred factoring by state
rxIndLinStrategyThis sets the inductive linearization strategy for matrix...
rxInitsInitial Values and State values for a rxode2 object
rxIntToBaseConvert a positive base
rxIntToLetterConvert a positive integer to a letter series
rxInvInvert matrix using RcppArmadillo.
rxIsCheck the type of an object using Rcpp
rxIsAutoSwitchCheck whether an ODE method string is an AutoSwitch composite...
rxIsCurrentChecks if the rxode2 object was built with the current build
rxIsDenseCheck whether an ODE solving method supports dense output
rxIsImplicitCheck whether an ODE solving method requires a Jacobian (is...
rxIsLoadedDetermine if the DLL associated with the rxode2 object is...
rxIsNonStiffCheck whether an ODE solving method is a purely non-stiff...
rxIsStiffCheck whether an ODE solving method is a purely stiff solver
rxLastCompileGet the last compiled model information as alist
rxLhsLeft handed Variables
rxLoadStateRestore a pre-integration rxode2 solver state from a binary...
rxLockLock/unlocking of rxode2 dll file
rxMd5Return the md5 of an rxode2 object or file
rxMemoryEstimateEstimate memory required by rxSolve() for a given dataset and...
rxMemSummaryCreate a per-ID event summary for memory estimation
rxModels_Get the rxModels information
rxModelVarsAll model variables for a rxode2 object
rxnbinomSimulate Binomial variable from threefry generator
rxNormGet the normalized model
rxnormVSimulate random normal variable from threefry generator
rxNumLoadedGet the number of loaded rxode2 DLLs
rxode2Create an ODE-based model specification
rxode2parseInternal translation to get model variables list
rxode2parseAssignPackagesToLoadControl the packages that are loaded when a 'rxode2' model...
rxode2parseAssignPointerTranslationThis sets function gets the currently assigned function...
rxode2parseAssignTranslationThis assigns the c level linkages for a roxde2 model
rxode2parseDThis gives the derivative table for rxode2
rxode2parseGetPointerAssignmentThis function gets the currently assigned function pointer...
rxode2parseGetTranslationThis function gets the currently assigned translations
rxode2-setSet the function body of an rxUi object while retaining other...
rxOldQsDesDeserialize a Raw Vector using qs
rxOmegaVarCovDerivVariance-covariance (non-Cholesky) Omega parameterization...
rxOmegaVarCovDeriv_Variance-covariance (non-Cholesky) Omega parameterization...
rxOptExprOptimize rxode2 for computer evaluation
rxordSimulate ordinal value
rxParamsParameters specified by the model
rxParseErrPrepare Error function for inclusion in rxode2
rxParsePkParse PK function for inclusion in rxode2
rxParsePredPrepare Pred function for inclusion in rxode2
rxParseSetSilentErrSilence some of rxode2's C/C++ messages
rxParseSuppressMsgRespect suppress messages
rxPkgCreates a package from compiled rxode2 models
rxpoisSimulate random Poisson variable from threefry generator
rxPpSimulate a from a Poisson process
rxPreferredDistributionNameChange distribution name to the preferred distribution name...
rxProgressrxode2 progress bar functions
rxPrunePrune branches (ie if/else) from rxode2
rxRateDurCreates a rxRateDur object
rxRawToCConvert a Raw Vector or R object to C Code
rxReloadReload rxode2 DLL
rxRemoveControlrxRemoveControl options for UI object
rxRenameRename items inside of a 'rxode2' ui model
rxRepR0_Rep R0 for foce
rxReqRequire namespace, otherwise throw error.
rxReservedKeywordsA list and description of rxode2 supported reserved keywords
rxResidualErrorA description of Rode2 supported residual errors
rxRmvnSimulate from a (truncated) multivariate normal
rxSLoad a model into a symengine environment
rxSaveStateSave the pre-integration rxode2 solver state to a binary file
rxSeedEngThis seeds the engine based on the number of cores used in...
rxSensMatExpDifferentiate and expand a matrix exponential model with...
rxSerializeSerialize an R Object to a Raw Vector
rxSetControlrxSetControl options for UI object
rxSetCovariateNamesForPipingAssign covariates for piping
rxSetIni0Set Initial conditions to time zero instead of the first...
rxSetPipingAutoSet the variables for the model piping automatic covarite...
rxSetProdDefunct setting of product
rxSetProgressBarSet timing for progress bar
rxSetSeedSet the parallel seed for rxode2 random number generation
rxSetSilentErrSilence some of rxode2's C/C++ messages
rxSetSumDefunct setting of sum
rxSetupIniSetup the initial conditions.
rxSetupScaleSetup the initial conditions.
rxShinyUse Shiny to help develop an rxode2 model
rxSimThetaOmegaSimulate Parameters from a Theta/Omega specification
rxSolveOptions, Solving & Simulation of an ODE/solved system
rxSolveAdjointSolve a model with adjoint (backward) sensitivities, drop-in...
rxSolveAdjointRk4Solve a model with an in-engine discrete-adjoint ('s') method
rxSolveChunkedSolve an ODE model in memory-safe chunks
rxSolveFreeFree the C solving/parsing information.
rxSolveSetupSee if the memory is installed for a solve
rxSplitPlusQThis function splits a function based on + or - terms
rxStackStack a solved object for things like default ggplot2 plot
rxStateState variables
rxStateOdeGet the ODE states only
rxSumProdModelRecast model in terms of sum/prod
rxSupportedFunsGet list of supported functions
rxSuppressMsgRespect suppress messages
rxSymInvCholGet Omega^-1 and derivatives
rxSymInvCholCreateCreates an object for calculating Omega/Omega^-1 and...
rxSymInvCholNReturn the dimension of the built-in derivatives/inverses
rxSyncOptionsSync options with rxode2 variables
rxSyntaxFunctionsA list and description of Rode supported syntax functions
rxtSimulate student t variable from threefry generator
rxTempDirGet the rxode2 temporary directory
rxThemerxTheme is the ggplot2 theme for rxode2 plots
rxToSErxode2 to symengine environment
rxTransTranslate the model to C code if needed
rxUdfUiThis function is called when processing rxode2 user functions...
rxUdfUiControlReturn the control that is being processed or setup control...
rxUdfUiDataReturn the data.frame that is being processed or setup...
rxUdfUiEstReturn the current estimation method for the UI processing
rxUdfUiExprGive the expression as a compressed model or expression
rxUdfUiFlagIs the expression actually a flag that can be used in the...
rxUdfUiIniDfGet the rxode2 iniDf of the current UI being processed (or...
rxUdfUiIniLhsReturn the lhs parsed language expression
rxUdfUiIsValueIs the expression actually equal to a value?
rxUdfUiMvReturn the model variables that is being processed or setup...
rxUdfUiNumThis gives the current number in the ui of the particular...
rxUdfUiParsingReturns if the current ui function is being parsed
rxUdfUiResetReset the rxode2 ui environment variables
rxUiDecompressCompress/Decompress 'rxode2' ui
rxUiDeparseThis is a generic function for deparsing certain objects when...
rxUiDeveloprxUiDevelop - Enable/Disable rxUi development. Here all $...
rxUiGetS3 for getting information from UI model
rxunifSimulate uniform variable from threefry generator
rxUnloadAllUnloads all rxode2 compiled DLLs
rxUseUse model object in your package
rxValidateValidate rxode2 This allows easy validation/qualification of...
rxVersionVersion and repository for this dparser package.
rxweibullSimulate Weibull variable from threefry generator
rxWithSeedPreserved seed and possibly set the seed
SELUScaled Exponential Linear Unit (SELU) Activation Function
setCvodeLinearSolverSet the CVODE linear solver
softplusSoftplus Activation Function
splitBolusSplit bolus doses across compartments inside an rxode2 model
stat_amtDosing/Amt geom/stat
stat_censCensoring geom/stat
summary.rxDllSummary of rxDll object
summary.rxode2Print expanded information about the rxode2 object.
swapMatListWithCubeSwaps the matrix list with a cube
SwishSwitch Activation Function
testIniDfThis function tests if this object is a iniDf as needed by...
testRxLinCmtTest if rxode2 uses linear solved systems
testRxUnboundedTest if the rxode2 model has any parameters with user defined...
toTrialDurationConvert event data to trial duration data A helper function...
update.rxUiUpdate for rxUi
uppergammauppergamma: upper incomplete gamma function
zeroReSet random effects and residual error to zero
rxode2 documentation built on July 28, 2026, 5:08 p.m.