Facilities for Simulating from ODE-Based Models

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Documentation for package ‘rxode2’ version 5.1.7

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.
• Package NEWS.

Help Pages

A B C D E F G I L M O P R S T U W Y Z misc

-- A --

add.dosing	Add dosing to eventTable
add.sampling	Add sampling to eventTable
as.arrow	Convert an rxSolveOom result to a lazy Arrow Dataset
as.arrow.rxSolveOom	Convert an rxSolveOom result to a lazy Arrow Dataset
as.character.rxEvid	EVID formatting for tibble and other places.
as.character.rxRateDur	Creates a rxRateDur object
as.data.table.rxEt	Convert an event table to a data.table
as.et	Coerce object to data.frame
as.et.default	Coerce object to data.frame
as.ini	Turn into an ini block for initialization
as.ini.call	Turn into an ini block for initialization
as.ini.character	Turn into an ini block for initialization
as.ini.data.frame	Turn into an ini block for initialization
as.ini.default	Turn into an ini block for initialization
as.ini.lotriFix	Turn into an ini block for initialization
as.ini.matrix	Turn into an ini block for initialization
as.model	Turn into a model expression
as.model.call	Turn into a model expression
as.model.character	Turn into a model expression
as.model.default	Turn into a model expression
as.model.list	Turn into a model expression
as.rxEvid	EVID formatting for tibble and other places.
as.rxRateDur	Creates a rxRateDur object
as.rxUi	As rxode2 ui
as.rxUi.default	As rxode2 ui
as.rxUi.function	As rxode2 ui
as.rxUi.rxModelVars	As rxode2 ui
as.rxUi.rxode2	As rxode2 ui
as.rxUi.rxode2tos	As rxode2 ui
as.rxUi.rxUi	As rxode2 ui
assertCompartmentExists	Verify that the compartment exists in a model
assertCompartmentName	Verify that a value is a valid nlmixr2 compartment name
assertCompartmentNew	Verify that a compartment would be new to the model
assertExists	Verify that a value is a valid nlmixr2 compartment name
assertIniDf	This function tests if this object is a iniDf as needed by the UI
assertParameterValue	Verify that a value is a valid nlmixr2 compartment name
assertRxLinCmt	Test if rxode2 uses linear solved systems
assertRxUi	Assert properties of the rxUi models
assertRxUiEstimatedResiduals	Assert properties of the rxUi models
assertRxUiIovNoCor	Assert properties of the rxUi models
assertRxUiMixedOnly	Assert properties of the rxUi models
assertRxUiMuRefOnly	Assert properties of the rxUi models
assertRxUiNoAutoregressive	Assert properties of the rxUi models
assertRxUiNoMix	Assert properties of the rxUi models
assertRxUiNoOmegaDf	Assert properties of the rxUi models
assertRxUiNoOmegaNormalPriors	Assert properties of the rxUi models
assertRxUiNoPriors	Assert properties of the rxUi models
assertRxUiNormal	Assert properties of the rxUi models
assertRxUiNormalPriors	Assert properties of the rxUi models
assertRxUiPopulationOnly	Assert properties of the rxUi models
assertRxUiPrediction	Assert properties of the rxUi models
assertRxUiRandomOnIdOnly	Assert properties of the rxUi models
assertRxUiSingleEndpoint	Assert properties of the rxUi models
assertRxUiTransformNormal	Assert properties of the rxUi models
assertRxUnbounded	Test if the rxode2 model has any parameters with user defined boundaries
assertVariableExists	Assert a variable exists in the model
assertVariableName	Verify that a value is a valid nlmixr2 compartment name
assertVariableNew	Assert a variable would be new to the model
as_tibble.rxEt	Convert to tbl

-- B --

binomProbs	Calculate expected confidence bands with binomial sampling distribution
binomProbs.default	Calculate expected confidence bands with binomial sampling distribution
bolus	Administer a bolus dose inside a rxode2 model
boxCox	boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions
boxCoxInv	boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions

-- C --

c.rxEvid	EVID formatting for tibble and other places.
c.rxRateDur	EVID formatting for tibble and other places.
coef.function	Extract the initial coefficients from an rxode2 model (rxUi)
coef.rxUi	Extract the initial coefficients from an rxode2 model (rxUi)
confint.rxSolve	Simulated percentiles, with confidence bands, from a solved rxode2 object
cvPost	Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

-- D --

d2aELU	Derivatives of the Exponential Linear Unit (ELU) Activation Function
d2ELU	Derivatives of the Exponential Linear Unit (ELU) Activation Function
d2ELUa	Derivatives of the Exponential Linear Unit (ELU) Activation Function
d2GELU	Derivatives of GELU
d2softplus	Default Softplus Activation Function
d3GELU	Derivatives of GELU
d3softplus	Default Softplus Activation Function
d4GELU	Derivatives of GELU
d4softplus	Default Softplus Activation Function
delay	Delayed state for delay differential equations
dELU	Derivatives of the Exponential Linear Unit (ELU) Activation Function
dELUa	Derivatives of the Exponential Linear Unit (ELU) Activation Function
dfWishart	This uses simulations to match the rse
dGELU	Derivatives of GELU
dlReLU	Derivative of Leaky ReLU activation function
dmexpit	mexpit - Convert log-scale numbers to probabilities
dPReLU	Derivatives Parametric ReLU Activation Function
dPReLUa	Derivatives Parametric ReLU Activation Function
dPReLUa1	Derivatives Parametric ReLU Activation Function
dReLU	Derivative of the Rectified Linear Unit (ReLU) Activation Function
dSELU	Derivative of the Scaled Exponential Linear Unit (SELU) Activation Function
dsoftplus	Default Softplus Activation Function
dSwish	Derivative of the Swish Activation Function

-- E --

ELU	Exponential Linear Unit (ELU) Activation Function
erf	Error function
et	Event Table Function
et.default	Event Table Function
et.function	Event Table Function
et.rxode2	Event Table Function
et.rxParams	Event Table Function
et.rxSolve	Event Table Function
et.rxUi	Event Table Function
etExpand	Expand additional doses
etRbind	Combining event tables
etRep	Repeat an rxode2 event table
etSeq	Sequence of event tables
eventTable	Create an event table object
evid_	Push a future dose or observation event from within an rxode2 model
expit	logit and inverse logit (expit) functions

-- F --

format.rxEvid	EVID formatting for tibble and other places.
format.rxRateDur	EVID formatting for tibble and other places.

-- G --

gammap	Gammap: normalized lower incomplete gamma function
gammapDer	gammapDer: derivative of gammap
gammapInv	gammapInv and gammapInva: Inverses of normalized gammap function
gammapInva	gammapInv and gammapInva: Inverses of normalized gammap function
gammaq	Gammaq: normalized upper incomplete gamma function
gammaqInv	gammaqInv and gammaqInva: Inverses of normalized gammaq function
gammaqInva	gammaqInv and gammaqInva: Inverses of normalized gammaq function
GELU	GELU activation function
genShinyApp.template	Generate an example (template) of a dosing regimen shiny app
geom_amt	Dosing/Amt geom/stat
geom_cens	Censoring geom/stat
getRxThreads	Get/Set the number of threads that rxode2 uses

-- I --

indLin	Transition ODEs written in d/dt() format to matrix exponential / inductive linearization format
infuse	Administer a infusion (with rate being fixed) inside a rxode2 model
infuseDur	Administer a infusion (with duration being fixed) inside a rxode2 model
ini	Ini block for rxode2/nlmixr models
ini.default	Ini block for rxode2/nlmixr models
ini.rxUi	Ini block for rxode2/nlmixr models
ini<-	Assign the ini block in the rxode2 related object
is.rxEt	Check if object is an rxEt event table
is.rxStackData	Return if the object can be stacked

-- L --

linMod	Linear model to replace in rxode2 ui model
linMod0	Linear model to replace in rxode2 ui model
linModA	Linear model to replace in rxode2 ui model
linModA0	Linear model to replace in rxode2 ui model
linModB	Linear model to replace in rxode2 ui model
linModB0	Linear model to replace in rxode2 ui model
linModD	Linear model to replace in rxode2 ui model
linModD0	Linear model to replace in rxode2 ui model
linModM	Linear model to replace in rxode2 ui model
linModM0	Linear model to replace in rxode2 ui model
linToOde	Convert linCmt rxUi models to ODE rxUi models
llikBeta	Calculate the log likelihood of the binomial function (and its derivatives)
llikBinom	Calculate the log likelihood of the binomial function (and its derivatives)
llikCauchy	log likelihood of Cauchy distribution and it's derivatives (from stan)
llikChisq	log likelihood and derivatives for chi-squared distribution
llikExp	log likelihood and derivatives for exponential distribution
llikF	log likelihood and derivatives for F distribution
llikGamma	log likelihood and derivatives for Gamma distribution
llikGeom	log likelihood and derivatives for Geom distribution
llikNbinom	Calculate the log likelihood of the negative binomial function (and its derivatives)
llikNbinomMu	Calculate the log likelihood of the negative binomial function (and its derivatives)
llikNorm	Log likelihood for normal distribution
llikPois	log-likelihood for the Poisson distribution
llikT	Log likelihood of T and it's derivatives (from stan)
llikUnif	log likelihood and derivatives for Unif distribution
llikWeibull	log likelihood and derivatives for Weibull distribution
logit	logit and inverse logit (expit) functions
logitNormInfo	logit and inverse logit (expit) functions
lowergamma	lowergamma: upper incomplete gamma function
lReLU	Leaky ReLU activation function

-- M --

meanProbs	Calculate expected confidence bands or prediction intreval with normal or t sampling distribution
meanProbs.default	Calculate expected confidence bands or prediction intreval with normal or t sampling distribution
mexpit	mexpit - Convert log-scale numbers to probabilities
mix	Specify a mixture model of variables
mlogit	mlogit - Convert multiple probabilities to log-scale numbers
model	Model block for rxode2/nlmixr models
model.default	Model block for rxode2/nlmixr models
model.function	Model block for rxode2/nlmixr models
model.rxModelVars	Model block for rxode2/nlmixr models
model.rxode2	Model block for rxode2/nlmixr models
model.rxUi	Model block for rxode2/nlmixr models
model<-	Assign the model block in the rxode2 related object
modelExtract	Extract model lines from a rxui model
modelExtract.default	Extract model lines from a rxui model
modelExtract.function	Extract model lines from a rxui model
modelExtract.rxModelVars	Extract model lines from a rxui model
modelExtract.rxode2	Extract model lines from a rxui model
modelExtract.rxUi	Extract model lines from a rxui model
multiply	Multiply dose the rxode2 system in the model

-- O --

obs	Add observations to a model
odeMethodToInt	Conversion between character and integer ODE integration methods for rxode2
odeToLin	Convert ODE-based linear compartment models to analytical linCmt() form

-- P --

phantom	Administer a phantom/transit dose inside a rxode2 model
phi	Cumulative distribution of standard normal
plot.rxSolve	Plot rxode2 objects
plot.rxSolveConfint1	Plot rxode2 objects
plot.rxSolveConfint2	Plot rxode2 objects
predict.function	Options, Solving & Simulation of an ODE/solved system
predict.rxEt	Options, Solving & Simulation of an ODE/solved system
predict.rxode2	Options, Solving & Simulation of an ODE/solved system
predict.rxParams	Options, Solving & Simulation of an ODE/solved system
predict.rxSolve	Options, Solving & Simulation of an ODE/solved system
predict.rxUi	Options, Solving & Simulation of an ODE/solved system
PReLU	Parametric ReLU Activation Function
print.rxEvid	EVID formatting for tibble and other places.
print.rxModelVars	Print Values
probit	probit and inverse probit functions
probitInv	probit and inverse probit functions
probitNormInfo	logit and inverse logit (expit) functions

-- R --

rbind.rxEt	Combining event tables
ReLU	Rectified Linear Unit (ReLU) Activation Function
rename.function	Rename items inside of a 'rxode2' ui model
rename.rxUi	Rename items inside of a 'rxode2' ui model
rep.rxEt	Repeat an rxode2 event table
replace	Replace dose the rxode2 system in the model
reset	Reset the rxode2 system in the model
rinvchisq	Scaled Inverse Chi Squared distribution
rxAllowUnload	Allow unloading of dlls
rxAppendModel	Append two rxui models together
rxAssignControlValue	Assign Control Variable
rxAssignPtr	Assign pointer based on model variables
rxbeta	Simulate beta variable from threefry generator
rxbinom	Simulate Binomial variable from threefry generator
rxcauchy	Simulate Cauchy variable from threefry generator
rxCbindStudyIndividual	Bind the study parameters and individual parameters
rxchisq	Simulate chi-squared variable from threefry generator
rxClean	Cleanup anonymous DLLs by unloading them
rxClearActiveParLoader	Activate a registered parameter loader for solves
rxCompile	Compile a model if needed
rxCompile.character	Compile a model if needed
rxCompile.rxDll	Compile a model if needed
rxCompile.rxModelVars	Compile a model if needed
rxCompile.rxode2	Compile a model if needed
rxControl	Options, Solving & Simulation of an ODE/solved system
rxControlUpdateSens	This updates the tolerances based on the sensitivity equations
rxCores	Get/Set the number of threads that rxode2 uses
rxCreateCache	This will create the cache directory for rxode2 to save between sessions
rxD	Add to rxode2's derivative tables
rxDelete	Delete the DLL for the model
rxDerived	Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.
rxDfdy	Jacobian and parameter derivatives
rxEtDispatchSolve	Dispatch solve to 'rxode2' solve
rxEtDispatchSolve.default	Dispatch solve to 'rxode2' solve
rxEventTableFile	Create a file-backed event table reference
rxEvid	EVID formatting for tibble and other places.
rxexp	Simulate exponential variable from threefry generator
rxf	Simulate F variable from threefry generator
rxFixPop	Apply the fixed population estimated parameters
rxFixRes	Literally fix residual parameters
rxForcedPars	Forced parameters carried by a model / ui
rxForcedPars<-	Forced parameters carried by a model / ui
rxFromSE	rxode2 to symengine environment
rxFun	Add/Create C functions for use in rxode2
rxgamma	Simulate gamma variable from threefry generator
rxgeom	Simulate geometric variable from threefry generator
rxGetControl	rxGetControl option from ui
rxGetDefaultSerialize	Get the Default Serialization Type
rxGetLin	Get the linear compartment model true function
rxGetrxode2	Get rxode2 model from object
rxGetSeed	Get the rxode2 seed
rxHasAr	Test if a model uses an autoregressive ('ar()') residual
rxHtml	Format rxSolve and related objects as html.
rxHtml.rxSolve	Format rxSolve and related objects as html.
rxIndLinState	Set the preferred factoring by state
rxIndLinStrategy	This sets the inductive linearization strategy for matrix building
rxInjectedPars	Parameters injected into a solve by a par-loader hook
rxIntToBase	Convert a positive base
rxIntToLetter	Convert a positive integer to a letter series
rxInv	Invert matrix using RcppArmadillo.
rxIsAutoSwitch	Check whether an ODE method string is an AutoSwitch composite pair
rxIsCurrent	Checks if the rxode2 object was built with the current build
rxIsDense	Check whether an ODE solving method supports dense output
rxIsImplicit	Check whether an ODE solving method requires a Jacobian (is implicit)
rxIsNonStiff	Check whether an ODE solving method is a purely non-stiff solver
rxIsStiff	Check whether an ODE solving method is a purely stiff solver
rxLastCompile	Get the last compiled model information as alist
rxLhs	Left handed Variables
rxLock	Lock/unlocking of rxode2 dll file
rxMemoryEstimate	Estimate memory required by rxSolve() for a given dataset and model
rxMemSummary	Create a per-ID event summary for memory estimation
rxModelName	Name a model from the function that created it
rxModelName.default	Name a model from the function that created it
rxModelNameLhs	Name a model from the left hand side of an assignment
rxnbinom	Simulate Binomial variable from threefry generator
rxnbinomMu	Simulate Binomial variable from threefry generator
rxNorm	Get the normalized model
rxnorm	Simulate random normal variable from threefry generator
rxnormV	Simulate random normal variable from threefry generator
rxNumLoaded	Get the number of loaded rxode2 DLLs
RxODE	Create an ODE-based model specification
rxode	Create an ODE-based model specification
rxode2	Create an ODE-based model specification
rxode2<-	Set the function body of an rxUi object while retaining other object information (like data)
rxode2<-.default	Set the function body of an rxUi object while retaining other object information (like data)
rxode2<-.function	Set the function body of an rxUi object while retaining other object information (like data)
rxode2parse	Internal translation to get model variables list
rxode2parseAssignPackagesToLoad	Control the packages that are loaded when a 'rxode2' model dll is loaded
rxode2parseAssignTranslation	This assigns the c level linkages for a roxde2 model
rxode2parseD	This gives the derivative table for rxode2
rxode2parseGetPackagesToLoad	Control the packages that are loaded when a 'rxode2' model dll is loaded
rxode2parseGetPointerAssignment	This function gets the currently assigned function pointer assignments
rxode2parseGetTranslation	This function gets the currently assigned translations
RxODE<-	Set the function body of an rxUi object while retaining other object information (like data)
rxode<-	Set the function body of an rxUi object while retaining other object information (like data)
rxOdeToIndLin	Transition ODEs written in d/dt() format to matrix exponential / inductive linearization format
rxOmegaVarCovDeriv	Variance-covariance (non-Cholesky) Omega parameterization derivatives
rxOptExpr	Optimize rxode2 for computer evaluation
rxord	Simulate ordinal value
rxParam	Parameters specified by the model
rxParams	Parameters specified by the model
rxParams.rxEt	Parameters specified by the model
rxParams.rxode2	Parameters specified by the model
rxParams.rxSolve	Parameters specified by the model
rxParLoader	Parameter-loader flag on a model
rxParLoader<-	Parameter-loader flag on a model
rxParseSuppressMsg	Respect suppress messages
rxPkg	Creates a package from compiled rxode2 models
rxpois	Simulate random Poisson variable from threefry generator
rxPp	Simulate a from a Poisson process
rxPreferredDistributionName	Change distribution name to the preferred distribution name term
rxPriorBuildSpec	Build the C spec 'rxPriorLogDensityEval()' (and the C API) evaluates
rxPriorLogDensity	Value and gradient of a model's prior log density, on the natural scale
rxPriorOmegaToCholOmegaInvGrad	Chain-rule a natural-scale omega gradient into FOCEI's cholOmegaInv scale
rxProgress	rxode2 progress bar functions
rxProgressAbort	rxode2 progress bar functions
rxProgressStop	rxode2 progress bar functions
rxRateDur	Creates a rxRateDur object
rxRegisterUiAssembled	Register or remove a ui assembly hook
rxRegisterUiPrep	Register or remove a solve-time ui preparation hook
rxRemoveControl	rxRemoveControl options for UI object
rxRemoveUiAssembled	Register or remove a ui assembly hook
rxRemoveUiPrep	Register or remove a solve-time ui preparation hook
rxRename	Rename items inside of a 'rxode2' ui model
rxRename.default	Rename items inside of a 'rxode2' ui model
rxRename.function	Rename items inside of a 'rxode2' ui model
rxRename.rxUi	Rename items inside of a 'rxode2' ui model
rxReservedKeywords	A list and description of rxode2 supported reserved keywords
rxResidualError	A description of Rode2 supported residual errors
rxRmFun	Add/Create C functions for use in rxode2
rxRmvn	Simulate from a (truncated) multivariate normal
rxS	Load a model into a symengine environment
rxSensMatExp	Differentiate and expand a matrix exponential model with forward sensitivities
rxSetActiveParLoader	Activate a registered parameter loader for solves
rxSetControl	rxSetControl options for UI object
rxSetCovariateNamesForPiping	Assign covariates for piping
rxSetIni0	Set Initial conditions to time zero instead of the first observed/dosed time
rxSetPipingAuto	Set the variables for the model piping automatic covarite selection
rxSetProd	Defunct setting of product
rxSetProgressBar	Set timing for progress bar
rxSetSeed	Set the parallel seed for rxode2 random number generation
rxSetSum	Defunct setting of sum
rxShiny	Use Shiny to help develop an rxode2 model
rxShiny.default	Use Shiny to help develop an rxode2 model
rxShiny.rxSolve	Use Shiny to help develop an rxode2 model
rxSimThetaOmega	Simulate Parameters from a Theta/Omega specification
rxSolve	Options, Solving & Simulation of an ODE/solved system
rxSolve.default	Options, Solving & Simulation of an ODE/solved system
rxSolve.function	Options, Solving & Simulation of an ODE/solved system
rxSolve.nlmixr2FitCore	Options, Solving & Simulation of an ODE/solved system
rxSolve.nlmixr2FitData	Options, Solving & Simulation of an ODE/solved system
rxSolve.rxode2tos	Options, Solving & Simulation of an ODE/solved system
rxSolve.rxSolve	Options, Solving & Simulation of an ODE/solved system
rxSolve.rxUi	Options, Solving & Simulation of an ODE/solved system
rxSolveAdjoint	Solve a model with adjoint (backward) sensitivities, drop-in for forward sens
rxSolveAdjointRk4	Solve a model with an in-engine discrete-adjoint ('s') method
rxSolveChunked	Solve an ODE model in memory-safe chunks
rxStack	Stack a solved object for things like default ggplot2 plot
rxState	State variables
rxStateOde	Get the ODE states only
rxSumProdModel	Recast model in terms of sum/prod
rxSupportedFuns	Get list of supported functions
rxSuppressMsg	Respect suppress messages
rxSymInvChol	Get Omega^-1 and derivatives
rxSyncOptions	Sync options with rxode2 variables
rxSyntaxFunctions	A list and description of Rode supported syntax functions
rxt	Simulate student t variable from threefry generator
rxTempDir	Get the rxode2 temporary directory
rxTest	Validate rxode2 This allows easy validation/qualification of nlmixr by running the testing suite on your system.
rxTheme	rxTheme is the ggplot2 theme for rxode2 plots
rxTick	rxode2 progress bar functions
rxToIndLin	Transition ODEs written in d/dt() format to matrix exponential / inductive linearization format
rxToSE	rxode2 to symengine environment
rxTrans	Translate the model to C code if needed
rxTrans.character	Translate the model to C code if needed
rxTrans.default	Translate the model to C code if needed
rxUdfUiControl	Return the control that is being processed or setup control for processing
rxUdfUiData	Return the data.frame that is being processed or setup data.frame for processing
rxUdfUiEst	Return the current estimation method for the UI processing
rxUdfUiExpr	Give the expression as a compressed model or expression
rxUdfUiFlag	Is the expression actually a flag that can be used in the rxUdfUi functions?
rxUdfUiIniDf	Get the rxode2 iniDf of the current UI being processed (or return NULL)
rxUdfUiIniLhs	Return the lhs parsed language expression
rxUdfUiIsValue	Is the expression actually equal to a value?
rxUdfUiMv	Return the model variables that is being processed or setup model variables for processing
rxUdfUiNum	This gives the current number in the ui of the particular function being called.
rxUdfUiParsing	Returns if the current ui function is being parsed
rxUiCompress	Compress/Decompress 'rxode2' ui
rxUiDecompress	Compress/Decompress 'rxode2' ui
rxUiDeparse	This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDeparse.default	This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDeparse.lotriFix	This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDeparse.rxControl	This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDevelop	rxUiDevelop - Enable/Disable rxUi development. Here all $ completions are given
rxUiGet	S3 for getting information from UI model
rxUiGet.allCovs	S3 for getting information from UI model
rxUiGet.cmtLines	S3 for getting information from UI model
rxUiGet.covLhs	S3 for getting information from UI model
rxUiGet.default	S3 for getting information from UI model
rxUiGet.dvidLine	S3 for getting information from UI model
rxUiGet.etaLhs	S3 for getting information from UI model
rxUiGet.fun	S3 for getting information from UI model
rxUiGet.funPartsDigest	S3 for getting information from UI model
rxUiGet.funPrint	S3 for getting information from UI model
rxUiGet.funTxt	S3 for getting information from UI model
rxUiGet.ini	S3 for getting information from UI model
rxUiGet.iniFun	S3 for getting information from UI model
rxUiGet.interpLines	S3 for getting information from UI model
rxUiGet.levelLhs	S3 for getting information from UI model
rxUiGet.levels	S3 for getting information from UI model
rxUiGet.lhsCov	S3 for getting information from UI model
rxUiGet.lhsEta	S3 for getting information from UI model
rxUiGet.lhsTheta	S3 for getting information from UI model
rxUiGet.lhsVar	S3 for getting information from UI model
rxUiGet.lstChr	S3 for getting information from UI model
rxUiGet.md5	S3 for getting information from UI model
rxUiGet.model	S3 for getting information from UI model
rxUiGet.modelDesc	S3 for getting information from UI model
rxUiGet.modelFun	S3 for getting information from UI model
rxUiGet.modelName	S3 for getting information from UI model
rxUiGet.multipleEndpoint	S3 for getting information from UI model
rxUiGet.muRefTable	S3 for getting information from UI model
rxUiGet.omega	S3 for getting information from UI model
rxUiGet.omegaSameMap	S3 for getting information from UI model
rxUiGet.paramsLine	S3 for getting information from UI model
rxUiGet.props	S3 for getting information from UI model
rxUiGet.sha1	S3 for getting information from UI model
rxUiGet.simulationIniModel	S3 for getting information from UI model
rxUiGet.simulationModel	S3 for getting information from UI model
rxUiGet.simulationSigma	S3 for getting information from UI model
rxUiGet.splitDose	S3 for getting information from UI model
rxUiGet.splitDoseLines	S3 for getting information from UI model
rxUiGet.state	S3 for getting information from UI model
rxUiGet.stateDf	S3 for getting information from UI model
rxUiGet.statePropDf	S3 for getting information from UI model
rxUiGet.symengineModelNoPrune	S3 for getting information from UI model
rxUiGet.symengineModelPrune	S3 for getting information from UI model
rxUiGet.theta	S3 for getting information from UI model
rxUiGet.thetaLhs	S3 for getting information from UI model
rxUiGet.thetaLower	S3 for getting information from UI model
rxUiGet.thetaUpper	S3 for getting information from UI model
rxUiGet.varLhs	S3 for getting information from UI model
rxUiPriors	Priors specified in a model
rxunif	Simulate uniform variable from threefry generator
rxUnloadAll	Unloads all rxode2 compiled DLLs
rxUnlock	Lock/unlocking of rxode2 dll file
rxUse	Use model object in your package
rxValidate	Validate rxode2 This allows easy validation/qualification of nlmixr by running the testing suite on your system.
rxweibull	Simulate Weibull variable from threefry generator
rxWithPreserveSeed	Preserved seed and possibly set the seed
rxWithSeed	Preserved seed and possibly set the seed

-- S --

SELU	Scaled Exponential Linear Unit (SELU) Activation Function
seq.rxEt	Sequence of event tables
setRxThreads	Get/Set the number of threads that rxode2 uses
simulate.rxode2	Options, Solving & Simulation of an ODE/solved system
simulate.rxParams	Options, Solving & Simulation of an ODE/solved system
simulate.rxSolve	Options, Solving & Simulation of an ODE/solved system
softplus	Softplus Activation Function
solve.function	Options, Solving & Simulation of an ODE/solved system
solve.rxEt	Options, Solving & Simulation of an ODE/solved system
solve.rxode2	Options, Solving & Simulation of an ODE/solved system
solve.rxParams	Options, Solving & Simulation of an ODE/solved system
solve.rxSolve	Options, Solving & Simulation of an ODE/solved system
solve.rxUi	Options, Solving & Simulation of an ODE/solved system
splitBolus	Split bolus doses across compartments inside an rxode2 model
stat_amt	Dosing/Amt geom/stat
stat_cens	Censoring geom/stat
summary.rxode2	Print expanded information about the rxode2 object.
swapMatListWithCube	Swaps the matrix list with a cube
Swish	Switch Activation Function

-- T --

testCompartmentExists	Verify that the compartment exists in a model
testExists	Verify that a value is a valid nlmixr2 compartment name
testIniDf	This function tests if this object is a iniDf as needed by the UI
testRxLinCmt	Test if rxode2 uses linear solved systems
testRxUiNormalPriors	Assert properties of the rxUi models
testRxUiOmegaDf	Assert properties of the rxUi models
testRxUiOmegaNormalPriors	Assert properties of the rxUi models
testRxUiPriors	Assert properties of the rxUi models
testRxUnbounded	Test if the rxode2 model has any parameters with user defined boundaries
testVariableExists	Assert a variable exists in the model
toTrialDuration	Convert event data to trial duration data A helper function to create a custom event table. The observation time will start from the first event time (baseline) and end at trial duration. The interval is the spacing between each observation.

-- U --

units<-.rxEvid	EVID formatting for tibble and other places.
update.rxSolve	Options, Solving & Simulation of an ODE/solved system
update.rxUi	Update for rxUi
uppergamma	uppergamma: upper incomplete gamma function

-- W --

warnRxBounded	Test if the rxode2 model has any parameters with user defined boundaries
write.template.server	Generate an example (template) of a dosing regimen shiny app
write.template.ui	Generate an example (template) of a dosing regimen shiny app

-- Y --

yeoJohnson	boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions
yeoJohnsonInv	boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions

-- Z --

zeroRe

Set random effects and residual error to zero

-- misc --

.cbindOme	cbind Ome
.collectWarnings	Collect warnings and just warn once.
.copyUi	This copies the rxode2 UI object so it can be modified
.handleSingleErrTypeNormOrTFoceiBase	Handle the single error for normal or t distributions
.matchesLangTemplate	Check if a language object matches a template language object
.modelHandleModelLines	Handle model lines
.quoteCallInfoLines	Returns quoted call information
.rxFromSE	rxode2 to symengine environment
.rxLinCmtGen	Internal function to generate the model variables for a linCmt() model
.rxode2ptrs	Get the rxode2 function pointers
.rxRename	Rename items inside of a 'rxode2' ui model
.rxSensStrippable	Get model properties without compiling it.
.rxToSE	rxode2 to symengine environment
.rxWithOptions	Temporarily set options then restore them while running code
.rxWithWd	Temporarily set options then restore them while running code
.toClassicEvid	This converts NONMEM-style EVIDs to classic RxODE events
.vecDf	Convert numeric vector to repeated data.frame
[.rxEvid	EVID formatting for tibble and other places.
[.rxRateDur	Creates a rxRateDur object
[[.rxEvid	EVID formatting for tibble and other places.
[[.rxRateDur	Creates a rxRateDur object