Function reference • RxODE

Creating RxODE compiled objects
`RxODE()`	Create an ODE-based model specification
Creating RxODE event tables/data frames
`et()`	Event Table Function
`etRbind()` `rbind(<rxEt>)`	Combining event tables
`etRep()` `rep(<rxEt>)`	Repeat an RxODE event table
`etSeq()` `seq(<rxEt>)`	Sequence of event tables
`as.et()`	Coerce object to data.frame
`eventTable()`	Create an event table object
`add.dosing()`	Add dosing to eventTable
`add.sampling()`	Add sampling to eventTable
Solving, Simulating and Solving options
`rxSolve()` `update(<rxSolve>)` `predict(<RxODE>)` `predict(<rxSolve>)` `predict(<rxEt>)` `predict(<rxParams>)` `simulate(<RxODE>)` `simulate(<rxSolve>)` `simulate(<rxParams>)` `solve(<rxSolve>)` `solve(<RxODE>)` `solve(<rxParams>)` `solve(<rxEt>)` `rxControl()`	Solving & Simulation of a ODE/solved system (and solving options) equation
Exploring RxODE and creating models with Shiny
`rxShiny()`	Use Shiny to help develop an RxODE model
`genShinyApp.template()` `write.template.server()` `write.template.ui()`	Generate an example (template) of a dosing regimen shiny app
Using RxODE in Packages
`rxUse()`	Use model object in your package
`rxPkg()`	Creates a package from compiled RxODE models
Specialized Simulation functions
`cvPost()`	Sample a covariance Matrix from the Posterior Inverse Wishart distribution.
`rinvchisq()`	Scaled Inverse Chi Squared distribution
`rxPp()`	Simulate a from a Poisson process
Optimizing models and/or adding precision
`rxOptExpr()`	Optimize RxODE for computer evaluation
`rxSumProdModel()`	Recast model in terms of sum/prod
`rxSetProd()`	Defunct setting of product
`rxSetSum()`	Defunct setting of sum
Running unit tests in RxODE
`rxValidate()` `rxTest()`	Validate RxODE This allows easy validation/qualification of nlmixr by running the testing suite on your system.
Internal functions
`RxODE()`	Create an ODE-based model specification
`add.dosing()`	Add dosing to eventTable
`add.sampling()`	Add sampling to eventTable
`as.data.table.rxEt()`	Convert an event table to a data.table
`as.et()`	Coerce object to data.frame
`as_tibble(<rxEt>)`	Convert to tbl
`coef(<RxODE>)`	Return the RxODE coefficients
`cvPost()`	Sample a covariance Matrix from the Posterior Inverse Wishart distribution.
`.rxFinalizeInner()`	Finalize inner RxODE based on symengine saved info
`.rxFinalizePred()`	Finalize RxODE pred based on symengine saved info
`.rxGenEBE()`	Generate pieces for EBE only problem
`.rxGenEtaS()`	Generate the ETA sensitivities for FO related methods
`.rxGenFoce()`	Generate FOCE without interaction
`.rxGenFocei()`	Generate pieces for FOCEi inner problem
`.rxGenFunState()`	Get the state information for the current model
`.rxGenHdEta()`	Generate the d(err)/d(eta) values for FO related methods
`.rxGenPred()`	Generate Augmented pred/err RxODE model
`.rxRmPrint()`	Remove print statements
`.rxWinRtoolsPath()`	Setup Rtools path
`.rxWithOptions()`	Temporarily set options then restore them while running code
`.rxWithWd()`	Temporarily set options then restore them while running code
`.setWarnIdSort()`	Turn on/off warnings for ID sorting.
`et()`	Event Table Function
`etExpand()`	Expand additional doses
`etRbind()` `rbind(<rxEt>)`	Combining event tables
`etRep()` `rep(<rxEt>)`	Repeat an RxODE event table
`etSeq()` `seq(<rxEt>)`	Sequence of event tables
`eventTable()`	Create an event table object
`forderForceBase()`	Force using base order for RxODE radix sorting
`gammap()`	Gammap: normalized lower incomplete gamma function
`gammapDer()`	gammapDer: derivative of gammap
`gammapInv()` `gammapInva()`	gammapInv and gammapInva: Inverses of normalized gammap function
`gammaq()`	Gammaq: normalized upper incomplete gamma function
`gammaqInv()` `gammaqInva()`	gammaqInv and gammaqInva: Inverses of normalized gammaq function
`genShinyApp.template()` `write.template.server()` `write.template.ui()`	Generate an example (template) of a dosing regimen shiny app
`getRxThreads()` `setRxThreads()` `rxCores()`	Get/Set the number of threads that RxODE uses
`guide_none()`	Empty Guide
`invWR1d()`	One correlation sample from the Inverse Wishart distribution
`is.rxEt()`	Check to see if this is an rxEt object.
`is.rxSolve()`	Check to see if this is an rxSolve object.
`logit()` `expit()` `logitNormInfo()` `probitNormInfo()`	logit and inverse logit (expit) functions
`lowergamma()`	lowergamma: upper incomplete gamma function
`phi()`	Cumulative distribution of standard normal
`print(<RxODE>)`	Print information about the RxODE object.
`probit()` `probitInv()`	probit and inverse probit functions
`rLKJ1()`	One correlation sample from the LKJ distribution
`rinvchisq()`	Scaled Inverse Chi Squared distribution
`rxAddReturn()`	Add a return statment to a function.
`rxAllowUnload()`	Allow unloading of dlls
`rxAssignPtr()`	Assign pointer based on model variables
`rxCbindStudyIndividual()`	Bind the study parameters and individual parameters
`rxChain()` `+`(<solveRxDll>)	rxChain Chain or add item to solved system of equations
`rxClean()`	Cleanup anonymous DLLs by unloading them
`rxCompile()`	Compile a model if needed
`rxCreateCache()`	This will create the cache directory for RxODE to save between sessions
`rxD()`	Add to RxODE'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
`rxEvid()` `as.rxEvid()` `c(<rxEvid>)` `[`(<rxEvid>) `as.character(<rxEvid>)` `[[`(<rxEvid>) `type_sum(<rxEvid>)` `pillar_shaft.rxEvid()` `c(<rxRateDur>)` `format(<rxEvid>)` `format(<rxRateDur>)` `print(<rxEvid>)`	EVID formatting for tibble and other places.
`rxFun()` `rxRmFun()`	Add user function to RxODE
`rxGenSaem()`	Generate pred-only SAEM RxODE model
`rxGetLin()`	Get the linear compartment model true function
`rxGetRxODE()`	Get RxODE model from object
`rxHtml()`	Format rxSolve and related objects as html.
`rxIndLinState()`	Set the preferred factoring by state
`rxIndLinStrategy()`	This sets the inductive linearization strategy for matrix building
`rxInv()`	Invert matrix using RcppArmadillo.
`rxIsCurrent()`	Checks if the RxODE object was built with the current build
`rxLhs()`	Left handed Variables
`rxLock()` `rxUnlock()`	Lock/unlocking of RxODE dll file
`rxNorm()`	Get the normalized model
`rxOptExpr()`	Optimize RxODE for computer evaluation
`rxParams()` `rxParam()`	Parameters specified by the model
`rxPkg()`	Creates a package from compiled RxODE models
`rxPp()`	Simulate a from a Poisson process
`rxProgress()` `rxTick()` `rxProgressStop()` `rxProgressAbort()`	RxODE progress bar functions
`rxRandNV()`	Create a random "normal" matrix using vandercorput generator
`rxRateDur()` `[`(<rxRateDur>) `as.rxRateDur()` `as.character(<rxRateDur>)` `[[`(<rxRateDur>) `type_sum(<rxRateDur>)` `pillar_shaft.rxRateDur()`	Creates a rxRateDur object
`rxReservedKeywords`	A list and description of Rode supported reserved keywords
`rxRmvn()`	Simulate from a (truncated) multivariate normal
`rxS()`	Load a model into a symengine environment
`rxSetIni0()`	Set Initial conditions to time zero instead of the first observed/dosed time
`rxSetProd()`	Defunct setting of product
`rxSetProgressBar()`	Set timing for progress bar
`rxSetSeed()`	Set the parallel seed for RxODE random number generation
`rxSetSum()`	Defunct setting of sum
`rxShiny()`	Use Shiny to help develop an RxODE model
`rxSimThetaOmega()`	Simulate Parameters from a Theta/Omega specification
`rxSolve()` `update(<rxSolve>)` `predict(<RxODE>)` `predict(<rxSolve>)` `predict(<rxEt>)` `predict(<rxParams>)` `simulate(<RxODE>)` `simulate(<rxSolve>)` `simulate(<rxParams>)` `solve(<rxSolve>)` `solve(<RxODE>)` `solve(<rxParams>)` `solve(<rxEt>)` `rxControl()`	Solving & Simulation of a ODE/solved system (and solving options) equation
`rxStack()`	Stack a solved object for things like ggplot
`rxState()`	State variables
`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 RxODE variables
`rxSyntaxFunctions`	A list and description of Rode supported syntax functions
`rxTempDir()`	Get the RxODE temporary directory
`rxTheme()`	rxTheme is the RxODE theme for plots
`rxToSE()` `.rxToSE()` `rxFromSE()` `.rxFromSE()`	RxODE to symengine environment
`rxTrans()`	Translate the model to C code if needed
`rxUnloadAll()`	Unloads all RxODE compiled DLLs
`rxUse()`	Use model object in your package
`rxValidate()` `rxTest()`	Validate RxODE This allows easy validation/qualification of nlmixr by running the testing suite on your system.
`rxWinSetup()`	Setup Windows components for RxODE
`rxbeta()`	Simulate beta variable from threefry generator
`rxbinom()`	Simulate Binomial variable from threefry generator
`rxcauchy()`	Simulate Cauchy variable from threefry generator
`rxchisq()`	Simulate chi-squared variable from threefry generator
`rxexp()`	Simulate exponential variable from threefry generator
`rxf()`	Simulate F variable from threefry generator
`rxgamma()`	Simulate gamma variable from threefry generator
`rxgeom()`	Simulate geometric variable from threefry generator
`rxnorm()` `rxnormV()`	Simulate random normal variable from threefry/vandercorput generator
`rxpois()`	Simulate random Poisson variable from threefry generator
`rxt()`	Simulate student t variable from threefry generator
`rxunif()`	Simulate uniform variable from threefry generator
`rxweibull()`	Simulate Weibull variable from threefry generator
`stat_amt()` `geom_amt()`	Dosing/Amt geom/stat
`stat_cens()` `geom_cens()`	Censoring geom/stat
`summary(<RxODE>)`	Print expanded information about the RxODE object.
`uppergamma()`	uppergamma: upper incomplete gamma function

Reference

Creating RxODE compiled objects

Creating RxODE event tables/data frames

Solving, Simulating and Solving options

Exploring RxODE and creating models with Shiny

Using RxODE in Packages

Specialized Simulation functions

Optimizing models and/or adding precision

Running unit tests in RxODE

Internal functions