# Facilities for Simulating from ODE-Based Models

## Documentation for package ‘rxode2’ version 2.0.13

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

## Help Pages

A E G I L M O P R S U W Z misc

## -- A --

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.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.rxUi | As rxode2 ui
assertRxUi | Assert properties of the rxUi models
assertRxUiEstimatedResiduals | Assert properties of the rxUi models
assertRxUiMixedOnly | Assert properties of the rxUi models
assertRxUiMuRefOnly | Assert properties of the rxUi models
assertRxUiNormal | 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

## -- E --

erf | Error function
expit | logit and inverse logit (expit) functions

## -- 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
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 --

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

## -- L --

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

## -- M --

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

## -- O --

odeMethodToInt | Conversion between character and integer ODE integration methods for rxode2

## -- P --

plot.rxSolve | Plot rxode2 objects
plot.rxSolveConfint1 | Plot rxode2 objects
plot.rxSolveConfint2 | Plot rxode2 objects
predict.rxEt | Solving & Simulation of a ODE/solved system (a options) equation
predict.rxode2 | Solving & Simulation of a ODE/solved system (a options) equation
predict.rxParams | Solving & Simulation of a ODE/solved system (a options) equation
predict.rxSolve | Solving & Simulation of a ODE/solved system (a options) equation
probit | probit and inverse probit functions
probitInv | probit and inverse probit functions
probitNormInfo | logit and inverse logit (expit) functions

## -- R --

rename.function | Rename items inside of a 'rxode2' ui model
rename.rxUi | Rename items inside of a 'rxode2' ui model
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
rxchisq | Simulate chi-squared variable from threefry generator
rxClean | Cleanup anonymous DLLs by unloading them
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 | Solving & Simulation of a ODE/solved system (a options) equation
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
rxDfdy | Jacobian and parameter derivatives
rxexp | Simulate exponential variable from threefry generator
rxf | Simulate F variable from threefry generator
rxFromSE | rxode2 to symengine environment
rxFun | Add user function to rxode2
rxgamma | Simulate gamma variable from threefry generator
rxgeom | Simulate geometric variable from threefry generator
rxGetControl | rxGetControl option from ui
rxGetLin | Get the linear compartment model true function
rxGetrxode2 | Get rxode2 model from object
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
rxIndLin_ | Inductive linearization solver
rxInv | Invert matrix using RcppArmadillo.
rxIsCurrent | Checks if the rxode2 object was built with the current build
rxLhs | Left handed Variables
rxLock | Lock/unlocking of rxode2 dll file
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
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)
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)
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
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
rxProgress | rxode2 progress bar functions
rxProgressAbort | rxode2 progress bar functions
rxProgressStop | rxode2 progress bar functions
rxRemoveControl | rxRemoveControl options for UI object
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 Rode supported reserved keywords
rxRmFun | Add user function to rxode2
rxS | Load a model into a symengine environment
rxSetControl | rxSetControl options for UI object
rxSetCovariateNamesForPiping | Assign covariates for piping
rxSetProd | Defunct setting of product
rxSetProgressBar | Set timing for progress bar
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 | Solving & Simulation of a ODE/solved system (a options) equation
rxSolve.default | Solving & Simulation of a ODE/solved system (a options) equation
rxSolve.function | Solving & Simulation of a ODE/solved system (a options) equation
rxSolve.nlmixr2FitCore | Solving & Simulation of a ODE/solved system (a options) equation
rxSolve.nlmixr2FitData | Solving & Simulation of a ODE/solved system (a options) equation
rxSolve.rxUi | Solving & Simulation of a ODE/solved system (a options) equation
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 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
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
rxUiCompress | Compress/Decompress 'rxode2' ui
rxUiDecompress | Compress/Decompress 'rxode2' ui
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.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.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.modelDesc | S3 for getting information from UI model
rxUiGet.modelFun | 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.paramsLine | 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.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
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

## -- S --

setRxThreads | Get/Set the number of threads that rxode2 uses
simulate.rxode2 | Solving & Simulation of a ODE/solved system (a options) equation
simulate.rxParams | Solving & Simulation of a ODE/solved system (a options) equation
simulate.rxSolve | Solving & Simulation of a ODE/solved system (a options) equation
solve.function | Solving & Simulation of a ODE/solved system (a options) equation
solve.rxEt | Solving & Simulation of a ODE/solved system (a options) equation
solve.rxode2 | Solving & Simulation of a ODE/solved system (a options) equation
solve.rxParams | Solving & Simulation of a ODE/solved system (a options) equation
solve.rxSolve | Solving & Simulation of a ODE/solved system (a options) equation
solve.rxUi | Solving & Simulation of a ODE/solved system (a options) equation
stat_amt | Dosing/Amt geom/stat
stat_cens | Censoring geom/stat
summary.rxode2 | Print expanded information about the rxode2 object.

## -- U --

update.rxSolve | Solving & Simulation of a ODE/solved system (a options) equation
update.rxUi | Update for rxUi
uppergamma | uppergamma: upper incomplete gamma function

## -- W --

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

## -- Z --

zeroRe | Set random effects and residual error to zero

## -- misc --

.copyUi | This copies the rxode2 UI object so it can be modified
.handleSingleErrTypeNormOrTFoceiBase | Handle the single error for normal or t distributions
.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
.rxRename | Rename items inside of a 'rxode2' ui model
.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