# Facilities for Simulating from ODE-Based Models

## Documentation for package ‘RxODE’ version 1.0.8

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

## Help Pages

A C E F G I L P R S T U W misc

## -- A --

add.dosing | Add dosing to eventTable
add.sampling | Add sampling to eventTable
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.rxEvid | EVID formatting for tibble and other places.
as.rxRateDur | Creates a rxRateDur object
as_tibble.rxEt | Convert to tbl

## -- C --

c.rxEvid | EVID formatting for tibble and other places.
c.rxRateDur | EVID formatting for tibble and other places.
coef.RxODE | Return the RxODE coefficients
cvPost | Sample a covariance Matrix from the Posterior Inverse Wishart distribution.

## -- E --

et | Event Table Function
et.default | Event Table Function
et.RxODE | Event Table Function
et.rxParams | Event Table Function
et.rxSolve | Event Table Function
etExpand | Expand additional doses
etRbind | Combining event tables
etRep | Repeat an RxODE event table
etSeq | Sequence of event tables
eventTable | Create an event table object
expit | logit and inverse logit (expit) functions

## -- F --

forderForceBase | Force using base order for RxODE radix sorting
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
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 RxODE uses
guide_none | Empty Guide

## -- I --

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.

## -- L --

logit | logit and inverse logit (expit) functions
logitNormInfo | logit and inverse logit (expit) functions
lowergamma | lowergamma: upper incomplete gamma function

## -- P --

phi | Cumulative distribution of standard normal
pillar_shaft.rxEvid | EVID formatting for tibble and other places.
pillar_shaft.rxRateDur | Creates a rxRateDur object
predict.rxEt | Solving & Simulation of a ODE/solved system (and solving options) equation
predict.RxODE | Solving & Simulation of a ODE/solved system (and solving options) equation
predict.rxParams | Solving & Simulation of a ODE/solved system (and solving options) equation
predict.rxSolve | Solving & Simulation of a ODE/solved system (and solving options) equation
print.rxEvid | EVID formatting for tibble and other places.
print.RxODE | Print information about the RxODE object.
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
rep.rxEt | Repeat an RxODE event table
rinvchisq | Scaled Inverse Chi Squared distribution
rLKJ1 | One correlation sample from the LKJ distribution
rxAddReturn | Add a return statment to a function.
rxAllowUnload | Allow unloading of dlls
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
rxChain | rxChain Chain or add item to solved system of equations
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.RxODE | Compile a model if needed
rxControl | Solving & Simulation of a ODE/solved system (and solving options) equation
rxCores | Get/Set the number of threads that RxODE uses
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 | EVID formatting for tibble and other places.
rxexp | Simulate exponential variable from threefry generator
rxf | Simulate F variable from threefry generator
rxFromSE | RxODE to symengine environment
rxFun | Add user function to RxODE
rxgamma | Simulate gamma variable from threefry generator
rxGenSaem | Generate pred-only SAEM RxODE model
rxgeom | Simulate geometric variable from threefry generator
rxGetLin | Get the linear compartment model true function
rxGetRxODE | Get RxODE 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
rxInv | Invert matrix using RcppArmadillo.
rxIsCurrent | Checks if the RxODE object was built with the current build
rxLhs | Left handed Variables
rxLock | Lock/unlocking of RxODE dll file
rxNorm | Get the normalized model
rxnorm | Simulate random normal variable from threefry/vandercorput generator
rxnormV | Simulate random normal variable from threefry/vandercorput generator
RxODE | Create an ODE-based model specification
rxOptExpr | Optimize RxODE for computer evaluation
rxParam | Parameters specified by the model
rxParams | Parameters specified by the model
rxParams.rxEt | Parameters specified by the model
rxParams.RxODE | Parameters specified by the model
rxParams.rxSolve | Parameters specified by the model
rxPkg | Creates a package from compiled RxODE models
rxpois | Simulate random Poisson variable from threefry generator
rxPp | Simulate a from a Poisson process
rxProgress | RxODE progress bar functions
rxProgressAbort | RxODE progress bar functions
rxProgressStop | RxODE progress bar functions
rxRandNV | Create a random "normal" matrix using vandercorput generator
rxRateDur | Creates a rxRateDur object
rxReservedKeywords | A list and description of Rode supported reserved keywords
rxRmFun | Add user function to RxODE
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
rxSetSum | Defunct setting of sum
rxShiny | Use Shiny to help develop an RxODE model
rxShiny.default | Use Shiny to help develop an RxODE model
rxShiny.rxSolve | Use Shiny to help develop an RxODE model
rxSimThetaOmega | Simulate Parameters from a Theta/Omega specification
rxSolve | Solving & Simulation of a ODE/solved system (and solving options) equation
rxSolve.default | 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
rxt | Simulate student t variable from threefry generator
rxTempDir | Get the RxODE temporary directory
rxTest | Validate RxODE This allows easy validation/qualification of nlmixr by running the testing suite on your system.
rxTheme | rxTheme is the RxODE theme for plots
rxTick | RxODE progress bar functions
rxToSE | RxODE 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
rxunif | Simulate uniform variable from threefry generator
rxUnloadAll | Unloads all RxODE compiled DLLs
rxUnlock | Lock/unlocking of RxODE dll file
rxUse | Use model object in your package
rxValidate | Validate RxODE This allows easy validation/qualification of nlmixr by running the testing suite on your system.
rxweibull | Simulate Weibull variable from threefry generator
rxWinSetup | Setup Windows components for RxODE

## -- S --

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

## -- T --

type_sum.rxEvid | EVID formatting for tibble and other places.
type_sum.rxRateDur | Creates a rxRateDur object

## -- U --

update.rxSolve | Solving & Simulation of a ODE/solved system (and solving options) equation
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

## -- misc --

+.solveRxDll | rxChain Chain or add item to solved system of equations
.rxFinalizeInner | Finalize inner RxODE based on symengine saved info
.rxFinalizePred | Finalize RxODE pred based on symengine saved info
.rxFromSE | RxODE to symengine environment
.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
.rxToSE | RxODE to symengine environment
.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.
[.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