R: Facilities for Simulating from ODE-Based Models

# Facilities for Simulating from ODE-Based Models

## Documentation for package ‘RxODE’ version 0.9.1-8

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

## Help Pages

A C E F G I 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.frame.rxEvid | Convert to data.frame
as.data.frame.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.tbl.rxEt | Convert to tbl
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.RxCompilationManager | Return the RxODE coefficients
coef.rxDll | Return the RxODE coefficients
coef.RxODE | Return the RxODE coefficients
coef.solveRxODE | 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

## -- 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.
format_type_sum.type_sum_units | type_sum function for units

## -- G --

genShinyApp.template | Generate an example (template) of a dosing regimen shiny app

## -- I --

is.rxEt | Check to see if this is an rxEt object.
is.rxSolve | Check to see if this is an rxSolve object.

## -- P --

pillar_shaft.mixed_units | type_sum function for units
pillar_shaft.rxEvid | EVID formatting for tibble and other places.
pillar_shaft.rxRateDur | Creates a rxRateDur object
pillar_shaft.units | type_sum function for units
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.rxCoefSolve | Print the rxCoefSolve object
print.rxEvid | EVID formatting for tibble and other places.
print.RxODE | Print information about the RxODE object.

## -- R --

rbind.rxEt | Combining event tables
rep.rxEt | Repeat an RxODE event table
rinvchisq | Scaled Inverse Chi Squared distribution
rxAddReturn | Add a return statement to a function.
rxAllowUnload | Allow unloading of dlls
rxAssignPtr | Assign pointer based on model variables
rxC14 | Setup C++14 support in windows (required for nlmixr)
rxChain | rxChain Chain or add item to solved system of equations
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.RxODE | Compile a model if needed
rxControl | Solving & Simulation of a ODE/solved system (and solving options) equation
rxCores | Get the number of cores in a system
rxDelete | Delete the DLL for the model
rxDfdy | Jacobian and parameter derivatives
rxEvid | EVID formatting for tibble and other places.
rxFoExpandEta | First Order Expansion of ETA
rxGetRxODE | Get RxODE model from object
rxHtml | Format rxSolve and related objects as html.
rxHtml.rxSolve | Format rxSolve and related objects as html.
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
RxODE | Create an ODE-based model specification
rxOptExpr | Optimize RxODE for computer evaluation
rxOptions | Options for RxODE
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
rxPermissive | Permissive or Strict RxODE syntax options
rxProgress | RxODE progress bar functions
rxProgressAbort | RxODE progress bar functions
rxProgressStop | RxODE progress bar functions
rxRateDur | Creates a rxRateDur object
rxSetIni0 | Set Initial conditions to time zero instead of the first observed/dosed time
rxSetProd | Choose the type of product to use in RxODE. These are used in the RxODE 'prod' blocks
rxSetProgressBar | Set timing for progress bar
rxSetSum | Choose the type of sums to use for RxODE.
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
rxStrict | Permissive or Strict RxODE syntax options
rxSumProdModel | Recast model in terms of sum/prod
rxSymInvChol | Get Omega^-1 and derivatives
rxSymPyFix | Fix SymPy expressions to be R parsable expressions
rxSymPySensitivity | Calculate the sensitivity equations for a model
rxSymPyVersion | Return the version of SymPy that is running
rxSyncOptions | Sync options with RxODE variables
rxTempDir | Get the RxODE temporary directory
rxTest | Validate RxODE
rxTick | RxODE progress bar functions
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
rxUnloadAll | Unload all RxODE Dlls that are not locked for solving.
rxUnlock | Lock/unlocking of RxODE dll file
rxUse | Use model object in your package
rxUseRadixSort | Use Radix Sort when possible
rxValidate | Validate RxODE
rxWinPythonSetup | Setup Python and SymPy for windows
rxWinSetup | Setup Windows components for RxODE

## -- S --

scale_type.units | type_sum function for units
seq.rxEt | Sequence of event tables
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
summary.RxODE | Print expanded information about the RxODE object.

## -- T --

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

## -- U --

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

## -- 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
.clearPipe | Clear/Set pipeline
.rxFindPow | Find power THETAs for appropriate scaling
.rxRmPrint | Remove print statements
.rxRmSens | Remove sensitivity equations
.rxSymPyJacobian | Calculate the full Jacobian for a model
.rxWinRtoolsPath | Setup Rtools path
.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