Facilities for Simulating from ODE-Based Models


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Documentation for package ‘RxODE’ version 1.1.1

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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
rxCbindStudyIndividual Bind the study parameters and individual parameters
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
rxSetSeed Set the parallel seed for RxODE random number generation
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