Facilities for Simulating from ODE-Based Models

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Documentation for package ‘rxode2’ version 2.0.7

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A C E F G I L M P R S 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.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
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

-- C --

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

-- E --

erf Error function
et Event Table Function
et.default Event Table Function
et.rxode2 Event Table Function
et.rxParams Event Table Function
et.rxSolve Event Table Function
etExpand Expand additional doses
etRbind Combining event tables
etRep Repeat an rxode2 event table
etSeq Sequence of event tables
eventTable Create an event table object
expit logit and inverse logit (expit) functions

-- F --

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 rxode2 uses

-- I --

ini Ini block for rxode2/nlmixr models
ini.default Ini block for rxode2/nlmixr models
ini.function Ini block for rxode2/nlmixr models
ini.rxUi Ini block for rxode2/nlmixr models

-- L --

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.rxUi Model block for rxode2/nlmixr models

-- P --

phi Cumulative distribution of standard normal
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
print.rxEvid EVID formatting for tibble and other places.
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
rename.function Rename items inside of a 'rxode2' ui model
rename.rxUi Rename items inside of a 'rxode2' ui model
rep.rxEt Repeat an rxode2 event table
rinvchisq Scaled Inverse Chi Squared distribution
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
rxCbindStudyIndividual Bind the study parameters and individual parameters
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
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 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
rxGetSeed Get the rxode2 seed
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
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
rxode Create an ODE-based model specification
rxode2 Create an ODE-based model specification
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
rxRandNV Create a random "normal" matrix using vandercorput generator
rxRateDur Creates a rxRateDur object
rxRemoveControl rxRemoveControl options for UI object
rxRename Rename items inside of a 'rxode2' ui model
rxReservedKeywords A list and description of Rode supported reserved keywords
rxRmFun Add user function to rxode2
rxRmvn Simulate from a (truncated) multivariate normal
rxS Load a model into a symengine environment
rxSetControl rxSetControl options for UI object
rxSetCovariateNamesForPiping Assign covariates for piping
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 rxode2 random number generation
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
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 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
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.default S3 for getting information from UI model
rxUiGet.dvidLine 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.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.thetaLower S3 for getting information from UI model
rxUiGet.thetaUpper 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
rxWinSetup Setup Windows components for rxode2
rxWithPreserveSeed Preserved seed and possibly set the seed
rxWithSeed Preserved seed and possibly set the seed

-- S --

seq.rxEt Sequence of event tables
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.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

-- 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
.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
[.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