Facilities for Simulating from ODE-Based Models

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Documentation for package ‘rxode2’ version 2.1.3

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A B 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.model.list 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.rxode2tos 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

-- B --

binomProbs Calculate expected confidence bands with binomial sampling distribution
binomProbs.default Calculate expected confidence bands with binomial sampling distribution

-- 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 --

meanProbs Calculate expected confidence bands or prediction intreval with normal or t sampling distribution
meanProbs.default Calculate expected confidence bands or prediction intreval with normal or t sampling distribution
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
modelExtract Extract model lines from a rxui model
modelExtract.default Extract model lines from a rxui model
modelExtract.function Extract model lines from a rxui model
modelExtract.rxModelVars Extract model lines from a rxui model
modelExtract.rxode2 Extract model lines from a rxui model
modelExtract.rxUi Extract model lines from a rxui model

-- 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.function Options, Solving & Simulation of an ODE/solved system
predict.rxEt Options, Solving & Simulation of an ODE/solved system
predict.rxode2 Options, Solving & Simulation of an ODE/solved system
predict.rxParams Options, Solving & Simulation of an ODE/solved system
predict.rxSolve Options, Solving & Simulation of an ODE/solved system
predict.rxUi Options, Solving & Simulation of an ODE/solved system
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 Options, Solving & Simulation of an ODE/solved system
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
rxFixPop Apply the fixed population estimated parameters
rxFromSE rxode2 to symengine environment
rxFun Add/Create C functions for use in 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 rxode2 supported reserved keywords
rxResidualError A description of Rode2 supported residual errors
rxRmFun Add/Create C functions for use in rxode2
rxS Load a model into a symengine environment
rxSetControl rxSetControl options for UI object
rxSetCovariateNamesForPiping Assign covariates for piping
rxSetPipingAuto Set the variables for the model piping automatic covarite selection
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 Options, Solving & Simulation of an ODE/solved system
rxSolve.default Options, Solving & Simulation of an ODE/solved system
rxSolve.function Options, Solving & Simulation of an ODE/solved system
rxSolve.nlmixr2FitCore Options, Solving & Simulation of an ODE/solved system
rxSolve.nlmixr2FitData Options, Solving & Simulation of an ODE/solved system
rxSolve.rxode2tos Options, Solving & Simulation of an ODE/solved system
rxSolve.rxUi Options, Solving & Simulation of an ODE/solved system
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.model 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.params S3 for getting information from UI model
rxUiGet.paramsLine S3 for getting information from UI model
rxUiGet.simulationIniModel 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.symengineModelNoPrune S3 for getting information from UI model
rxUiGet.symengineModelPrune 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 Options, Solving & Simulation of an ODE/solved system
simulate.rxParams Options, Solving & Simulation of an ODE/solved system
simulate.rxSolve Options, Solving & Simulation of an ODE/solved system
solve.function Options, Solving & Simulation of an ODE/solved system
solve.rxEt Options, Solving & Simulation of an ODE/solved system
solve.rxode2 Options, Solving & Simulation of an ODE/solved system
solve.rxParams Options, Solving & Simulation of an ODE/solved system
solve.rxSolve Options, Solving & Simulation of an ODE/solved system
solve.rxUi Options, Solving & Simulation of an ODE/solved system
stat_amt Dosing/Amt geom/stat
stat_cens Censoring geom/stat
summary.rxode2 Print expanded information about the rxode2 object.

-- U --

update.rxSolve Options, Solving & Simulation of an ODE/solved system
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
.matchesLangTemplate Check if a language object matches a template language object
.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