# Facilities for Simulating from ODE-Based Models

## Documentation for package ‘rxode2’ version 4.1.1

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

## Help Pages

A B C D E F G I L M O P R S T U W Y Z 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.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.rxEvid | EVID formatting for tibble and other places.
as.rxRateDur | Creates a rxRateDur object
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
assertCompartmentExists | Verify that the compartment exists in a model
assertCompartmentName | Verify that a value is a valid nlmixr2 compartment name
assertCompartmentNew | Verify that a compartment would be new to the model
assertExists | Verify that a value is a valid nlmixr2 compartment name
assertIniDf | This function tests if this object is a iniDf as needed by the UI
assertParameterValue | Verify that a value is a valid nlmixr2 compartment name
assertRxLinCmt | Test if rxode2 uses linear solved systems
assertRxUi | Assert properties of the rxUi models
assertRxUiEstimatedResiduals | Assert properties of the rxUi models
assertRxUiIovNoCor | Assert properties of the rxUi models
assertRxUiMixedOnly | Assert properties of the rxUi models
assertRxUiMuRefOnly | Assert properties of the rxUi models
assertRxUiNoMix | 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
assertRxUnbounded | Test if the rxode2 model has any parameters with user defined boundaries
assertVariableExists | Assert a variable exists in the model
assertVariableName | Verify that a value is a valid nlmixr2 compartment name
assertVariableNew | Assert a variable would be new to the model

## -- B --

binomProbs | Calculate expected confidence bands with binomial sampling distribution
binomProbs.default | Calculate expected confidence bands with binomial sampling distribution
boxCox | boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions
boxCoxInv | boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions

## -- 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.

## -- D --

d2aELU | Derivatives of the Exponential Linear Unit (ELU) Activation Function
d2ELU | Derivatives of the Exponential Linear Unit (ELU) Activation Function
d2ELUa | Derivatives of the Exponential Linear Unit (ELU) Activation Function
d2GELU | Derivatives of GELU
d2softplus | Default Softplus Activation Function
d3GELU | Derivatives of GELU
d3softplus | Default Softplus Activation Function
d4GELU | Derivatives of GELU
d4softplus | Default Softplus Activation Function
dELU | Derivatives of the Exponential Linear Unit (ELU) Activation Function
dELUa | Derivatives of the Exponential Linear Unit (ELU) Activation Function
dfWishart | This uses simulations to match the rse
dGELU | Derivatives of GELU
dlReLU | Derivative of Leaky ReLU activation function
dPReLU | Derivatives Parametric ReLU Activation Function
dPReLUa | Derivatives Parametric ReLU Activation Function
dPReLUa1 | Derivatives Parametric ReLU Activation Function
dReLU | Derivative of the Rectified Linear Unit (ReLU) Activation Function
dSELU | Derivative of the Scaled Exponential Linear Unit (SELU) Activation Function
dsoftplus | Default Softplus Activation Function
dSwish | Derivative of the Swish Activation Function

## -- E --

ELU | Exponential Linear Unit (ELU) Activation Function
erf | Error function
et | Event Table Function
et.default | Event Table Function
et.function | Event Table Function
et.rxode2 | Event Table Function
et.rxParams | Event Table Function
et.rxSolve | Event Table Function
et.rxUi | 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
GELU | GELU activation 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
is.rxStackData | Return if the object can be stacked

## -- L --

linMod | Linear model to replace in rxode2 ui model
linMod0 | Linear model to replace in rxode2 ui model
linModA | Linear model to replace in rxode2 ui model
linModA0 | Linear model to replace in rxode2 ui model
linModB | Linear model to replace in rxode2 ui model
linModB0 | Linear model to replace in rxode2 ui model
linModD | Linear model to replace in rxode2 ui model
linModD0 | Linear model to replace in rxode2 ui model
linModM | Linear model to replace in rxode2 ui model
linModM0 | Linear model to replace in rxode2 ui model
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
lReLU | Leaky ReLU activation 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
mexpit | mexpit - Convert log-scale numbers to probabilities
mix | Specify a mixture model of variables
mlogit | mlogit - Convert multiple probabilities to log-scale numbers
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 --

phi | Cumulative distribution of standard normal
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
PReLU | Parametric ReLU Activation Function
print.rxEvid | EVID formatting for tibble and other places.
print.rxModelVars | Print Values
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
ReLU | Rectified Linear Unit (ReLU) Activation Function
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 | 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
rxDerived | Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.
rxDfdy | Jacobian and parameter derivatives
rxEtDispatchSolve | Dispatch solve to 'rxode2' solve
rxEtDispatchSolve.default | Dispatch solve to 'rxode2' solve
rxEvid | EVID formatting for tibble and other places.
rxexp | Simulate exponential variable from threefry generator
rxf | Simulate F variable from threefry generator
rxFixPop | Apply the fixed population estimated parameters
rxFixRes | Literally fix residual 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
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
rxIntToBase | Convert a positive base
rxIntToLetter | Convert a positive integer to a letter series
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)
rxode2parse | Internal translation to get model variables list
rxode2parseAssignPackagesToLoad | Control the packages that are loaded when a 'rxode2' model dll is loaded
rxode2parseAssignTranslation | This assigns the c level linkages for a roxde2 model
rxode2parseD | This gives the derivative table for rxode2
rxode2parseGetPackagesToLoad | Control the packages that are loaded when a 'rxode2' model dll is loaded
rxode2parseGetPointerAssignment | This function gets the currently assigned function pointer assignments
rxode2parseGetTranslation | This function gets the currently assigned translations
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
rxParseSuppressMsg | Respect suppress messages
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
rxRateDur | Creates a rxRateDur object
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
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
rxSetPipingAuto | Set the variables for the model piping automatic covarite selection
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 | 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
rxStack | Stack a solved object for things like default ggplot2 plot
rxState | State variables
rxStateOde | Get the ODE states only
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
rxUdfUiControl | Return the control that is being processed or setup control for processing
rxUdfUiData | Return the data.frame that is being processed or setup data.frame for processing
rxUdfUiEst | Return the current estimation method for the UI processing
rxUdfUiIniDf | Get the rxode2 iniDf of the current UI being processed (or return NULL)
rxUdfUiIniLhs | Return the lhs parsed language expression
rxUdfUiMv | Return the model variables that is being processed or setup model variables for processing
rxUdfUiNum | This gives the current number in the ui of the particular function being called.
rxUdfUiParsing | Returns if the current ui function is being parsed
rxUiCompress | Compress/Decompress 'rxode2' ui
rxUiDecompress | Compress/Decompress 'rxode2' ui
rxUiDeparse | This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDeparse.default | This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDeparse.lotriFix | This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDeparse.rxControl | This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information
rxUiDevelop | rxUiDevelop - Enable/Disable rxUi development. Here all $ completions are given
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.funPartsDigest | 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.interpLines | S3 for getting information from UI model
rxUiGet.levelLhs | S3 for getting information from UI model
rxUiGet.levels | 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.paramsLine | S3 for getting information from UI model
rxUiGet.props | S3 for getting information from UI model
rxUiGet.sha1 | 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.state | S3 for getting information from UI model
rxUiGet.stateDf | S3 for getting information from UI model
rxUiGet.statePropDf | 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
rxWithPreserveSeed | Preserved seed and possibly set the seed
rxWithSeed | Preserved seed and possibly set the seed

## -- S --

SELU | Scaled Exponential Linear Unit (SELU) Activation Function
seq.rxEt | Sequence of event tables
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
softplus | Softplus Activation Function
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.
swapMatListWithCube | Swaps the matrix list with a cube
Swish | Switch Activation Function

## -- T --

testCompartmentExists | Verify that the compartment exists in a model
testExists | Verify that a value is a valid nlmixr2 compartment name
testIniDf | This function tests if this object is a iniDf as needed by the UI
testRxLinCmt | Test if rxode2 uses linear solved systems
testRxUnbounded | Test if the rxode2 model has any parameters with user defined boundaries
testVariableExists | Assert a variable exists in the model
toTrialDuration | Convert event data to trial duration data A helper function to create a custom event table. The observation time will start from the first event time (baseline) and end at trial duration. The interval is the spacing between each observation.

## -- U --

units<-.rxEvid | EVID formatting for tibble and other places.
update.rxSolve | Options, Solving & Simulation of an ODE/solved system
update.rxUi | Update for rxUi
uppergamma | uppergamma: upper incomplete gamma function

## -- W --

warnRxBounded | Test if the rxode2 model has any parameters with user defined boundaries
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

## -- Y --

yeoJohnson | boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions
yeoJohnsonInv | boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions

## -- Z --

zeroRe | Set random effects and residual error to zero

## -- misc --

.cbindOme | cbind Ome
.collectWarnings | Collect warnings and just warn once.
.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
.rxode2ptrs | Get the rxode2 function pointers
.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
.toClassicEvid | This converts NONMEM-style EVIDs to classic RxODE events
.vecDf | Convert numeric vector to repeated data.frame
[.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