.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
.rxLinCmtGen            Internal function to generate the model
                        variables for a linCmt() model
.rxWithOptions          Temporarily set options then restore them while
                        running code
.rxWithWd               Temporarily set options then restore them while
                        running code
.rxode2ptrs             Get the rxode2 function pointers
.toClassicEvid          This converts NONMEM-style EVIDs to classic
                        RxODE events
.vecDf                  Convert numeric vector to repeated data.frame
ELU                     Exponential Linear Unit (ELU) Activation
                        Function
GELU                    GELU activation function
PReLU                   Parametric ReLU Activation Function
ReLU                    Rectified Linear Unit (ReLU) Activation
                        Function
SELU                    Scaled Exponential Linear Unit (SELU)
                        Activation Function
Swish                   Switch Activation Function
add.dosing              Add dosing to eventTable
add.sampling            Add sampling to eventTable
as.data.table.rxEt      Convert an event table to a data.table
as.et                   Coerce object to data.frame
as.ini                  Turn into an ini block for initialization
as.model                Turn into a model expression
as.rxUi                 As rxode2 ui
as_tibble.rxEt          Convert to tbl
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
assertRxUi              Assert properties of the rxUi models
assertVariableExists    Assert a variable exists in the model
assertVariableNew       Assert a variable would be new to the model
binomProbs              Calculate expected confidence bands with
                        binomial sampling distribution
bolus                   Administer a bolus dose inside a rxode2 model
boxCox                  boxCox/yeoJohnson and inverse boxCox/yeoJohnson
                        functions
cvPost                  Sample a covariance Matrix from the Posterior
                        Inverse Wishart distribution.
dELU                    Derivatives of the Exponential Linear Unit
                        (ELU) Activation Function
dGELU                   Derivatives of GELU
dPReLU                  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
dSwish                  Derivative of the Swish Activation Function
dfWishart               This uses simulations to match the rse
dlReLU                  Derivative of Leaky ReLU activation function
dsoftplus               Default Softplus Activation Function
erf                     Error function
et                      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
evid_                   Push a future dose or observation event from
                        within an rxode2 model
gammap                  Gammap: normalized lower incomplete gamma
                        function
gammapDer               gammapDer: derivative of gammap
gammapInv               gammapInv and gammapInva: Inverses of
                        normalized gammap function
gammaq                  Gammaq: normalized upper incomplete gamma
                        function
gammaqInv               gammaqInv and gammaqInva: Inverses of
                        normalized gammaq function
genShinyApp.template    Generate an example (template) of a dosing
                        regimen shiny app
getRxThreads            Get/Set the number of threads that rxode2 uses
infuse                  Administer a infusion (with rate being fixed)
                        inside a rxode2 model
infuseDur               Administer a infusion (with duration being
                        fixed) inside a rxode2 model
ini.rxUi                Ini block for rxode2/nlmixr models
ini<-                   Assign the ini block in the rxode2 related
                        object
is.rxEt                 Check if object is an rxEt event table
is.rxStackData          Return if the object can be stacked
lReLU                   Leaky ReLU activation function
linMod                  Linear model to replace in rxode2 ui model
linToOde                Convert linCmt rxUi models to ODE rxUi models
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
lowergamma              lowergamma: upper incomplete gamma function
meanProbs               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.function          Model block for rxode2/nlmixr models
model<-                 Assign the model block in the rxode2 related
                        object
modelExtract            Extract model lines from a rxui model
multiply                Multiply dose the rxode2 system in the model
obs                     Add observations to a model
odeMethodToInt          Conversion between character and integer ODE
                        integration methods for rxode2
phantom                 Administer a phantom/transit dose inside a
                        rxode2 model
phi                     Cumulative distribution of standard normal
plot.rxSolve            Plot rxode2 objects
print.rxModelVars       Print Values
probit                  probit and inverse probit functions
replace                 Replace dose the rxode2 system in the model
reset                   Reset the rxode2 system in the model
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
rxCbindStudyIndividual
                        Bind the study parameters and individual
                        parameters
rxClean                 Cleanup anonymous DLLs by unloading them
rxCompile               Compile a model if needed
rxControlUpdateSens     This updates the tolerances based on the
                        sensitivity equations
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
rxEvid                  EVID formatting for tibble and other places.
rxFixPop                Apply the fixed population estimated parameters
rxFixRes                Literally fix residual parameters
rxFun                   Add/Create C functions for use in rxode2
rxGetControl            rxGetControl option from ui
rxGetDefaultSerialize   Get the Default Serialization Type
rxGetLin                Get the linear compartment model true function
rxGetSeed               Get the rxode2 seed
rxGetrxode2             Get rxode2 model from object
rxHtml                  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
rxLastCompile           Get the last compiled model information as
                        alist
rxLhs                   Left handed Variables
rxLock                  Lock/unlocking of rxode2 dll file
rxMemSummary            Create a per-ID event summary for memory
                        estimation
rxMemoryEstimate        Estimate memory required by rxSolve() for a
                        given dataset and model
rxNorm                  Get the normalized model
rxNumLoaded             Get the number of loaded rxode2 DLLs
rxOptExpr               Optimize rxode2 for computer evaluation
rxParams                Parameters specified by the model
rxParseSuppressMsg      Respect suppress messages
rxPkg                   Creates a package from compiled rxode2 models
rxPp                    Simulate a from a Poisson process
rxPreferredDistributionName
                        Change distribution name to the preferred
                        distribution name term
rxProgress              rxode2 progress bar functions
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 rxode2 supported
                        reserved keywords
rxResidualError         A description of Rode2 supported residual
                        errors
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
rxSimThetaOmega         Simulate Parameters from a Theta/Omega
                        specification
rxSolve                 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
rxTempDir               Get the rxode2 temporary directory
rxTheme                 rxTheme is the ggplot2 theme for rxode2 plots
rxToSE                  rxode2 to symengine environment
rxTrans                 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
rxUdfUiExpr             Give the expression as a compressed model or
                        expression
rxUdfUiFlag             Is the expression actually a flag that can be
                        used in the rxUdfUi functions?
rxUdfUiIniDf            Get the rxode2 iniDf of the current UI being
                        processed (or return NULL)
rxUdfUiIniLhs           Return the lhs parsed language expression
rxUdfUiIsValue          Is the expression actually equal to a value?
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
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
rxUiDevelop             rxUiDevelop - Enable/Disable rxUi development.
                        Here all $ completions are given
rxUiGet.cmtLines        S3 for getting information from UI model
rxUnloadAll             Unloads all rxode2 compiled DLLs
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.
rxWithSeed              Preserved seed and possibly set the seed
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
rxexp                   Simulate exponential variable from threefry
                        generator
rxf                     Simulate F variable from threefry generator
rxgamma                 Simulate gamma variable from threefry generator
rxgeom                  Simulate geometric variable from threefry
                        generator
rxnbinom                Simulate Binomial variable from threefry
                        generator
rxnormV                 Simulate random normal variable from threefry
                        generator
rxode2                  Create an ODE-based model specification
rxode2<-                Set the function body of an rxUi object while
                        retaining other object information (like data)
rxode2parse             Internal translation to get model variables
                        list
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
rxord                   Simulate ordinal value
rxpois                  Simulate random Poisson variable from threefry
                        generator
rxt                     Simulate student t variable from threefry
                        generator
rxunif                  Simulate uniform variable from threefry
                        generator
rxweibull               Simulate Weibull variable from threefry
                        generator
softplus                Softplus Activation Function
splitBolus              Split bolus doses across compartments inside an
                        rxode2 model
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
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
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.
update.rxUi             Update for rxUi
uppergamma              uppergamma: upper incomplete gamma function
zeroRe                  Set random effects and residual error to zero
