.augPredIpredModel      Augment Prediction for Ipred Model
.nlmFamilyFitGeneric    Shared fit driver for the nlm-family estimation
                        methods
.nlmixr0preProcessCovariatesPresent
                        Preprocess Covariates needed (or other data
                        items)
.nlmixr0preProcessNpMuExpand
                        Preprocessing hook: mu-expand non-mu structural
                        fixed-effect thetas for the nonparametric
                        engines, before the rest of the pipeline builds
                        on the ui.  Doing it here (rather than mutating
                        the ui mid-setup) keeps the injected
                        pseudo-etas consistent through covariate/mu
                        processing and model compilation.  Off when
                        control$muExpand is FALSE.
.nlmixrPreprocessLiteralFix
                        This literally fixes parameters in the model
.preProcessDataUi       Preprocess the zero omegas
.preProcessLinCmtOde    Translate a mixed 'linCmt()'/ODE model to
                        all-ODEs
.preProcessVaeNonMuTheta
                        VAE preprocessing hook: inject etas for
                        non-mu-referenced thetas per
                        vaeControl(nonMuTheta=).
.preProcessZeroOmega    Preprocess the zero omegas
.preProcessZeroTheta    Nudge exactly-zero theta initial estimates off
                        zero (FOCEi family)
aaaCranNlmixrThreads    This function is to set the number of threads
                        to 2
addCwres                Add CWRES
addNpde                 NPDE calculation for nlmixr2
addTable                Add table information to nlmixr2 fit object
                        without tables
agqControl              Control options for the agq estimation method
assertNlmixrFit         Assert that this is a nlmixr2 fit object
assertNlmixrFitData     Assert that this is a nlmixr2 fit data object
bobyqaControl           Control for bobyqa estimation method in nlmixr2
boxCox                  Cox Box, Yeo Johnson and inverse transformation
cholSE                  Generalized Cholesky Matrix Decomposition
emviControl             Control for the variational inference methods
                        emvi and fbvi in nlmixr2
fbviControl             Control for the fbvi (full-Bayes variational
                        inference) method
foControl               Control options for the FO estimation method
foceControl             Control options for the foce estimation method
foceiControl            Control Options for FOCEi
foceiLikLoad            Load a general FOCE-family likelihood into
                        memory
foceiLikRun             Evaluate a loaded general FOCE-family
                        likelihood at supplied etas
foceiLikUnload          Unload the general FOCE-family likelihood from
                        memory
focepControl            Control options for the focep (FOCE+)
                        estimation method
foiControl              Control options foir the FOI estimation method
formatMinWidth          Format numeric values to minimize the printing
                        width
getValidNlmixrCtl.agq   Get valid nlmixr control object
iagqControl             Control options for the iagq estimation method
ifoceControl            Control options for the ifoce estimation method
ifoceiControl           Control options for the ifocei estimation
                        method
ifocepControl           Control options for the ifocep (IRLS FOCE+)
                        estimation method
ilaplaceControl         Control options for the ilaplace estimation
                        method
impControl              Control for the imp (importance-sampling EM
                        without MAP search) method
impmapControl           Control options for the impmap
                        (importance-sampling EM) estimation method
iterPrintControl        Control iteration-time print formatting
laplaceControl          Control options for the Laplace estimation
                        method
lbfgsb3cControl         Control for lbfgsb3c estimation method in
                        nlmixr2
magqControl             Control options for the magq estimation method
mfoceControl            Control options for the mfoce estimation method
mfoceiControl           Control options for the mfocei estimation
                        method
mfocepControl           Control options for the mfocep (mu-referenced
                        FOCE+) estimation method
mlaplaceControl         Control options for the mlaplace estimation
                        method
n1qn1Control            Control for n1qn1 estimation method in nlmixr2
newuoaControl           Control for newuoa estimation method in nlmixr2
nlmControl              nlmixr2 defaults controls for nlm
nlminbControl           nlmixr2 nlminb defaults
nlmixr2                 nlmixr2 fits population PK and PKPD non-linear
                        mixed effects models.
nlmixr2AllEst           Show all the current estimation methods
nlmixr2AllEstType       Tagged list of the available nlmixr2 estimation
                        methods
nlmixr2AugPredSolve     Augmented Prediction for nlmixr2 fit
nlmixr2CreateOutputFromUi
                        Create nlmixr output from the UI
nlmixr2Est.agq          Generic for nlmixr2 estimation methods
nlmixr2Gill83           Get the optimal forward difference interval by
                        Gill83 method
nlmixr2Hess             Calculate Hessian
nlmixr2Keywords         A list and description of the fields in the
                        nlmxir2 object
nlmixr2Logo             Messages the nlmixr2 logo...
nlmixr2NlmeControl      Control Values for nlme Fit with extra options
                        for nlmixr
nlmixr2Validate         Validate nlmixr2
nlmixr2Version          Display nlmixr2's version
nlmixr2fix              Try to fix a nlmixr2 fit
nlmixrAddObjectiveFunctionDataFrame
                        Add objective function data frame to the
                        current objective function
nlmixrAddTiming         Manually add time to a nlmixr2 object
nlmixrCbind             nlmixrCbind
nlmixrClone             Clone nlmixr environment
nlmixrWithTiming        Time a part of a nlmixr operation and add to
                        nlmixr object
nlsControl              nlmixr2 defaults controls for nls
nmNearPD                C++ implementation of Matrix's nearPD
nmObjGetControl.agq     Get control object from fit
nmObjGetEstimationModel
                        Get the estimation model for a fit object
                        depending on the object type
nmObjGetFoceiControl.agq
                        Method for getting focei compatible control
                        object from nlmixr object
nmObjGetIpredModel      Get the ipred model for a fit object depending
                        on the object type
nmObjGetPredOnly        Get the pred-only model for a fit depending on
                        the object type
nmObjHandleControlObject.agqControl
                        Handle the control object
nmObjHandleModelObject
                        Handle Model Object
nmObjUiSetCompressed    Set if the nlmixr2 object will return a
                        compressed ui
nmsimplex               Nelder-Mead simplex search
npagControl             Control for the npag (nonparametric adaptive
                        grid) method
npbControl              Control for the npb (nonparametric Bayes)
                        method
ofv                     Return the objective function
optimControl            nlmixr2 optim defaults
posthocControl          Control options for the posthoc estimation
                        method
predict.nlmixr2FitCore
                        Predict method for nlmixr2 fit core objects
print.saemFit           Print an SAEM model fit summary
qrpemControl            Control for the qrpem (quasi-random parametric
                        EM) estimation method
residuals.nlmixr2FitData
                        Extract residuals from the FOCEI fit
rmEta                   Remove an eta from the model
saemControl             Control Options for SAEM
setCov                  Set the covariance type based on prior
                        calculated covariances
setOfv                  Set/get Objective function type for a nlmixr2
                        object
sqrtm                   Return the square root of general square matrix
                        A
summary.saemFit         Print an SAEM model fit summary
tableControl            Output table/data.frame options
uobyqaControl           Control for uobyqa estimation method in nlmixr2
vaeControl              Control for vae (variational autoencoder)
                        estimation method in nlmixr2
vaeCovariates           Covariates explored by the VAE covariate search
vpcSim                  VPC simulation
