Package index • nlmixr2est

All functions

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() iBoxCox() yeoJohnson() iYeoJohnson(): Cox Box, Yeo Johnson and inverse transformation
cholSE(): Generalized Cholesky Matrix Decomposition
.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)
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
getValidNlmixrControl() getValidNlmixrCtl(): 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() nlmixr(): 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() augPred(<nlmixr2FitData>): Augmented Prediction for nlmixr2 fit
nlmixr2CreateOutputFromUi(): Create nlmixr output from the UI
nlmixr2Est(): 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() nlmeControl(): Control Values for nlme Fit with extra options for nlmixr
nlmixr2Validate() nmTest(): 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(): Get control object from fit
nmObjGetEstimationModel(): Get the estimation model for a fit object depending on the object type
nmObjGetFoceiControl(): Method for getting focei compatible control object from nlmixr object
nmObjGetIpredModel() nmObjGetEstimationModel(<saem>) nmObjGetEstimationModel(<default>): 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(): 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() getOfvType(): 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