# Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

## Documentation for package ‘nlmixr2est’ version 4.1.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C F G I L N O P R S T U V Y misc

## -- A --

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
augPred.nlmixr2FitData | Augmented Prediction for nlmixr2 fit

## -- B --

bobyqaControl | Control for bobyqa estimation method in nlmixr2
boxCox | Cox Box, Yeo Johnson and inverse transformation

## -- C --

cholSE | Generalized Cholesky Matrix Decomposition

## -- F --

foceControl | Control options for the foce estimation method
foceiControl | Control Options for FOCEi
foControl | Control options for the FO estimation method
foiControl | Control options foir the FOI estimation method

## -- G --

getOfvType | Set/get Objective function type for a nlmixr2 object
getValidNlmixrControl | Get valid nlmixr control object
getValidNlmixrCtl | Get valid nlmixr control object
getValidNlmixrCtl.agq | Get valid nlmixr control object
getValidNlmixrCtl.bobyqa | Get valid nlmixr control object
getValidNlmixrCtl.default | Get valid nlmixr control object
getValidNlmixrCtl.fo | Get valid nlmixr control object
getValidNlmixrCtl.foce | Get valid nlmixr control object
getValidNlmixrCtl.focei | Get valid nlmixr control object
getValidNlmixrCtl.foi | Get valid nlmixr control object
getValidNlmixrCtl.laplace | Get valid nlmixr control object
getValidNlmixrCtl.lbfgsb3c | Get valid nlmixr control object
getValidNlmixrCtl.n1qn1 | Get valid nlmixr control object
getValidNlmixrCtl.newuoa | Get valid nlmixr control object
getValidNlmixrCtl.nlm | Get valid nlmixr control object
getValidNlmixrCtl.nlme | Get valid nlmixr control object
getValidNlmixrCtl.nlminb | Get valid nlmixr control object
getValidNlmixrCtl.nls | Get valid nlmixr control object
getValidNlmixrCtl.optim | Get valid nlmixr control object
getValidNlmixrCtl.posthoc | Get valid nlmixr control object
getValidNlmixrCtl.predict | Get valid nlmixr control object
getValidNlmixrCtl.rxSolve | Get valid nlmixr control object
getValidNlmixrCtl.saem | Get valid nlmixr control object
getValidNlmixrCtl.simulate | Get valid nlmixr control object
getValidNlmixrCtl.simulation | Get valid nlmixr control object
getValidNlmixrCtl.tableControl | Get valid nlmixr control object
getValidNlmixrCtl.uobyqa | Get valid nlmixr control object

## -- I --

iBoxCox | Cox Box, Yeo Johnson and inverse transformation
iYeoJohnson | Cox Box, Yeo Johnson and inverse transformation

## -- L --

laplaceControl | Control options for the Laplace estimation method
lbfgsb3cControl | Control for lbfgsb3c estimation method in nlmixr2

## -- N --

n1qn1Control | Control for n1qn1 estimation method in nlmixr2
newuoaControl | Control for newuoa estimation method in nlmixr2
nlmControl | nlmixr2 defaults controls for nlm
nlmeControl | Control Values for nlme Fit with extra options for nlmixr
nlminbControl | nlmixr2 nlminb defaults
nlmixr | nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2 | nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.function | nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.nlmixr2FitCore | nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.nlmixr2FitData | nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.rxUi | nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2AllEst | Show all the current estimation methods
nlmixr2AugPredSolve | Augmented Prediction for nlmixr2 fit
nlmixr2CreateOutputFromUi | Create nlmixr output from the UI
nlmixr2Est | Generic for nlmixr2 estimation methods
nlmixr2Est.agq | Generic for nlmixr2 estimation methods
nlmixr2Est.bobyqa | Generic for nlmixr2 estimation methods
nlmixr2Est.default | Generic for nlmixr2 estimation methods
nlmixr2Est.fo | Generic for nlmixr2 estimation methods
nlmixr2Est.foce | Generic for nlmixr2 estimation methods
nlmixr2Est.focei | Generic for nlmixr2 estimation methods
nlmixr2Est.foi | Generic for nlmixr2 estimation methods
nlmixr2Est.laplace | Generic for nlmixr2 estimation methods
nlmixr2Est.lbfgsb3c | Generic for nlmixr2 estimation methods
nlmixr2Est.n1qn1 | Generic for nlmixr2 estimation methods
nlmixr2Est.newuoa | Generic for nlmixr2 estimation methods
nlmixr2Est.nlm | Generic for nlmixr2 estimation methods
nlmixr2Est.nlme | Generic for nlmixr2 estimation methods
nlmixr2Est.nlminb | Generic for nlmixr2 estimation methods
nlmixr2Est.nls | Generic for nlmixr2 estimation methods
nlmixr2Est.optim | Generic for nlmixr2 estimation methods
nlmixr2Est.output | Generic for nlmixr2 estimation methods
nlmixr2Est.posthoc | Generic for nlmixr2 estimation methods
nlmixr2Est.predict | Generic for nlmixr2 estimation methods
nlmixr2Est.rxSolve | Generic for nlmixr2 estimation methods
nlmixr2Est.saem | Generic for nlmixr2 estimation methods
nlmixr2Est.simulate | Generic for nlmixr2 estimation methods
nlmixr2Est.simulation | Generic for nlmixr2 estimation methods
nlmixr2Est.uobyqa | Generic for nlmixr2 estimation methods
nlmixr2fix | Try to fix a nlmixr2 fit
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
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
nmObjGetControl.agq | Get control object from fit
nmObjGetControl.bobyqa | Get control object from fit
nmObjGetControl.default | Get control object from fit
nmObjGetControl.fo | Get control object from fit
nmObjGetControl.foce | Get control object from fit
nmObjGetControl.focei | Get control object from fit
nmObjGetControl.foi | Get control object from fit
nmObjGetControl.laplace | Get control object from fit
nmObjGetControl.lbfgsb3c | Get control object from fit
nmObjGetControl.n1qn1 | Get control object from fit
nmObjGetControl.newuoa | Get control object from fit
nmObjGetControl.nlm | Get control object from fit
nmObjGetControl.nlme | Get control object from fit
nmObjGetControl.nlminb | Get control object from fit
nmObjGetControl.nls | Get control object from fit
nmObjGetControl.optim | Get control object from fit
nmObjGetControl.posthoc | Get control object from fit
nmObjGetControl.saem | Get control object from fit
nmObjGetControl.uobyqa | Get control object from fit
nmObjGetEstimationModel | Get the estimation model for a fit object depending on the object type
nmObjGetEstimationModel.default | Get the ipred model for a fit object depending on the object type
nmObjGetEstimationModel.saem | Get the ipred model for a fit object depending on the object type
nmObjGetFoceiControl | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.agq | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.default | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.foce | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.laplace | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.nlme | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.posthoc | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.saem | Method for getting focei compatible control object from nlmixr object
nmObjGetIpredModel | Get the ipred model for a fit object depending on the object type
nmObjGetIpredModel.default | Get the ipred model for a fit object depending on the object type
nmObjGetIpredModel.saem | 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
nmObjGetPredOnly.default | Get the pred-only model for a fit depending on the object type
nmObjGetPredOnly.saem | Get the pred-only model for a fit depending on the object type
nmObjHandleControlObject | Handle the control object
nmObjHandleControlObject.agqControl | Handle the control object
nmObjHandleControlObject.bobyqaControl | Handle the control object
nmObjHandleControlObject.default | Handle the control object
nmObjHandleControlObject.foceControl | Handle the control object
nmObjHandleControlObject.foceiControl | Handle the control object
nmObjHandleControlObject.foControl | Handle the control object
nmObjHandleControlObject.foiControl | Handle the control object
nmObjHandleControlObject.laplaceControl | Handle the control object
nmObjHandleControlObject.lbfgsb3cControl | Handle the control object
nmObjHandleControlObject.n1qn1Control | Handle the control object
nmObjHandleControlObject.newuoaControl | Handle the control object
nmObjHandleControlObject.nlmControl | Handle the control object
nmObjHandleControlObject.nlmeControl | Handle the control object
nmObjHandleControlObject.nlminbControl | Handle the control object
nmObjHandleControlObject.nlsControl | Handle the control object
nmObjHandleControlObject.optimControl | Handle the control object
nmObjHandleControlObject.posthocControl | Handle the control object
nmObjHandleControlObject.saemControl | Handle the control object
nmObjHandleControlObject.uobyqaControl | Handle the control object
nmObjHandleModelObject | Handle Model Object
nmObjHandleModelObject.default | Handle Model Object
nmObjHandleModelObject.foceiModelList | Handle Model Object
nmObjHandleModelObject.saemModelList | Handle Model Object
nmObjUiSetCompressed | Set if the nlmixr2 object will return a compressed ui
nmsimplex | Nelder-Mead simplex search
nmTest | Validate nlmixr2

## -- O --

ofv | Return the objective function
optimControl | nlmixr2 optim defaults

## -- P --

posthocControl | Control options for the posthoc estimation method
print.saemFit | Print an SAEM model fit summary

## -- R --

residuals.nlmixr2FitData | Extract residuals from the FOCEI fit

## -- S --

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

## -- T --

tableControl | Output table/data.frame options

## -- U --

uobyqaControl | Control for uobyqa estimation method in nlmixr2

## -- V --

vpcSim | VPC simulation

## -- Y --

yeoJohnson | Cox Box, Yeo Johnson and inverse transformation

## -- misc --

.augPredIpredModel | Augment Prediction for Ipred Model
.nlmixr0preProcessCovariatesPresent | Preprocess Covariates needed (or other data items)
.nlmixrPreprocessLiteralFix | This literally fixes parameters in the model
.preProcessDataUi | Preprocess the zero omegas
.preProcessZeroOmega | Preprocess the zero omegas