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

## Documentation for package ‘nlmixr2est’ version 2.1.8

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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

## -- A --

addCwres | Add CWRES
addNpde | NPDE calculation for nlmixr2
addTable | Add table information to nlmixr2 fit object without tables
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 --

boxCox | Cox Box, Yeo Johnson and inverse transformation

## -- C --

cholSE | Generalized Cholesky Matrix Decomposition

## -- F --

foceiControl | Control Options for FOCEi

## -- G --

getOfvType | Set/get Objective function type for a nlmixr2 object
getValidNlmixrControl | Get valid nlmixr control object
getValidNlmixrCtl | 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.nlme | Get valid nlmixr control object
getValidNlmixrCtl.posthoc | 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

## -- I --

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

## -- N --

nlmeControl | Control Values for nlme Fit with extra options for nlmixr
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.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.nlme | 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
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
nmNearPD | C++ implementation of Matrix's nearPD
nmObjGetControl | 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.nlme | Get control object from fit
nmObjGetControl.posthoc | Get control object from fit
nmObjGetControl.saem | 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.default | Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.nlme | 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.default | Handle the control object
nmObjHandleControlObject.foceiControl | Handle the control object
nmObjHandleControlObject.nlmeControl | Handle the control object
nmObjHandleControlObject.saemControl | 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

## -- P --

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

## -- V --

vpcSim | VPC simulation

## -- Y --

yeoJohnson | Cox Box, Yeo Johnson and inverse transformation