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

Documentation for package ‘nlmixr2est’ version 3.0.4

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-- 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 --

bobyqaControl	Control for bobyqa estimation method in nlmixr2
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.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.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 --

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.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.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
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.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.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.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.bobyqaControl	Handle the control object
nmObjHandleControlObject.default	Handle the control object
nmObjHandleControlObject.foceiControl	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.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 --

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
.nlmixrPreprocessLiteralFix	This literally fixes parameters in the model
.preProcessDataUi	Preprocess the zero omegas
.preProcessZeroOmega	Preprocess the zero omegas