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nlmixr2est (version 5.0.2)

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

Description

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 ). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 ).

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Install

install.packages('nlmixr2est')

Monthly Downloads

1,651

Version

5.0.2

License

GPL (>= 3)

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Repository

https://github.com/nlmixr2/nlmixr2est

Homepage

https://nlmixr2.github.io/nlmixr2est/

Maintainer

Matthew Fidler

Last Published

November 28th, 2025

Functions in nlmixr2est (5.0.2)

.deparseDifferent

Identify Differences Between Standard and New Objects but used in rxUiDeparse

Collect warnings and just warn once.

A surrogate function for nlme to call for ode solving

A surrogate function for nlm to call for ode solving

Adjust covariance matrix based on scaling parameters

.nlmixrPreprocessLiteralFix

This literally fixes parameters in the model

.nlmixrNlsFunVal

Internal nls functions for minpack.lm

.nlmixrOptimFunC

A surrogate function for optim to call for ode solving

A surrogate function for nls to call for ode solving

.nlmFinalizeList

Finalizes output list

.nlmixr2objectNameAssign

Allows external methods (like those in nlmixr2) to assign object name

.nlmixr2estLastPredSimulationInfo

Get the least prediction simulation information for VPC

Setup a nonlinear system for optimization

.nlmixr0preProcessCovariatesPresent

Preprocess Covariates needed (or other data items)

Frees nlm environment

.preProcessZeroOmega

Preprocess the zero omegas

.preProcessDataUi

Preprocess the zero omegas

.nlmixr2FitUpdateParams

Update model to have final parameter estimates for piping and save orig data

.rxGetDVFTransform

Get the DV transformation

.saemDropMuRefFromModel

Drop mu referenced etas and covariates

Returns the data currently setup to run nls

Control Options for FOCEi

getValidNlmixrCtl.agq

Get valid nlmixr control object

Control options for the Laplace estimation method

This is an internal function for modifying the UI to apply mu2 referencing

This is an internal function for replacing the ui with original model and dropping artificial data in output

Control options for the FO estimation method

Control options for the foce estimation method

lbfgsb3cControl

Control for lbfgsb3c estimation method in nlmixr2

Control for n1qn1 estimation method in nlmixr2

Fit/Evaluate FOCEi

getBaseSimModelFit

Method for getting simulation rxode2 classic models based on fits

Control options foir the FOI estimation method

nlmixr2AugPredSolve

Augmented Prediction for nlmixr2 fit

nlmixr2 nlminb defaults

nlmixr2 defaults controls for nlm

Generic for nlmixr2 estimation methods

nlmixr2CreateOutputFromUi

Create nlmixr output from the UI

Create a gradient function based on gill numerical differences

Control for newuoa estimation method in nlmixr2

Show all the current estimation methods

Get the optimal forward difference interval by Gill83 method

nlmixr2 fits population PK and PKPD non-linear mixed effects models.

nlmixr2iovLogvarCv

Transform the estimated value to %CV for IOV

Calculate Hessian

Try to fix a nlmixr2 fit

nlmixr2NlmeControl

Control Values for nlme Fit with extra options for nlmixr

Display nlmixr2's version

nlmixrAddObjectiveFunctionDataFrame

Add objective function data frame to the current objective function

Print x using the message facility

nlmixr2Validate

Validate nlmixr2

Messages the nlmixr2 logo...

nlmixr2Keywords

A list and description of the fields in the nlmxir2 object

nlmixrAddTiming

Manually add time to a nlmixr2 object

Get an item from a nlmixr core object

Clone nlmixr environment

nlmixr2 defaults controls for nls

nmObjGetControl.agq

Get control object from fit

nlmixrWithTiming

Time a part of a nlmixr operation and add to nlmixr object

nlmixrUpdateObject

Update the nlmixr2 object with new fit information

nmGetDistributionSaemLines

This is a S3 method for getting the distribution lines for a base rxode2 saem problem

C++ implementation of Matrix's nearPD

nmObjHandleControlObject.agqControl

Handle the control object

nmObjUiSetCompressed

Set if the nlmixr2 object will return a compressed ui

nmObjGetPredOnly

Get the pred-only model for a fit depending on the object type

nmObjGetFoceiControl.agq

Method for getting focei compatible control object from nlmixr object

nmObjGetEstimationModel

Get the estimation model for a fit object depending on the object type

nmObjGetData.addCwres

Get an item from a nlmixr2FitData object

nmObjHandleModelObject

Handle Model Object

nmObjGetRxSolve

Get an option for the estimation method

nmObjGetIpredModel

Get the ipred model for a fit object depending on the object type

Respect suppress messages for nlmixr2 C functions

Nelder-Mead simplex search

nlmixr2 optim defaults

preProcessHooks

Return a list of all pre-processing hooks

preProcessHooksAdd

This adds a pre-processing hook to nlmixr2est

Return the objective function

rxGetDistributionNlmeLines

This is a S3 method for getting the distribution lines for a base rxode2 nlme problem

Set/get Objective function type for a nlmixr2 object

Return the square root of general square matrix A

Output table/data.frame options

summary.saemFit

Print an SAEM model fit summary

residuals.nlmixr2FitData

Extract residuals from the FOCEI fit

rxGetDistributionNlsLines

This is a S3 method for getting the distribution lines for a base rxode2 nls problem

Objects exported from other packages

Control options for the posthoc estimation method

Remove an eta from the model

rxGetDistributionFoceiLines

This is a S3 method for getting the distribution lines for a base rxode2 focei problem

Set the covariance type based on prior calculated covariances

Print an SAEM model fit summary

Expand a VPC simulation

Control for uobyqa estimation method in nlmixr2

Control Options for SAEM

preProcessHooksRm

Remove the hook from nlmixr2est

vpcNameDataCmts

Name the data and compartments

Add table information to nlmixr2 fit object without tables

assertNlmixrFit

Assert that this is a nlmixr2 fit object

Generalized Cholesky Matrix Decomposition

assertNlmixrFitData

Assert that this is a nlmixr2 fit data object

Cox Box, Yeo Johnson and inverse transformation

Control options for the agq estimation method

Control for bobyqa estimation method in nlmixr2

Adds a package to the nlmixr2's $sessioninfo inside the fit

NPDE calculation for nlmixr2

.augPredIpredModel

Augment Prediction for Ipred Model

Initialize S3 methods

Deparse finalize a control or related object into a language object

Get the adaptive Gauss-Hermite quadrature points and weights

This downgrades the UI for any of the zero etas in the model

.foceiPreProcessData

This function process the data for use in focei

.nlmixrNlminbFunC

A surrogate function for nlminb to call for ode solving