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nlmixr (version 2.0.4)

Nonlinear Mixed Effects Models in Population PK/PD

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 'RxODE' package (Wang, Hallow, and James 2015 ).

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Install

install.packages('nlmixr')

Monthly Downloads

78

Version

2.0.4

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

April 17th, 2021

Functions in nlmixr (2.0.4)

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

Add multiple covariates to a given model, sequentially or all at once

Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016

Simulated Data Set for comparing objective functions

2 Compartment Model with Michaelis-Menten Clearance

Adding covariate to a given variable in an nlmixr model expression

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme

2 Compartment Model

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

1 Compartment Model w/ Michaelis-Menten Elimination

Add covariate expression to a function string

as.focei.dynmodel

Output nlmixr format for dynmodel

Convert fit to FOCEi style fit

Generalized Cholesky Matrix Decomposition

Convert fit to classic dynmodel object

Calculate gnlmm variance-covariance matrix of fixed effects

Log-likelihood using Gaussian Quadrature

Return composite saem/focei to saem

Backward covariate search

Covariance matrix by Fisher Information Matrix via linearization

Produce trace-plot for fit if applicable

NPDE calculation for nlmixr

Bootstrap nlmixr fit

Return composite nlme/focei to nlme

Cox Box, Yeo Johnson and inverse transformation

Control Options for FOCEi

covarSearchAuto

Stepwise Covariate Model-selection (SCM) method

Configure an SAEM model

This gets the parsed data in the lower-level manner that nlmixr expects.

instant.stan.extension

instant.stan.extension.

Fit a non-population dynamic model

Add table information to nlmixr fit object without tables

Fit a non-population dynamic model using mcmc

Inverse Guassian absorption model

dynmodelControl

Control Options for dynmodel

Forward covariate search

Get the FOCEi theta or eta specification for model.

Fit/Evaulate FOCEi

gen_saem_user_fn

Generate an SAEM model

Create categorical covariates

concentrations from a linear compartment model

Get the optimal forward difference interval by Gill83 method

Forward covariate selection for nlme-base non-linear mixed effect models

nlmixrBounds.eta.names

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

initializeCovars

Initializing covariates before estimation

nlmixr ini block handling

Sets nodes and weights of Gauss-Hermite quadrature

GOF plots for nlme-based mixed-effect models

makeHockeyStick

Creating Hockey-stick covariates

Prepares the UI function and returns a list.

nlmixTest function for testing

Get the FOCEi theta specification for the model

Plot of a non-population dynamic model fit

Simulate a nlmixr solved system

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

Fit a generalized nonlinear mixed-effect model

Fit nlme-based mixed-effect model using ODE implementation

Print x using the message facility

Augmented Prediction for nlmixr fit

Calculate Hessian

Extract the nlmixr bound information from a function.

Fit nlme-based linear compartment mixed-effect model using closed form solution

Create a gradient function based on gill numerical differences

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

nlmixrUI.saem.fit

Generate saem.fit user function.

Validate nlmixr

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

nlmixrUI.focei.inits

Get the FOCEi initializations

nlmixrUI.dynmodelfun2

Return dynmodel variable translation function

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

nlmixrUI.focei.fixed

Get parameters that are fixed

nlmixrUI.saem.init.omega

SAEM's init$omega

Calculate gnlmm variance-covariance matrix of random effects

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

Parent/Metabolite dataset

Access the model list information for nlmixr's nlme user functions

nlmixrUI.saem.distribution

Get SAEM distribution

nlmixrBoundsParser

Functions to assist with setting initial conditions and boundaries

nlmixrUI.saem.cres

Get initial estimate for bres SAEM.

nlmixr model block

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

Convert/Format the data appropriately for nlmixr

Messages the nlmixr logo...

Set/get Objective function type for a nlmixr object

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

nlmixrUI.saem.init

Get saem initilization list

Create a run summary word document

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

Fit a nlmixr model

Convert data to RxODE format (depreciated)

Create a large output based on a nlmixr fit

Return the square root of general square matrix A

VPC based on ui model

VPC for nlmixr saemFit objects

Find the assignments in R expression

Objects exported from other packages

Nelder-Mead simplex search

removeCovMultiple

Removing multiple covariates

Control Options for SAEM

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

nlmixrUI.saem.model

Generate SAEM model list

Display nlmixr's version

Set the covariance type based on prior calculated covariances

Warfarin PK/PD data

Plot an SAEM model fit

plot.nlmixrFitData

Plot a nlmixr data object

Pump failure example dataset

Return the objective function

Perform normalization of the covariate

Plot of a non-population dynamic model fit using mcmc

summary.dyn.mcmc

Print summary of a non-population dynamic model fit using mcmc

Single Dose Phenobarbitol PK/PD

Pregnant Rat Diet Experiment

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

Prediction after a gnlmm fit

Print a non-population dynamic model fit object

print.gnlmm.fit

Print a gnlmm fit

Remove covariate from function string

removeCovariate

Remove covariate expression from a function string

nlmixrDynmodelConvert

Converting nlmixr objects to dynmodel objects

Multiple dose theophylline PK data

Output table/data.frame options

Vpc function for nlmixr

Summary of a non-population dynamic model fit

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

summary.saemFit

Print an SAEM model fit summary

nlmixrUI.saem.model.omega

Get the SAEM model Omega

Get a posthoc estimate of x

Predict a nlmixr solved system

Generic for nlmixr estimation methods

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

nlmixrUI.saem.res.name

Get error names for SAEM

nlmixrUI.saem.rx1

Return RxODE model with predictions appended

Print UI function

preconditionFit

Linearly re-parameterize the model to be less sensitive to rounding errors

Calculate the inverse preconditioning matrix

Print an SAEM model fit summary

Fit an SAEM model

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

Multiple dose theophylline PK data

bootplot.nlmixrFitCore

Produce trace-plot for fit if applicable