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nlmixr (version 2.0.7)

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

54

Version

2.0.7

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

March 27th, 2022

Functions in nlmixr (2.0.7)

Simulated Data Set for comparing objective functions

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

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme

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

2 Compartment Model with Michaelis-Menten Clearance

2 Compartment Model

1 Compartment Model w/ Michaelis-Menten Elimination

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

as.focei.dynmodel

Output nlmixr format for dynmodel

Add covariate expression to a function string

Adding covariate to a given variable in an nlmixr model expression

Return composite nlme/focei to nlme

Backward covariate search

Log-likelihood using Gaussian Quadrature

Return composite saem/focei to saem

Cox Box, Yeo Johnson and inverse transformation

Bootstrap nlmixr fit

Control Options for FOCEi

Configure an SAEM model

Convert fit to classic dynmodel object

Add table information to nlmixr fit object without tables

Get the FOCEi theta specification for the model

NPDE calculation for nlmixr

Get the FOCEi theta or eta specification for model.

nlmixr ini block handling

Calculate gnlmm variance-covariance matrix of fixed effects

Generalized Cholesky Matrix Decomposition

Convert fit to FOCEi style fit

Inverse Guassian absorption model

instant.stan.extension

instant.stan.extension.

Forward covariate search

Fit/Evaulate FOCEi

gen_saem_user_fn

Generate an SAEM model

Produce trace-plot for fit if applicable

Calculate gnlmm variance-covariance matrix of random effects

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

nlmixrUI.dynmodelfun2

Return dynmodel variable translation function

dynmodelControl

Control Options for dynmodel

Fit a non-population dynamic model using mcmc

nlmixr model block

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

covarSearchAuto

Stepwise Covariate Model-selection (SCM) method

Fit a non-population dynamic model

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

makeHockeyStick

Creating Hockey-stick covariates

Covariance matrix by Fisher Information Matrix via linearization

Sets nodes and weights of Gauss-Hermite quadrature

Parent/Metabolite dataset

Plot of a non-population dynamic model fit

Fit a generalized nonlinear mixed-effect model

initializeCovars

Initializing covariates before estimation

Convert/Format the data appropriately for nlmixr

nlmixrBoundsParser

Functions to assist with setting initial conditions and boundaries

Simulate a nlmixr solved system

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

Get the optimal forward difference interval by Gill83 method

nlmixrUI.saem.cres

Get initial estimate for bres SAEM.

nlmixrUI.saem.distribution

Get SAEM distribution

Fit nlme-based mixed-effect model using ODE implementation

Create a gradient function based on gill numerical differences

Print x using the message facility

GOF plots for nlme-based mixed-effect models

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

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

concentrations from a linear compartment model

nlmixrUI.saem.res.name

Get error names for SAEM

nlmixrUI.saem.init

Get saem initilization list

nlmixrUI.saem.rx1

Return RxODE model with predictions appended

Perform normalization of the covariate

summary.dyn.mcmc

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

print.gnlmm.fit

Print a gnlmm fit

Return the objective function

Create categorical covariates

Augmented Prediction for nlmixr fit

Summary of a non-population dynamic model fit

summary.saemFit

Print an SAEM model fit summary

Calculate Hessian

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

Extract the nlmixr bound information from a function.

Predict a nlmixr solved system

nlmixrUI.focei.fixed

Get parameters that are fixed

Messages the nlmixr logo...

Get a posthoc estimate of x

nlmixrUI.focei.inits

Get the FOCEi initializations

plot.nlmixrFitData

Plot a nlmixr data object

Fit a nlmixr model

nlmixrBounds.eta.names

Find the assignments in R expression

Plot an SAEM model fit

Create a run summary word document

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

nlmixrUI.saem.init.omega

SAEM's init$omega

Single Dose Phenobarbitol PK/PD

Print an SAEM model fit summary

Print UI function

Plot of a non-population dynamic model fit using mcmc

nlmixrDynmodelConvert

Converting nlmixr objects to dynmodel objects

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

Convert data to RxODE format (depreciated)

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

Fit an SAEM model

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

nlmixrUI.saem.model.omega

Get the SAEM model Omega

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

Vpc function for nlmixr

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

nlmixTest function for testing

Generic for nlmixr estimation methods

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

nlmixrUI.saem.fit

Generate saem.fit user function.

Prepares the UI function and returns a list.

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

Validate nlmixr

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

Display nlmixr's version

nlmixrUI.saem.model

Generate SAEM model list

Output table/data.frame options

Create a large output based on a nlmixr fit

preconditionFit

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

removeCovMultiple

Removing multiple covariates

Return the square root of general square matrix A

Objects exported from other packages

Calculate the inverse preconditioning matrix

Set/get Objective function type for a nlmixr object

Multiple dose theophylline PK data

Prediction after a gnlmm fit

Print a non-population dynamic model fit object

Control Options for SAEM

Multiple dose theophylline PK data

Remove covariate from function string

Nelder-Mead simplex search

Pump failure example dataset

bootplot.nlmixrFitCore

Produce trace-plot for fit if applicable

removeCovariate

Remove covariate expression from a function string

Pregnant Rat Diet Experiment

VPC for nlmixr saemFit objects

VPC based on ui model

Set the covariance type based on prior calculated covariances

Warfarin PK/PD data