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nlmixr (version 1.1.1-2)

Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics

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

124

Version

1.1.1-2

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

August 29th, 2019

Functions in nlmixr (1.1.1-2)

2 Compartment Model with Michelis Menton Clearance

2 Compartment Model

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

Cox Box, Yeo Johnson and inverse transformation

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

NPDE calculation for nlmixr

Log-likelihood using Gaussian Quadrature

Covariance matrix by Fisher Information Matrix via linearization

Convert fit to FOCEi style fit

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme

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

Calculate gnlmm variance-covariance matrix of fixed effects

Simulated Data Set for comparing objective functions

Fit a non-population dynamic model using mcmc

asHux.nlmixrFitCore

Change a nlmixr fit object to a huxtable

Return composite saem/focei to saem

Generalized Cholesky Matrix Decomposition

Get the FOCEi theta specification for the model

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

Control Options for FOCEi

gen_saem_user_fn

Generate an SAEM model

Get the FOCEi theta or eta specification for model.

instant.stan.extension

instant.stan.extension.

Inverse Guassian absorption model

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

1 Compartment Model w/ Michelis Menton Elimination

Parent/Metabolite dataset

Fit/Evaulate FOCEi

Return composite nlme/focei to nlme

concentrations from a linear compartment model

Fit a non-population dynamic model

nlmixr model block

Extract the Nlmixr bound information from a function.

Sets nodes and weigts of Gauss-Hermite quadrature

Fit a generalized nonlinear mixed-effect model

Configure an SAEM model

nlmixr ini block handling

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

Print x using the message facility

Augmented Prediction for nlmixr fit

constructLinCmt

Construct RxODE linCmt function

Simulate a nlmixr solved system

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

Cleanup saem_fit environment by removing dll after the object is no logner used by R.

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

nlmixrUI.saem.init.omega

SAEM's init$omega

Control Options for SAEM

plot.nlmixrFitData

Plot a nlmixr data object

nlmixrUI.saem.init

Get saem initilization list

Plot of a non-population dynamic model fit using mcmc

Fit an SAEM model

Calculate gnlmm variance-covariance matrix of random effects

nlmixrUI.saem.fit

Generate saem.fit user function.

nlmixrBounds.eta.names

Prepares the UI function and returns a list.

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

Convert/Format the data appropriately for nlmixr

Messages the nlmixr logo...

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

Predict a nlmixr solved system

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

Fit nlme-based mixed-effect model using ODE implementation

Fit a nlmixr model

Get a list of directories for inclusion

Find the assignments in R expression

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

nlmixrUI.saem.distribution

Get SAEM distribution

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

Create a gradient function based on gill numerical differences

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

Calculate Hessian

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

Print a non-population dynamic model fit object

Return the objective function

Summary of a non-population dynamic model fit using mcmc

Summary of a non-population dynamic model fit

GOF plots for nlme-based mixed-effect models

nlmixrUI.saem.model

Generate SAEM model list

Parameters for a linear compartment model for SAEM

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

Clear memoise cache for nlmixr

nlmixrUI.saem.model.omega

Get the SAEM model Omega

summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc

Create a run summary word document

Create a large output based on a nlmixr fit

Convert data to RxODE format (depreciated)

Plot of a non-population dynamic model fit

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

Pregnant Rat Diet Experiment

Single Dose Phenobarbitol PK/PD

Nelder-Mead of simplex search

Pump failure example dataset

Print an SAEM model fit summary

nlmixrUI.focei.fixed

Get parameters that are fixed

Get the optimal forward difference interval by Gill83 method

Objects exported from other packages

Multiple dose Theophiline PK data

Multiple dose Theophiline PK data

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

Prediction after a gnlmm fit

Print UI function

print.gnlmm.fit

Print a gnlmm fit

Produce trace-plot for fit if applicable

Plot an SAEM model fit

nlmixrUI.saem.res.name

Get error names for SAEM

nlmixrUI.focei.inits

Get the FOCEi initializations

Set Objective function type for a nlmixr object

Return the square root of general square matrix A

Vpc function for nlmixr

Dispaly nlmixr's version

summary.saemFit

Print an SAEM model fit summary

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

Output table/data.frame options

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

Validate nlmixr

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

VPC for nlmixr saemFit objects

Warfarin PK/PD data

VPC based on ui model