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nlmixr (version 1.1.1-6)

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

39

Version

1.1.1-6

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

March 14th, 2020

Functions in nlmixr (1.1.1-6)

Log-likelihood using Gaussian Quadrature

Covariance matrix by Fisher Information Matrix via linearization

Fit a non-population dynamic model

Fit a non-population dynamic model using mcmc

Return composite nlme/focei to nlme

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

Convert fit to FOCEi style fit

Configure an SAEM model

Calculate gnlmm variance-covariance matrix of fixed effects

constructLinCmt

Construct RxODE linCmt function

Fit/Evaulate FOCEi

nlmixr ini block handling

Extract the Nlmixr bound information from a function.

Augmented Prediction for nlmixr fit

instant.stan.extension

instant.stan.extension.

Fit nlme-based mixed-effect model using ODE implementation

Predict a nlmixr solved system

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

Clear memoise cache for nlmixr

Simulated Data Set for comparing objective functions

Return composite saem/focei to saem

Get the FOCEi theta specification for the model

Get the FOCEi theta or eta specification for model.

Cox Box, Yeo Johnson and inverse transformation

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

concentrations from a linear compartment model

Convert/Format the data appropriately for nlmixr

Generalized Cholesky Matrix Decomposition

asHux.nlmixrFitCore

Change a nlmixr fit object to a huxtable

SAEM dll prodection from garbage collection

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

Calculate gnlmm variance-covariance matrix of random effects

Fit a generalized nonlinear mixed-effect model

Control Options for FOCEi

gen_saem_user_fn

Generate an SAEM model

Print UI function

Sets nodes and weigts of Gauss-Hermite quadrature

Multiple dose Theophilline PK data

GOF plots for nlme-based mixed-effect models

Print x using the message facility

nlmixrUI.focei.inits

Get the FOCEi initializations

Simulate a nlmixr solved system

Multiple dose Theophilline PK data

Create a gradient function based on gill numerical differences

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

Get the optimal forward difference interval by Gill83 method

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

Calculate Hessian

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

nlmixrUI.saem.model.omega

Get the SAEM model Omega

Inverse Guassian absorption model

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

nlmixrUI.focei.fixed

Get parameters that are fixed

nlmixrUI.saem.model

Generate SAEM model list

Convert data to RxODE format (depreciated)

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

nlmixrUI.saem.init.omega

SAEM's init$omega

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

Print a non-population dynamic model fit object

Plot of a non-population dynamic model fit

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

nlmixrUI.saem.res.name

Get error names for SAEM

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

Parameters for a linear compartment model for SAEM

nlmixrBounds.eta.names

Summary of a non-population dynamic model fit using mcmc

print.gnlmm.fit

Print a gnlmm fit

Nelder-Mead of simplex search

VPC for nlmixr saemFit objects

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

Parent/Metabolite dataset

Get a list of directories for inclusion

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

Prepares the UI function and returns a list.

Fit a nlmixr model

Dispaly nlmixr's version

Create a large output based on a nlmixr fit

Create a run summary word document

nlmixrUI.saem.fit

Generate saem.fit user function.

Validate nlmixr

Warfarin PK/PD data

Objects exported from other packages

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

Fit an SAEM model

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

Messages the nlmixr logo...

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

nlmixr model block

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

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

Plot of a non-population dynamic model fit using mcmc

Prediction after a gnlmm fit

Vpc function for nlmixr

Pump failure example dataset

VPC based on ui model

Return the square root of general square matrix A

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

Summary of a non-population dynamic model fit

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc

summary.saemFit

Print an SAEM model fit summary

nlmixrUI.saem.init

Get saem initilization list

Plot an SAEM model fit

nlmixrUI.saem.distribution

Get SAEM distribution

Set Objective function type for a nlmixr object

Return the objective function

plot.nlmixrFitData

Plot a nlmixr data object

Pregnant Rat Diet Experiment

Control Options for SAEM

Single Dose Phenobarbitol PK/PD

Produce trace-plot for fit if applicable

Print an SAEM model fit summary

Output table/data.frame options

Find the assignments in R expression

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

1 Compartment Model w/ Michelis Menton Elimination

2 Compartment Model with Michelis Menton Clearance

2 Compartment Model

NPDE calculation for nlmixr

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

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme