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nlmixr (version 1.1.1-7)

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

1.1.1-7

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

March 18th, 2020

Functions in nlmixr (1.1.1-7)

NPDE calculation for nlmixr

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme

2 Compartment Model

Calculate gnlmm variance-covariance matrix of fixed effects

Simulated Data Set for comparing objective functions

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

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

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

2 Compartment Model with Michelis Menton Clearance

Return composite saem/focei to saem

Control Options for FOCEi

Generalized Cholesky Matrix Decomposition

Cox Box, Yeo Johnson and inverse transformation

Configure an SAEM model

Calculate gnlmm variance-covariance matrix of random effects

constructLinCmt

Construct RxODE linCmt function

Log-likelihood using Gaussian Quadrature

asHux.nlmixrFitCore

Change a nlmixr fit object to a huxtable

Covariance matrix by Fisher Information Matrix via linearization

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

nlmixr ini block handling

SAEM dll prodection from garbage collection

instant.stan.extension

instant.stan.extension.

Get the FOCEi theta or eta specification for model.

Parameters for a linear compartment model for SAEM

Convert fit to FOCEi style fit

Return composite nlme/focei to nlme

Fit a generalized nonlinear mixed-effect model

nlmixr model block

nlmixrBounds.eta.names

Get the FOCEi theta specification for the model

1 Compartment Model w/ Michelis Menton Elimination

Fit a non-population dynamic model

Parent/Metabolite dataset

Fit a non-population dynamic model using mcmc

gen_saem_user_fn

Generate an SAEM model

Sets nodes and weigts of Gauss-Hermite quadrature

GOF plots for nlme-based mixed-effect models

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

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

Fit/Evaulate FOCEi

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

Fit nlme-based mixed-effect model using ODE implementation

Print x using the message facility

concentrations from a linear compartment model

Augmented Prediction for nlmixr fit

nlmixrUI.focei.inits

Get the FOCEi initializations

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

Predict a nlmixr solved system

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

Inverse Guassian absorption model

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

Get the optimal forward difference interval by Gill83 method

nlmixrUI.saem.fit

Generate saem.fit user function.

Extract the Nlmixr bound information from a function.

Create a gradient function based on gill numerical differences

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

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

Find the assignments in R expression

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

nlmixrUI.saem.distribution

Get SAEM distribution

Simulate a nlmixr solved system

nlmixrUI.saem.res.name

Get error names for SAEM

Convert/Format the data appropriately for nlmixr

Clear memoise cache for nlmixr

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

Prepares the UI function and returns a list.

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

Dispaly nlmixr's version

print.gnlmm.fit

Print a gnlmm fit

nlmixrUI.saem.model

Generate SAEM model list

Control Options for SAEM

Summary of a non-population dynamic model fit using mcmc

Plot an SAEM model fit

plot.nlmixrFitData

Plot a nlmixr data object

Fit a nlmixr model

Calculate Hessian

Convert data to RxODE format (depreciated)

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

Return the objective function

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

nlmixrUI.saem.init.omega

SAEM's init$omega

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

Messages the nlmixr logo...

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

nlmixrUI.saem.model.omega

Get the SAEM model Omega

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

Nelder-Mead of simplex search

nlmixrUI.focei.fixed

Get parameters that are fixed

Get a list of directories for inclusion

Create a run summary word document

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

Objects exported from other packages

Single Dose Phenobarbitol PK/PD

Summary of a non-population dynamic model fit

Print UI function

Print an SAEM model fit summary

Return the square root of general square matrix A

Vpc function for nlmixr

Set Objective function type for a nlmixr object

nlmixrUI.saem.init

Get saem initilization list

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

Validate nlmixr

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

Plot of a non-population dynamic model fit

summary.saemFit

Print an SAEM model fit summary

summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc

Create a large output based on a nlmixr fit

Prediction after a gnlmm fit

Plot of a non-population dynamic model fit using mcmc

VPC for nlmixr saemFit objects

VPC based on ui model

Output table/data.frame options

Print a non-population dynamic model fit object

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

Fit an SAEM model

Produce trace-plot for fit if applicable

Multiple dose Theophilline PK data

Multiple dose Theophilline PK data

Pump failure example dataset

Warfarin PK/PD data

Pregnant Rat Diet Experiment