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nlmixr (version 1.1.1-9)

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

54

Version

1.1.1-9

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

June 22nd, 2020

Functions in nlmixr (1.1.1-9)

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

2 Compartment Model

NPDE calculation for nlmixr

Cox Box, Yeo Johnson and inverse transformation

Covariance matrix by Fisher Information Matrix via linearization

Return composite saem/focei to saem

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

Convert fit to FOCEi style fit

Return composite nlme/focei to nlme

Fit a non-population dynamic model using mcmc

2 Compartment Model with Michelis Menton Clearance

Get the FOCEi theta or eta specification for model.

Calculate gnlmm variance-covariance matrix of fixed effects

Log-likelihood using Gaussian Quadrature

constructLinCmt

Construct RxODE linCmt function

Calculate gnlmm variance-covariance matrix of random effects

gen_saem_user_fn

Generate an SAEM model

Control Options for FOCEi

Get the FOCEi theta specification for the model

Parameters for a linear compartment model for SAEM

concentrations from a linear compartment model

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

Fit nlme-based mixed-effect model using ODE implementation

GOF plots for nlme-based mixed-effect models

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

Fit a non-population dynamic model

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

instant.stan.extension

instant.stan.extension.

SAEM dll prodection from garbage collection

Create a gradient function based on gill numerical differences

Calculate Hessian

nlmixrUI.saem.fit

Generate saem.fit user function.

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

Inverse Guassian absorption model

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

Simulate a nlmixr solved system

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

Print x using the message facility

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

Create a large output based on a nlmixr fit

Nelder-Mead of simplex search

Create a run summary word document

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

Sets nodes and weigts of Gauss-Hermite quadrature

Convert data to RxODE format (depreciated)

Print an SAEM model fit summary

nlmixrBounds.eta.names

Convert/Format the data appropriately for nlmixr

Extract the Nlmixr bound information from a function.

summary.saemFit

Print an SAEM model fit summary

Output table/data.frame options

nlmixrUI.focei.fixed

Get parameters that are fixed

nlmixrUI.focei.inits

Get the FOCEi initializations

Generalized Cholesky Matrix Decomposition

Pump failure example dataset

Produce trace-plot for fit if applicable

Fit a nlmixr model

nlmixrUI.saem.init

Get saem initilization list

Plot an SAEM model fit

nlmixrUI.saem.init.omega

SAEM's init$omega

Prediction after a gnlmm fit

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

Validate nlmixr

Parent/Metabolite dataset

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

Dispaly nlmixr's version

nlmixrUI.saem.model.omega

Get the SAEM model Omega

nlmixrUI.saem.model

Generate SAEM model list

Configure an SAEM model

nlmixr model block

Get the optimal forward difference interval by Gill83 method

Clear memoise cache for nlmixr

Vpc function for nlmixr

Return the objective function

Find the assignments in R expression

Print a non-population dynamic model fit object

Summary of a non-population dynamic model fit using mcmc

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

Get a list of directories for inclusion

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

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

Single Dose Phenobarbitol PK/PD

Fit/Evaulate FOCEi

nlmixrUI.saem.res.name

Get error names for SAEM

Set Objective function type for a nlmixr object

Objects exported from other packages

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

Return the square root of general square matrix A

Fit a generalized nonlinear mixed-effect model

nlmixr ini block handling

Plot of a non-population dynamic model fit

Summary of a non-population dynamic model fit

VPC for nlmixr saemFit objects

Pregnant Rat Diet Experiment

summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc

VPC based on ui model

Multiple dose Theophilline PK data

Multiple dose Theophilline PK data

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

Augmented Prediction for nlmixr fit

Messages the nlmixr logo...

Predict a nlmixr solved system

Warfarin PK/PD data

Prepares the UI function and returns a list.

nlmixrUI.saem.distribution

Get SAEM distribution

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

Plot of a non-population dynamic model fit using mcmc

print.gnlmm.fit

Print a gnlmm fit

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

plot.nlmixrFitData

Plot a nlmixr data object

Print UI function

Control Options for SAEM

Fit an SAEM model

Simulated Data Set for comparing objective functions

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

1 Compartment Model w/ Michelis Menton Elimination