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nlmixr (version 1.1.1-3)

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

1.1.1-3

License

GPL (>= 2)

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Repository

https://github.com/nlmixrdevelopment/nlmixr

Maintainer

Wenping Wang

Last Published

November 13th, 2019

Functions in nlmixr (1.1.1-3)

Convert fit to FOCEi style fit

Covariance matrix by Fisher Information Matrix via linearization

SAEM dll prodection from garbage collection

gen_saem_user_fn

Generate an SAEM model

Sets nodes and weigts of Gauss-Hermite quadrature

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

Log-likelihood using Gaussian Quadrature

nlmixr model block

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

Return composite nlme/focei to nlme

Control Options for FOCEi

Convert/Format the data appropriately for nlmixr

Fit/Evaulate FOCEi

Calculate gnlmm variance-covariance matrix of fixed effects

Return composite saem/focei to saem

1 Compartment Model w/ Michelis Menton Elimination

asHux.nlmixrFitCore

Change a nlmixr fit object to a huxtable

Clear memoise cache for nlmixr

Get the FOCEi theta or eta specification for model.

Cox Box, Yeo Johnson and inverse transformation

Fit a non-population dynamic model

Configure an SAEM model

Generalized Cholesky Matrix Decomposition

Fit a non-population dynamic model using mcmc

constructLinCmt

Construct RxODE linCmt function

nlmixrUI.focei.inits

Get the FOCEi initializations

Inverse Guassian absorption model

nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving

concentrations from a linear compartment model

nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM

GOF plots for nlme-based mixed-effect models

Calculate gnlmm variance-covariance matrix of random effects

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

Predict a nlmixr solved system

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

Print x using the message facility

Fit nlme-based mixed-effect model using ODE implementation

nlmixrUI.dynmodelfun

Return dynmodel variable translation function

nlmixrUI.focei.fixed

Get parameters that are fixed

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

nlmixrUI.saem.fit

Generate saem.fit user function.

nlmixrUI.rxode.pred

Return RxODE model with predictions appended

nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs

nlmixrUI.saem.ares

Get initial estimate for ares SAEM.

nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.

nlmixrBounds.eta.names

nlmixrUI.saem.init.omega

SAEM's init$omega

Dispaly nlmixr's version

Fit a nlmixr model

Plot of a non-population dynamic model fit

Plot of a non-population dynamic model fit using mcmc

nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined

Nelder-Mead of simplex search

Validate nlmixr

nlmixrUI.saem.log.eta

Get model$log.eta for SAEM

Get a list of directories for inclusion

Objects exported from other packages

Pump failure example dataset

plot.nlmixrFitData

Plot a nlmixr data object

nlmixrUI.saem.model

Generate SAEM model list

nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code

Plot an SAEM model fit

nlmixrUI.saem.model.omega

Get the SAEM model Omega

residuals.nlmixrFitData

Extract residuals from the FOCEI fit

Get the FOCEi theta specification for the model

Calculate Hessian

Parent/Metabolite dataset

Parameters for a linear compartment model for SAEM

Pregnant Rat Diet Experiment

Fit a generalized nonlinear mixed-effect model

instant.stan.extension

instant.stan.extension.

Augmented Prediction for nlmixr fit

Messages the nlmixr logo...

nlmixr ini block handling

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

Prediction after a gnlmm fit

Print a non-population dynamic model fit object

Fit an SAEM model

Extract the Nlmixr bound information from a function.

Get the optimal forward difference interval by Gill83 method

Control Options for SAEM

nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.

nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI

vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects

Vpc function for nlmixr

Set Objective function type for a nlmixr object

Create a gradient function based on gill numerical differences

Single Dose Phenobarbitol PK/PD

nlmixrUI.saem.init

Get saem initilization list

Convert data to RxODE format (depreciated)

summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc

Prepares the UI function and returns a list.

Find the assignments in R expression

nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM

nlmixrUI.saem.bres

Get initial estimate for bres SAEM.

Return the objective function

Simulate a nlmixr solved system

Print an SAEM model fit summary

Output table/data.frame options

Print UI function

nlmixrUI.saem.distribution

Get SAEM distribution

summary.saemFit

Print an SAEM model fit summary

Warfarin PK/PD data

Multiple dose Theophilline PK data

nlmixrUI.saem.res.name

Get error names for SAEM

Create a large output based on a nlmixr fit

nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM

Summary of a non-population dynamic model fit using mcmc

Create a run summary word document

print.gnlmm.fit

Print a gnlmm fit

Produce trace-plot for fit if applicable

Multiple dose Theophilline PK data

Return the square root of general square matrix A

Summary of a non-population dynamic model fit

VPC based on ui model

VPC for nlmixr saemFit objects

NPDE calculation for nlmixr

VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme

Simulated Data Set for comparing objective functions

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

2 Compartment Model

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

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

2 Compartment Model with Michelis Menton Clearance