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nlmixr (version 1.0.0-7)

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

1.0.0-7

License

GPL (>= 2)

Issues

69

Pull Requests

1

Stars

119

Forks

45

Maintainer

Wenping Wang

Last Published

September 23rd, 2018

Functions in nlmixr (1.0.0-7)

focei.theta

Get the FOCEi theta specification for the model
nlmixrLogo

Messages the nlmixr logo...
nlmixrPred

Predict a nlmixr solved system
nmDataConvert

Convert NONMEM/Monolix data to RxODE/nlmixr style data
foceiControl

Control Options for FOCEi
nlmixrUI.focei.fixed

Get parameters that are fixed
nlmixrUI

Prepares the UI function and returns a list.
Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination
nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM
nlmixrUI.saem.fit

Generate saem.fit user function.
nmsimplex

Nelder-Mead of simplex search
as.nlme

Return composite nlme/focei to nlme
bootdata

Bootstrap data
getOMEGA

Calculate gnlmm variance-covariance matrix of random effects
.collectWarnings

Collect warnings and just warn once.
as.saem

Return composite saem/focei to saem
dynmodel

Fit a non-population dynamic model
dynmodel.mcmc

Fit a non-population dynamic model using mcmc
configsaem

Configure an SAEM model
gnlmm

Fit a generalized nonlinear mixed-effect model
constructLinCmt

Construct RxODE linCmt function
calcCov

Calculate gnlmm variance-covariance matrix of fixed effects
lincmt

Parameters for a linear compartment model for SAEM
foceiFit

FOCEi fit
focei.eta

Get the FOCEi theta or eta specification for model.
ini

nlmixr ini block handling
instant.stan.extension

instant.stan.extension.
model

nlmixr model block
summary.saemFit

Print an SAEM model fit summary
metabolite

Parent/Metabolite dataset
nlmeModList

Access the model list information for nlmixr's nlme user functions
nlmixrUI.rxode.pred

Return RxODE model with predictions appended
nlmixrData

Convert/Format the data appropriately for nlmixr
gauss.quad

Sets nodes and weigts of Gauss-Hermite quadrature
gen_saem_user_fn

Generate an SAEM model
nlmixrForget

Clear memoise cache for nlmixr
nlme_gof

GOF plots for nlme-based mixed-effect models
frwd_selection

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

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

Fit nlme-based mixed-effect model using ODE implementation
tableControl

Output table/data.frame options
nlmixrUI.saem.model.omega

Get the SAEM model Omega
nlmixrSim

Simulate a nlmixr solved system
nlmixr

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

Print x using the message facility
invgaussian

Inverse Guassian absorption model
nlmixrUI.saem.ares

Get initial estimate for ares SAEM.
nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code
nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined
nlmixrUI.focei.inits

Get the FOCEi initializations
nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI
nlmixrBounds.eta.names

Get ETA names
nlmixrUILinCmt

Build linear solved information based on defined parameters.
nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs
print.gnlmm.fit

Print a gnlmm fit
plot.saemFit

Plot an SAEM model fit
lin_cmt

concentrations from a linear compartment model
prediction

Prediction after a gnlmm fit
print.nlmixrUI

Print UI function
nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.
nlmixrAugPred

Augmented Prediction for nlmixr fit
nlmixrBounds

Extract the Nlmixr bound information from a function.
nlmixrUI.saem.log.eta

Get model$log.eta for SAEM
saem.fit

Fit an SAEM model
print.saemFit

Print an SAEM model fit summary
nlmixrUI.saem.bres

Get initial estimate for bres SAEM.
nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving
nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM
pump

Pump failure example dataset
nlmixrUI.saem.model

Generate SAEM model list
nlmixrUI.saem.init

Get saem initilization list
nlmixrUI.saem.distribution

Get SAEM distribution
nlmixrUI.saem.init.omega

SAEM's init$omega
nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.
nlmixr_fit

Fit a nlmixr model
saemControl

Control Options for SAEM
nlmixrUI.saem.res.name

Get error names for SAEM
nmxInclude

Get a list of directories for inclusion
vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects
nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM
plot.dyn.ID

Plot of a non-population dynamic model fit
nlmixrValidate

Validate nlmixr
nlmixrfindLhs

Find the assignments in R expression
nlmixrVersion

Dispaly nlmixr's version
residuals.nlmixrFitData

Extract residuals from the FOCEI fit
vpc_saemFit

VPC for nlmixr saemFit objects
saem.cleanup

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

Print a non-population dynamic model fit object
print.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc
traceplot

Produce trace-plot for fit if applicable
vpc

Vpc function for nlmixr
plot.dyn.mcmc

Plot of a non-population dynamic model fit using mcmc
summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc
summary.dyn.ID

Summary of a non-population dynamic model fit
vpc_ui

VPC based on ui model
plot.nlmixrFitData

Plot a nlmixr data object
reexports

Objects exported from other packages
theo_md

Multiple dose Theophiline PK data
rats

Pregnant Rat Diet Experiment
theo_sd

Multiple dose Theophiline PK data
Bolus_2CPTMM

2 Compartment Model with Michelis Menton Clearance
Bolus_2CPT

2 Compartment Model
addCwres

Add CWRES
Wang2007

Simulated Data Set for comparing objective functions
Bolus_1CPT

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
Infusion_1CPT

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
as.focei

Convert fit to FOCEi style fit
addNpde

NPDE calculation for nlmixr
Oral_1CPT

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