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nlmixr (version 0.9.1-3)

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

53

Version

0.9.1-3

License

GPL (>= 2)

Issues

69

Pull Requests

1

Stars

119

Forks

46

Maintainer

Wenping Wang

Last Published

June 21st, 2018

Functions in nlmixr (0.9.1-3)

focei.theta

Get the FOCEi theta specification for the model
getOMEGA

Calculate gnlmm variance-covariance matrix of random effects
as.data.frame.focei.fit

Convert focei fit to a data.frame
focei.eta

Get the FOCEi theta or eta specification for model.
nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM
lincmt

Parameters for a linear compartment model for SAEM
summary.saemFit

Print an SAEM model fit summary
nlmixrUI.saem.bres

Get initial estimate for bres SAEM.
nlmixrUILinCmt

Build linear solved information based on defined parameters.
nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM
nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined
focei.fit

FOCEI Fit for nlmixr
lin_cmt

concentrations from a linear compartment model
plot.dyn.mcmc

Plot of a non-population dynamic model fit using mcmc
rxFoceiGrad

Calculate the Gradient for an individual
nlmixr

nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrUI.saem.res.name

Get error names for SAEM
nlmixrAugPred

Augmented Prediction for nlmixr fit
dynmodel.mcmc

Fit a non-population dynamic model using mcmc
rxGrad

Returns the gradient for FOCEi environment
gnlmm

Fit a generalized nonlinear mixed-effect model
frwd_selection

Forward covariate selection for nlme-base non-linear mixed effect models
plot.focei.fit

Plot a focei.fit plot
nlmixrBounds

Extract the Nlmixr bound information from a function.
nlme_lin_cmpt

Fit nlme-based linear compartment mixed-effect model using closed form solution
nlmixrUI.saem.ares

Get initial estimate for ares SAEM.
nlme_ode

Fit nlme-based mixed-effect model using ODE implementation
nlmixrUI.saem.init

Get saem initilization list
gauss.quad

Sets nodes and weigts of Gauss-Hermite quadrature
nlmixrUI.nlmefun

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

Generate an SAEM model
as.nlme

Return composite nlme/focei to nlme
metabolite

Parent/Metabolite dataset
rxUpdateEtas

Update ETAs based on d(eta)/d(theta)
rxFoceiEta

FOCEI ETA setup,
prediction

Prediction after a gnlmm fit
fitted.focei.fit

Extract the fitted values from the model
logLik.focei.fit

Extract log likelihood for focei fit
nlmeModList

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

Visual predictive check (VPC) for nlmixr nlme objects
nlmixrValidate

Validate nlmixr
nmxInclude

Get a list of directories for inclusion
nlmixrPred

Predict a nlmixr solved system
nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving
nlmixrLogo

Messages the nlmixr logo...
nlmixrBounds.eta.names

Get ETA names
plot.dyn.ID

Plot of a non-population dynamic model fit
nlmixrUI.saem.fit

Generate saem.fit user function.
nlmixrUI.focei.inits

Get the FOCEi initilizations
nlmixrForget

Clear memoise cache for nlmixr
instant.stan.extension

instant.stan.extension.
rxHessian

Get the Hessian for the environment
nlmixrData

Convert/Format the data appropriately for nlmixr
nlme_gof

GOF plots for nlme-based mixed-effect models
theo_md

Multiple dose Theophiline PK data
nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs
nlmixrUI.saem.model

Generate SAEM model list
nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI
nlmixrUI.saem.log.eta

Get model$log.eta for SAEM
nlmixrUI.rxode.pred

Return RxODE model with predictions appended
nobs.focei.fit

Extract the number of observations for the focei fit
nmDataConvert

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

Inverse Guassian absorption model
nmsimplex

Nelder-Mead of simplex search
vpc_saemFit

VPC for nlmixr saemFit objects
nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.
vpc_ui

VPC based on ui model
print.focei.fit

Print a focei fit
nlmixrPrint

Print x using the message facility
reexports

Objects exported from other packages
print.gnlmm.fit

Print a gnlmm fit
nlmixrUI.saem.model.omega

Get the SAEM model Omega
pump

Pump failure example dataset
nlmixrSim

Simulate a nlmixr solved system
rxFoceiLp

Get -Grad for individual
nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code
nlmixrUI.saem.init.omega

SAEM's init$omega
nlmixrUI

Prepares the UI function and returns a list.
par.hist

Parameter history extraction
summary.dyn.mcmc

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

Control Options for SAEM
saem.cleanup

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

Pregnant Rat Diet Experiment
print.nlmixrUI

Print UI function
plot.saemFit

Plot an SAEM model fit
nlmixr_fit

Fit a nlmixr model
nlmixrfindLhs

Find the assignments in R expression
nlmixrVersion

Dispaly nlmixr's version
vpc

Vpc function for nlmixr
vcov.focei.fit

Extract variance/covariance matrix for FOCEI fit
print.dyn.ID

Print a non-population dynamic model fit object
print.saemFit

Print an SAEM model fit summary
print.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc
residuals.focei.fit

Extract residuals from the FOCEI fit
saem.fit

Fit an SAEM model
rxFoceiInner

Solve the FOCEI inner problem
rxFoceiLik

Get -LLIK for individual
rxFoceiTheta

FOCEI THETA setup,
summary.dyn.ID

Summary of a non-population dynamic model fit
theo_sd

Multiple dose Theophiline PK data
traceplot

Produce trace-plot for fit if applicable
RxODE_focei_eta_lp

Get the likelihood slope for ETA
RxODE_focei_eta

Get the Function pointers for the LBJ'S routine
Bolus_1CPT

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
Bolus_2CPT

2 Compartment Model
Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination
Bolus_2CPTMM

2 Compartment Model with Michelis Menton Clearance
as.focei

Convert fit to FOCEi style fit
RxODE_focei_eta_lik

Get the likelihood for ETA
Wang2007

Simulated Data Set for comparing objective functions
RxODE_focei_finalize_llik

Finalize likelihood environment
Oral_1CPT

Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016
Infusion_1CPT

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

Return composite saem/focei to saem
bootdata

Bootstrap data
calcCov

Calculate gnlmm variance-covariance matrix of fixed effects
configsaem

Configure an SAEM model
dynmodel

Fit a non-population dynamic model
constructLinCmt

Construct RxODE linCmt function