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nlmixr (version 0.9.1-2)

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

0.9.1-2

License

GPL (>= 2)

Issues

69

Pull Requests

1

Stars

119

Forks

46

Maintainer

Wenping Wang

Last Published

May 21st, 2018

Functions in nlmixr (0.9.1-2)

Bolus_1CPT

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
instant.stan.extension

instant.stan.extension.
nlmixrAugPred

Augmented Prediction for nlmixr fit
nlmixrBounds

Extract the Nlmixr bound information from a function.
nlmixrPrint

Print x using the message facility
as.focei

Convert fit to FOCEi style fit
nlmixrSim

Simulate a nlmixr solved system
as.nlme

Return composite nlme/focei to nlme
dynmodel

Fit a non-population dynamic model
dynmodel.mcmc

Fit a non-population dynamic model using mcmc
nlmixrLogo

Messages the nlmixr logo...
lin_cmt

concentrations from a linear compartment model
invgaussian

Inverse Guassian absorption model
nlmixrPred

Predict a nlmixr solved system
Bolus_2CPT

2 Compartment Model
nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving
nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.
Bolus_2CPTMM

2 Compartment Model with Michelis Menton Clearance
nlmixrUI.saem.log.eta

Get model$log.eta for SAEM
as.saem

Return composite saem/focei to saem
Infusion_1CPT

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

Plot a focei.fit plot
bootdata

Bootstrap data
plot.saemFit

Plot an SAEM model fit
RxODE_focei_eta_lik

Get the likelihood for ETA
rats

Pregnant Rat Diet Experiment
RxODE_focei_eta

Get the Function pointers for the LBJ'S routine
reexports

Objects exported from other packages
nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI
nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code
calcCov

Calculate gnlmm variance-covariance matrix of fixed effects
fitted.focei.fit

Extract the fitted values from the model
Oral_1CPT

Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016
nlmixrUI.saem.res.name

Get error names for SAEM
constructLinCmt

Construct RxODE linCmt function
configsaem

Configure an SAEM model
focei.eta

Get the FOCEi theta or eta specification for model.
collectWarnings

Collect warnings and just warn once.
nlmixr_fit

Fit a nlmixr model
nlmixrVersion

Dispaly nlmixr's version
rxFoceiGrad

Calculate the Gradient for an individual
gen_saem_user_fn

Generate an SAEM model
rxFoceiInner

Solve the FOCEI inner problem
nlmixrUI.saem.init

Get saem initilization list
getOMEGA

Calculate gnlmm variance-covariance matrix of random effects
vpc

Vpc function for nlmixr
rxHessian

Get the Hessian for the environment
nlmixrUI.saem.init.omega

SAEM's init$omega
rxUpdateEtas

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

Parent/Metabolite dataset
vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects
frwd_selection

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

Find the assignments in R expression
nobs.focei.fit

Extract the number of observations for the focei fit
nlmeModList

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

Convert NONMEM/Monolix data to RxODE/nlmixr style data
nlmixrBounds.eta.names

Get ETA names
gauss.quad

Sets nodes and weigts of Gauss-Hermite quadrature
par.hist

Parameter history extraction
lincmt

Parameters for a linear compartment model for SAEM
logLik.focei.fit

Extract log likelihood for focei fit
nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs
residuals.focei.fit

Extract residuals from the FOCEI fit
rxFoceiEta

FOCEI ETA setup,
nlme_ode

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

FOCEI THETA setup,
rxGrad

Returns the gradient for FOCEi environment
summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc
nlmixrUI.saem.ares

Get initial estimate for ares SAEM.
nlmixr

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

Create the nlme parameter transform function from the UI object.
summary.saemFit

Print an SAEM model fit summary
nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM
nlmixrUILinCmt

Build linear solved information based on defined parameters.
nlmixrUI.saem.bres

Get initial estimate for bres SAEM.
nlmixrUI.rxode.pred

Return RxODE model with predictions appended
nlmixrValidate

Validate nlmixr
nlmixrUI.saem.fit

Generate saem.fit user function.
nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM
print.dyn.mcmc

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

Print a focei fit
nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined
plot.dyn.ID

Plot of a non-population dynamic model fit
print.gnlmm.fit

Print a gnlmm fit
print.nlmixrUI

Print UI function
saem.cleanup

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

Summary of a non-population dynamic model fit
saemControl

Control Options for SAEM
plot.dyn.mcmc

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

Fit an SAEM model
theo_sd

Multiple dose Theophiline PK data
theo_md

Multiple dose Theophiline PK data
traceplot

Produce trace-plot for fit if applicable
vcov.focei.fit

Extract variance/covariance matrix for FOCEI fit
RxODE_focei_eta_lp

Get the likelihood slope for ETA
RxODE_focei_finalize_llik

Finalize likelihood environment
as.data.frame.focei.fit

Convert focei fit to a data.frame
nlme_lin_cmpt

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

GOF plots for nlme-based mixed-effect models
nlmixrData

Convert/Format the data appropriately for nlmixr
Wang2007

Simulated Data Set for comparing objective functions
nlmixrUI

Prepares the UI function and returns a list.
nlmixrForget

Clear memoise cache for nlmixr
nlmixrUI.focei.inits

Get the FOCEi initilizations
nlmixrUI.saem.model

Generate SAEM model list
nmsimplex

Nelder-Mead of simplex search
nlmixrUI.saem.model.omega

Get the SAEM model Omega
nmxInclude

Get a list of directories for inclusion
prediction

Prediction after a gnlmm fit
pump

Pump failure example dataset
print.saemFit

Print an SAEM model fit summary
rxFoceiLik

Get -LLIK for individual
rxFoceiLp

Get -Grad for individual
print.dyn.ID

Print a non-population dynamic model fit object
vpc_saemFit

VPC for nlmixr saemFit objects
vpc_ui

VPC based on ui model
Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination
gnlmm

Fit a generalized nonlinear mixed-effect model
focei.fit

FOCEI Fit for nlmixr
focei.theta

Get the FOCEi theta specification for the model