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nlmixr (version 0.9.1-0)

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

0.9.1-0

License

GPL (>= 2)

Issues

69

Pull Requests

1

Stars

119

Forks

46

Maintainer

Wenping Wang

Last Published

May 19th, 2018

Functions in nlmixr (0.9.1-0)

calcCov

Calculate gnlmm variance-covariance matrix of fixed effects
gen_saem_user_fn

Generate an SAEM model
frwd_selection

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

Sets nodes and weigts of Gauss-Hermite quadrature
nlmixrLogo

Messages the nlmixr logo...
lincmt

Parameters for a linear compartment model for SAEM
lin_cmt

concentrations from a linear compartment model
logLik.focei.fit

Extract log likelihood for focei fit
dynmodel.mcmc

Fit a non-population dynamic model using mcmc
nlmixrPred

Predict a nlmixr solved system
nlmixrUI

Prepares the UI function and returns a list.
dynmodel

Fit a non-population dynamic model
invgaussian

Inverse Guassian absorption model
nlmixrData

Convert/Format the data appropriately for nlmixr
gnlmm

Fit a generalized nonlinear mixed-effect model
fitted.focei.fit

Extract the fitted values from the model
constructLinCmt

Construct RxODE linCmt function
nlmixrBounds.eta.names

Get ETA names
focei.eta

Get the FOCEi theta or eta specification for model.
instant.stan.extension

instant.stan.extension.
metabolite

Parent/Metabolite dataset
nlmixrUI.focei.inits

Get the FOCEi initilizations
nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving
nmsimplex

Nelder-Mead of simplex search
getOMEGA

Calculate gnlmm variance-covariance matrix of random effects
nlmixrAugPred

Augmented Prediction for nlmixr fit
nlmixrForget

Clear memoise cache for nlmixr
nlmeModList

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

FOCEI Fit for nlmixr
nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs
focei.theta

Get the FOCEi theta specification for the model
nlmixrUI.saem.init

Get saem initilization list
nmxInclude

Get a list of directories for inclusion
nlmixrPrint

Print x using the message facility
nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI
rats

Pregnant Rat Diet Experiment
nlmixrUI.saem.init.omega

SAEM's init$omega
nlme_gof

GOF plots for nlme-based mixed-effect models
nlmixrSim

Simulate a nlmixr solved system
reexports

Objects exported from other packages
nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code
nlme_lin_cmpt

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

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

Print an SAEM model fit summary
summary.dyn.mcmc

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

Build linear solved information based on defined parameters.
nlmixrUI.rxode.pred

Return RxODE model with predictions appended
plot.focei.fit

Plot a focei.fit plot
nlmixrValidate

Validate nlmixr
nlmixrBounds

Extract the Nlmixr bound information from a function.
nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.
nlme_ode

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

Get model$log.eta for SAEM
nlmixrVersion

Dispaly nlmixr's version
nlmixr

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

Get initial estimate for ares SAEM.
plot.saemFit

Plot an SAEM model fit
nlmixrUI.saem.eta.trans

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

Generate saem.fit user function.
nlmixrUI.saem.bres

Get initial estimate for bres SAEM.
residuals.focei.fit

Extract residuals from the FOCEI fit
nlmixrUI.saem.res.name

Get error names for SAEM
saemControl

Control Options for SAEM
rxFoceiEta

FOCEI ETA setup,
nlmixrUI.saem.model

Generate SAEM model list
vpc_saemFit

VPC for nlmixr saemFit objects
summary.dyn.ID

Summary of a non-population dynamic model fit
vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects
nlmixr_fit

Fit a nlmixr model
nlmixrUI.saem.model.omega

Get the SAEM model Omega
nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM
nobs.focei.fit

Extract the number of observations for the focei fit
par.hist

Parameter history extraction
plot.dyn.ID

Plot of a non-population dynamic model fit
nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined
rxFoceiGrad

Calculate the Gradient for an individual
nlmixrfindLhs

Find the assignments in R expression
nmDataConvert

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

Prediction after a gnlmm fit
plot.dyn.mcmc

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

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

Print a focei fit
rxFoceiInner

Solve the FOCEI inner problem
print.saemFit

Print an SAEM model fit summary
print.dyn.ID

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

Print a gnlmm fit
print.nlmixrUI

Print UI function
rxFoceiLik

Get -LLIK for individual
pump

Pump failure example dataset
rxFoceiLp

Get -Grad for individual
saem.cleanup

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

Fit an SAEM model
rxHessian

Get the Hessian for the environment
traceplot

Produce trace-plot for fit if applicable
rxUpdateEtas

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

Multiple dose Theophiline PK data
vcov.focei.fit

Extract variance/covariance matrix for FOCEI fit
rxFoceiTheta

FOCEI THETA setup,
rxGrad

Returns the gradient for FOCEi environment
vpc_ui

VPC based on ui model
theo_sd

Multiple dose Theophiline PK data
as.focei

Convert fit to FOCEi style fit
Bolus_2CPTMM

2 Compartment Model with Michelis Menton Clearance
RxODE_focei_eta

Get the Function pointers for the LBJ'S routine
RxODE_focei_finalize_llik

Finalize likelihood environment
configsaem

Configure an SAEM model
RxODE_focei_eta_lik

Get the likelihood for ETA
bootdata

Bootstrap data
Bolus_2CPT

2 Compartment Model
Wang2007

Simulated Data Set for comparing objective functions
Oral_1CPT

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

Get the likelihood slope for ETA
Infusion_1CPT

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

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination
as.saem

Return composite saem/focei to saem
collectWarnings

Collect warnings and just warn once.
as.data.frame.focei.fit

Convert focei fit to a data.frame
as.nlme

Return composite nlme/focei to nlme