# Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics

## Documentation for package ‘nlmixr’ version 0.9.0-3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F G I L M N O P R S T V W

## -- A --

as.data.frame.focei.fit | Convert focei fit to a data.frame
as.focei | Convert fit to FOCEi style fit
as.focei.nlmixr_nlme | Convert fit to FOCEi style fit

## -- B --

Bolus_1CPT | Bolus_1CPT - 1 Compartment Model Simulated Data from ACOP 2016
Bolus_1CPTMM | 1 Compartment Model w/ Michelis Menton Elimination
Bolus_2CPT | 2 Compartment Model
Bolus_2CPTMM | 2 Compartment Model with Michelis Menton Clearance
bootdata | Bootstrap data

## -- C --

calcCov | Calculate gnlmm variance-covariance matrix of fixed effects
collectWarnings | Collect warnings and just warn once.
configsaem | Configure an SAEM model

## -- D --

dynmodel | Fit a non-population dynamic model
dynmodel.mcmc | Fit a non-population dynamic model using mcmc

## -- F --

fitted.focei.fit | Extract the fitted values from the model
focei.eta | Get the FOCEi theta or eta specification for model.
focei.eta.nlmixr_nlme | Get the FOCEi theta or eta specification for model.
focei.fit | FOCEI Fit for nlmixr
focei.fit.data.frame | FOCEI Fit for nlmixr
focei.fit.function | FOCEI Fit for nlmixr
focei.fit.nlmixr.ui.focei.fit | FOCEI Fit for nlmixr
focei.fit.nlmixr.ui.nlme | FOCEI Fit for nlmixr
focei.fit.nlmixrUI | FOCEI Fit for nlmixr
focei.theta | Get the FOCEi theta specification for the model
focei.theta.nlmixr_nlme | Get the FOCEi theta specification for the model
frwd_selection | Forward covariate selection for nlme-base non-linear mixed effect models

## -- G --

gauss.quad | Sets nodes and weigts of Gauss-Hermite quadrature
gen_saem_user_fn | Generate an SAEM model
getOMEGA | Calculate gnlmm variance-covariance matrix of random effects
gnlmm | Fit a generalized nonlinear mixed-effect model
gnlmm2 | Fit a generalized nonlinear mixed-effect model

## -- I --

Infusion_1CPT | Infusion_1CPT - 1 Compartment Model Simulated Data from ACOP 2016
instant.stan.extension | instant.stan.extension.
invgaussian | Inverse Guassian absorption model

## -- L --

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

## -- M --

metabolite | Parent/Metabolite dataset

## -- N --

nlme_gof | GOF plots for nlme-based 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
nlmixr | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixr.function | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixr.nlmixr.ui.focei.fit | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixr.nlmixr.ui.nlme | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixr.nlmixr.ui.saem | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixr.nlmixrUI | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrBounds.eta.names | Get ETA names
nlmixrBounds.focei.upper.lower | Get upper/lower/names for THETAs
nlmixrLogo | Messages the nlmixr logo...
nlmixrUI.focei.inits | Get the FOCEi initilizations
nlmixrUI.nlme.specs | Create the nlme specs list for nlmixr nlme solving
nlmixrUI.rxode.pred | Return RxODE model with predictions appended
nlmixrUI.saem.ares | Get initial estimate for ares SAEM.
nlmixrUI.saem.bres | Get initial estimate for bres SAEM.
nlmixrUI.saem.eta.trans | Get the eta->eta.trans for SAEM
nlmixrUI.saem.fit | Generate saem.fit user function.
nlmixrUI.saem.init | Get saem initilization list
nlmixrUI.saem.init.omega | SAEM's init$omega
nlmixrUI.saem.init.theta | Generate SAEM initial estimates for THETA.
nlmixrUI.saem.log.eta | Get model$log.eta for SAEM
nlmixrUI.saem.model | Generate SAEM model list
nlmixrUI.saem.model.omega | Get the SAEM model Omega
nlmixrUI.saem.res.mod | Get the SAEM model$res.mod code
nlmixrUI.saem.res.name | Get error names for SAEM
nlmixrUI.saem.theta.name | Get THETA names for nlmixr's SAEM
nlmixrUI.theta.pars | Get the Parameter function with THETA/ETAs defined
nlmixrUILinCmt | Build linear solved information based on defined parameters.
nlmixrValidate | Validate nlmixr
nlmixrVersion | Dispaly nlmixr's version
nlmixr_fit | Fit a nlmixr model
nmDataConvert | Convert NONMEM/Monolix data to RxODE/nlmixr style data
nmsimplex | Nelder-Mead of simplex search
nobs.focei.fit | Extract the number of observations for the focei fit

## -- O --

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

## -- P --

par.hist | Parameter history extraction
par.hist.nlmixr.ui.focei.fit | Parameter history extraction
par.hist.nlmixr.ui.saem | Parameter history extraction
plot.dyn.ID | Plot of a non-population dynamic model fit
plot.dyn.mcmc | Plot of a non-population dynamic model fit using mcmc
plot.focei.fit | Plot a focei.fit plot
plot.saemFit | Plot an SAEM model fit
prediction | Prediction after a gnlmm fit
print.dyn.ID | Print a non-population dynamic model fit object
print.dyn.mcmc | Summary of a non-population dynamic model fit using mcmc
print.focei.fit | Print a focei fit
print.gnlmm.fit | Print a gnlmm fit
print.nlmixrUI | Print UI function
print.saemFit | Print an SAEM model fit summary
pump | Pump failure example dataset

## -- R --

rats | Pregnant Rat Diet Experiment
residuals.focei.fit | Extract residuals from the FOCEI fit

## -- S --

saem | Fit an SAEM model
saem.cleanup | Cleanup saem_fit environment by removing dll after the object is no logner used by R.
saem.fit | Fit an SAEM model
saem.fit.default | Fit an SAEM model
saem.fit.function | Fit an SAEM model
saem.fit.nlmixr.ui.nlme | Fit an SAEM model
saem.fit.nlmixrUI | Fit an SAEM model
saem.fit.RxODE | Fit an SAEM model
saemControl | Control Options for SAEM
simulate.focei.fit | Simulate response based on FOCEi model's datathe fitted object's dataset
summary.dyn.ID | Summary of a non-population dynamic model fit
summary.dyn.mcmc | Summary of a non-population dynamic model fit using mcmc
summary.saemFit | Print an SAEM model fit summary

## -- T --

theo_md | Multiple dose Theophiline PK data
theo_sd | Multiple dose Theophiline PK data
traceplot | Produce trace-plot for fit if applicable
traceplot.focei.fit | Produce trace-plot for fit if applicable

## -- V --

vcov.focei.fit | Extract variance/covariance matrix for FOCEI fit
vpc | Visual predictive check (VPC)

## -- W --

Wang2007 | Simulated Data Set for comparing objective functions