# Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics

## Documentation for package ‘nlmixr’ version 1.1.1-7

- DESCRIPTION file.

## Help Pages

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

## -- A --

addCwres | Add CWRES
addNpde | NPDE calculation for nlmixr
as.focei | Convert fit to FOCEi style fit
as.focei.nlmixrNlme | Convert fit to FOCEi style fit
asHux.nlmixrFitCore | Change a nlmixr fit object to a huxtable
augPred.nlmixrFitData | Augmented Prediction for nlmixr 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
boxCox | Cox Box, Yeo Johnson and inverse transformation

## -- C --

calc.2LL | Log-likelihood using Gaussian Quadrature
calc.COV | Covariance matrix by Fisher Information Matrix via linearization
calcCov | Calculate gnlmm variance-covariance matrix of fixed effects
cholSE | Generalized Cholesky Matrix Decomposition
configsaem | Configure an SAEM model

## -- D --

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

## -- F --

focei.eta | Get the FOCEi theta or eta specification for model.
focei.eta.nlmixrNlme | Get the FOCEi theta or eta specification for model.
focei.fit | FOCEi fit
focei.theta | Get the FOCEi theta specification for the model
focei.theta.nlmixrNlme | Get the FOCEi theta specification for the model
foceiControl | Control Options for FOCEi
foceiFit | FOCEi fit
foceiFit.data.frame | FOCEi fit
foceiFit.data.frame0 | FOCEi fit
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 --

iBoxCox | Cox Box, Yeo Johnson and inverse transformation
Infusion_1CPT | Infusion_1CPT - 1 Compartment Model Simulated Data from ACOP 2016
ini | nlmixr ini block handling
instant.stan.extension | instant.stan.extension.
invgaussian | Inverse Guassian absorption model
iYeoJohnson | Cox Box, Yeo Johnson and inverse transformation

## -- L --

lincmt | Parameters for a linear compartment model for SAEM
lin_cmt | concentrations from a linear compartment model

## -- M --

metabolite | Parent/Metabolite dataset
model | nlmixr model block

## -- N --

nlmeLinCmpt | Fit nlme-based linear compartment mixed-effect model using closed form solution
nlmeLinCmt | Fit nlme-based linear compartment mixed-effect model using closed form solution
nlmeOde | Fit nlme-based mixed-effect model using ODE implementation
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.nlmixrFitCore | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixr.nlmixrUI | nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrAugPred | Augmented Prediction for nlmixr fit
nlmixrBounds.eta.names | Get ETA names
nlmixrBounds.focei.upper.lower | Get upper/lower/names for THETAs
nlmixrEval_ | Create a gradient function based on gill numerical differences
nlmixrGill83 | Get the optimal forward difference interval by Gill83 method
nlmixrGradFun | Create a gradient function based on gill numerical differences
nlmixrGrad_ | Create a gradient function based on gill numerical differences
nlmixrHess | Calculate Hessian
nlmixrLogo | Messages the nlmixr logo...
nlmixrParHist_ | Create a gradient function based on gill numerical differences
nlmixrPred | Predict a nlmixr solved system
nlmixrSim | Simulate a nlmixr solved system
nlmixrUI.dynmodelfun | Return dynmodel variable translation function
nlmixrUI.focei.fixed | Get parameters that are fixed
nlmixrUI.focei.inits | Get the FOCEi initializations
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.distribution | Get SAEM distribution
nlmixrUI.saem.eta.trans | Get the eta->eta.trans for SAEM
nlmixrUI.saem.fit | Generate saem.fit user function.
nlmixrUI.saem.fixed | Get parameters that are fixed for SAEM
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
nlmixrValidate | Validate nlmixr
nlmixrVersion | Dispaly nlmixr's version
nlmixr_fit | Fit a nlmixr model
nmDocx | Create a run summary word document
nmLst | Create a large output based on a nlmixr fit
nmSave | Create a run summary word document
nmsimplex | Nelder-Mead of simplex search
nmTest | Validate nlmixr

## -- O --

ofv | Return the objective function
Oral_1CPT | Oral_1CPT - 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016

## -- P --

pheno_sd | Single Dose Phenobarbitol PK/PD
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.nlmixrFitData | Plot a nlmixr data object
plot.saemFit | Plot an SAEM model fit
predict.nlmixrFitData | Predict a nlmixr solved system
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.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.nlmixrFitData | Extract residuals from the FOCEI fit
rxSolve.nlmixrFitData | Simulate a nlmixr solved system

## -- 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
setOfv | Set Objective function type for a nlmixr object
simulate.nlmixrFitData | Simulate a nlmixr solved system
solve.nlmixrFitData | Simulate a nlmixr solved system
sqrtm | Return the square root of general square matrix A
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 --

tableControl | Output table/data.frame options
theo_md | Multiple dose Theophilline PK data
theo_sd | Multiple dose Theophilline PK data
traceplot | Produce trace-plot for fit if applicable
traceplot.nlmixrFitCore | Produce trace-plot for fit if applicable

## -- V --

VarCorr.nlmixrNlme | Return VarCorr for nlmixr nlme
vpc | Vpc function for nlmixr
vpc.default | Vpc function for nlmixr
vpc.nlmixrFitData | VPC based on ui model
vpc.nlmixrNlme | Visual predictive check (VPC) for nlmixr nlme objects
vpc.nlmixrVpc | VPC based on ui model
vpc.saemFit | VPC for nlmixr saemFit objects
vpc.ui | VPC based on ui model
vpcNlmixrNlme | Visual predictive check (VPC) for nlmixr nlme objects
vpc_nlmixr_nlme | Visual predictive check (VPC) for nlmixr nlme objects
vpc_saemFit | VPC for nlmixr saemFit objects
vpc_ui | VPC based on ui model

## -- W --

Wang2007 | Simulated Data Set for comparing objective functions
warfarin | Warfarin PK/PD data

## -- Y --

yeoJohnson | Cox Box, Yeo Johnson and inverse transformation

## -- misc --

.protectSaem | SAEM dll prodection from garbage collection