Nonlinear Mixed Effects Models in Population PK/PD

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Documentation for package ‘nlmixr’ version 2.0.7

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

-- A --

addCovariate Add covariate expression to a function string
addCovVar Adding covariate to a given variable in an nlmixr model expression
addCwres Add CWRES
addNpde NPDE calculation for nlmixr
addTable Add table information to nlmixr fit object without tables
as.dynmodel Convert fit to classic dynmodel object
as.focei Convert fit to FOCEi style fit
as.focei.nlmixrNlme Convert fit to FOCEi style fit
augPred.nlmixrFitData Augmented Prediction for nlmixr fit

-- B --

backwardSearch Backward covariate search
Bolus_1CPT Bolus_1CPT - 1 Compartment Model Simulated Data from ACOP 2016
Bolus_1CPTMM 1 Compartment Model w/ Michaelis-Menten Elimination
Bolus_2CPT 2 Compartment Model
Bolus_2CPTMM 2 Compartment Model with Michaelis-Menten Clearance
bootdata Bootstrap data
bootplot Produce trace-plot for fit if applicable
bootplot.nlmixrFitCore Produce trace-plot for fit if applicable
bootstrapFit Bootstrap nlmixr fit
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
covarSearchAuto Stepwise Covariate Model-selection (SCM) method

-- D --

dynmodel Fit a non-population dynamic model
dynmodel.mcmc Fit a non-population dynamic model using mcmc
dynmodelControl Control Options for dynmodel

-- 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
forwardSearch Forward covariate search
frwd_selection Forward covariate selection for nlme-base non-linear mixed effect models

-- G --

gauss.quad Sets nodes and weights of Gauss-Hermite quadrature
getOfvType Set/get Objective function type for a nlmixr object
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
gof Plot of a non-population dynamic model fit

-- 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
initializeCovars Initializing covariates before estimation
instant.stan.extension instant.stan.extension.
invgaussian Inverse Guassian absorption model
iYeoJohnson Cox Box, Yeo Johnson and inverse transformation

-- L --

lin_cmt concentrations from a linear compartment model

-- M --

makeDummies Create categorical covariates
makeHockeyStick Creating Hockey-stick covariates
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 Extract the nlmixr bound information from a function.
nlmixrBounds.eta.names Get ETA names
nlmixrBounds.focei.upper.lower Get upper/lower/names for THETAs
nlmixrBoundsParser Functions to assist with setting initial conditions and boundaries
nlmixrBoundsParser.( Functions to assist with setting initial conditions and boundaries
nlmixrDynmodelConvert Converting nlmixr objects to dynmodel objects
nlmixrEst Generic for nlmixr estimation methods
nlmixrEst.dynmodel Generic for nlmixr estimation methods
nlmixrEst.fo Generic for nlmixr estimation methods
nlmixrEst.foce Generic for nlmixr estimation methods
nlmixrEst.focei Generic for nlmixr estimation methods
nlmixrEst.foi Generic for nlmixr estimation methods
nlmixrEst.nlme Generic for nlmixr estimation methods
nlmixrEst.nlme.free Generic for nlmixr estimation methods
nlmixrEst.nlme.mu Generic for nlmixr estimation methods
nlmixrEst.nlme.mu.cov Generic for nlmixr estimation methods
nlmixrEst.nlmixrEst Generic for nlmixr estimation methods
nlmixrEst.posthoc Generic for nlmixr estimation methods
nlmixrEst.saem Generic for nlmixr estimation methods
nlmixrGill83 Get the optimal forward difference interval by Gill83 method
nlmixrHess Calculate Hessian
nlmixrLogo Messages the nlmixr logo...
nlmixrPred Predict a nlmixr solved system
nlmixrSim Simulate a nlmixr solved system
nlmixrTest nlmixTest function for testing
nlmixrUI.dynmodelfun Return dynmodel variable translation function
nlmixrUI.dynmodelfun2 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.cres 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.rx1 Return RxODE model with predictions appended
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 Display 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 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 --

performNorm Perform normalization of the covariate
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
preCondInv Calculate the inverse preconditioning matrix
preconditionFit Linearly re-parameterize the model to be less sensitive to rounding errors
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 Print 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
removeCovariate Remove covariate expression from a function string
removeCovMultiple Removing multiple covariates
removeCovVar Remove covariate from function string
residuals.nlmixrFitData Extract residuals from the FOCEI fit
rxSolve.nlmixrFitData Simulate a nlmixr solved system

-- S --

saem Fit an SAEM model
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
setCov Set the covariance type based on prior calculated covariances
setOfv Set/get 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 Print 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 theophylline PK data
theo_sd Multiple dose theophylline 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