Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics


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Documentation for package ‘nlmixr’ version 1.0.0-7

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

-- C --

calcCov Calculate gnlmm variance-covariance matrix of fixed effects
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.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 --

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

-- 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.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
nlmixrLogo Messages the nlmixr logo...
nlmixrPred Predict a nlmixr solved system
nlmixrSim Simulate a nlmixr solved system
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
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

-- O --

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

-- P --

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
simulate.nlmixrFitData Simulate a nlmixr solved system
solve.nlmixrFitData Simulate a nlmixr solved system
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 Theophiline PK data
theo_sd Multiple dose Theophiline PK data
traceplot Produce trace-plot for fit if applicable
traceplot.nlmixrFitCore Produce trace-plot for fit if applicable

-- V --

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

-- misc --

.collectWarnings Collect warnings and just warn once.