Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics


[Up] [Top]

Documentation for package ‘nlmixr’ version 0.9.0-3

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