nlmixr v1.0.0-7

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Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'RxODE' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).

Functions in nlmixr

Name Description
focei.theta Get the FOCEi theta specification for the model
nlmixrLogo Messages the nlmixr logo...
nlmixrPred Predict a nlmixr solved system
nmDataConvert Convert NONMEM/Monolix data to RxODE/nlmixr style data
foceiControl Control Options for FOCEi
nlmixrUI.focei.fixed Get parameters that are fixed
nlmixrUI Prepares the UI function and returns a list.
Bolus_1CPTMM 1 Compartment Model w/ Michelis Menton Elimination
nlmixrUI.saem.eta.trans Get the eta->eta.trans for SAEM
nlmixrUI.saem.fit Generate saem.fit user function.
nmsimplex Nelder-Mead of simplex search
as.nlme Return composite nlme/focei to nlme
bootdata Bootstrap data
getOMEGA Calculate gnlmm variance-covariance matrix of random effects
.collectWarnings Collect warnings and just warn once.
as.saem Return composite saem/focei to saem
dynmodel Fit a non-population dynamic model
dynmodel.mcmc Fit a non-population dynamic model using mcmc
configsaem Configure an SAEM model
gnlmm Fit a generalized nonlinear mixed-effect model
constructLinCmt Construct RxODE linCmt function
calcCov Calculate gnlmm variance-covariance matrix of fixed effects
lincmt Parameters for a linear compartment model for SAEM
foceiFit FOCEi fit
focei.eta Get the FOCEi theta or eta specification for model.
ini nlmixr ini block handling
instant.stan.extension instant.stan.extension.
model nlmixr model block
summary.saemFit Print an SAEM model fit summary
metabolite Parent/Metabolite dataset
nlmeModList Access the model list information for nlmixr's nlme user functions
nlmixrUI.rxode.pred Return RxODE model with predictions appended
nlmixrData Convert/Format the data appropriately for nlmixr
gauss.quad Sets nodes and weigts of Gauss-Hermite quadrature
gen_saem_user_fn Generate an SAEM model
nlmixrForget Clear memoise cache for nlmixr
nlme_gof GOF plots for nlme-based mixed-effect models
frwd_selection Forward covariate selection for nlme-base non-linear 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
tableControl Output table/data.frame options
nlmixrUI.saem.model.omega Get the SAEM model Omega
nlmixrSim Simulate a nlmixr solved system
nlmixr nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrPrint Print x using the message facility
invgaussian Inverse Guassian absorption model
nlmixrUI.saem.ares Get initial estimate for ares SAEM.
nlmixrUI.saem.res.mod Get the SAEM model$res.mod code
nlmixrUI.theta.pars Get the Parameter function with THETA/ETAs defined
nlmixrUI.focei.inits Get the FOCEi initializations
nlmixrUI.nlme.var Get the variance for the nlme fit process based on UI
nlmixrBounds.eta.names Get ETA names
nlmixrUILinCmt Build linear solved information based on defined parameters.
nlmixrBounds.focei.upper.lower Get upper/lower/names for THETAs
print.gnlmm.fit Print a gnlmm fit
plot.saemFit Plot an SAEM model fit
lin_cmt concentrations from a linear compartment model
prediction Prediction after a gnlmm fit
print.nlmixrUI Print UI function
nlmixrUI.nlmefun Create the nlme parameter transform function from the UI object.
nlmixrAugPred Augmented Prediction for nlmixr fit
nlmixrBounds Extract the Nlmixr bound information from a function.
nlmixrUI.saem.log.eta Get model$log.eta for SAEM
saem.fit Fit an SAEM model
print.saemFit Print an SAEM model fit summary
nlmixrUI.saem.bres Get initial estimate for bres SAEM.
nlmixrUI.nlme.specs Create the nlme specs list for nlmixr nlme solving
nlmixrUI.saem.fixed Get parameters that are fixed for SAEM
pump Pump failure example dataset
nlmixrUI.saem.model Generate SAEM model list
nlmixrUI.saem.init Get saem initilization list
nlmixrUI.saem.distribution Get SAEM distribution
nlmixrUI.saem.init.omega SAEM's init$omega
nlmixrUI.saem.init.theta Generate SAEM initial estimates for THETA.
nlmixr_fit Fit a nlmixr model
saemControl Control Options for SAEM
nlmixrUI.saem.res.name Get error names for SAEM
nmxInclude Get a list of directories for inclusion
vpc_nlmixr_nlme Visual predictive check (VPC) for nlmixr nlme objects
nlmixrUI.saem.theta.name Get THETA names for nlmixr's SAEM
plot.dyn.ID Plot of a non-population dynamic model fit
nlmixrValidate Validate nlmixr
nlmixrfindLhs Find the assignments in R expression
nlmixrVersion Dispaly nlmixr's version
residuals.nlmixrFitData Extract residuals from the FOCEI fit
vpc_saemFit VPC for nlmixr saemFit objects
saem.cleanup Cleanup saem_fit environment by removing dll after the object is no logner used by R.
print.dyn.ID Print a non-population dynamic model fit object
print.dyn.mcmc Summary of a non-population dynamic model fit using mcmc
traceplot Produce trace-plot for fit if applicable
vpc Vpc function for nlmixr
plot.dyn.mcmc Plot of a non-population dynamic model fit using mcmc
summary.dyn.mcmc Summary of a non-population dynamic model fit using mcmc
summary.dyn.ID Summary of a non-population dynamic model fit
vpc_ui VPC based on ui model
plot.nlmixrFitData Plot a nlmixr data object
reexports Objects exported from other packages
theo_md Multiple dose Theophiline PK data
rats Pregnant Rat Diet Experiment
theo_sd Multiple dose Theophiline PK data
Bolus_2CPTMM 2 Compartment Model with Michelis Menton Clearance
Bolus_2CPT 2 Compartment Model
addCwres Add CWRES
Wang2007 Simulated Data Set for comparing objective functions
Bolus_1CPT Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
Infusion_1CPT Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
as.focei Convert fit to FOCEi style fit
addNpde NPDE calculation for nlmixr
Oral_1CPT Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016
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Vignettes of nlmixr

Name
VignetteDemo.R
cwres_vs_pred.png
dv_vs_ipred.png
dv_vs_pred.png
etas.png
fitplots.png
igab.png
ind_plots.png
installing_nlmixr.Rmd
iter.png
iwres_vs_pred.png
logo.png
nlmixr_RxODE_shinyMixR_combo.jpg
pmetab.png
running_nlmixr.Rmd
theo_inf.txt
theo_sd.dat
theo_sd.png
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