nlmixr v1.1.1-2

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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
Bolus_2CPTMM 2 Compartment Model with Michelis Menton Clearance
Bolus_2CPT 2 Compartment Model
Infusion_1CPT Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
bootdata Bootstrap data
boxCox Cox Box, Yeo Johnson and inverse transformation
Oral_1CPT Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016
addNpde NPDE calculation for nlmixr
addCwres Add CWRES
calc.2LL Log-likelihood using Gaussian Quadrature
calc.COV Covariance matrix by Fisher Information Matrix via linearization
as.focei Convert fit to FOCEi style fit
VarCorr.nlmixrNlme Return VarCorr for nlmixr nlme
.nmGetData This gets the parsed data in the lower-level manner that nlmixr expects.
calcCov Calculate gnlmm variance-covariance matrix of fixed effects
Wang2007 Simulated Data Set for comparing objective functions
dynmodel.mcmc Fit a non-population dynamic model using mcmc
asHux.nlmixrFitCore Change a nlmixr fit object to a huxtable
as.saem Return composite saem/focei to saem
cholSE Generalized Cholesky Matrix Decomposition
focei.theta Get the FOCEi theta specification for the model
frwd_selection Forward covariate selection for nlme-base non-linear mixed effect models
foceiControl Control Options for FOCEi
gen_saem_user_fn Generate an SAEM model
focei.eta Get the FOCEi theta or eta specification for model.
instant.stan.extension instant.stan.extension.
invgaussian Inverse Guassian absorption model
Bolus_1CPT Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
Bolus_1CPTMM 1 Compartment Model w/ Michelis Menton Elimination
foceiFit FOCEi fit
metabolite Parent/Metabolite dataset
foceiFitCpp_ Fit/Evaulate FOCEi
as.nlme Return composite nlme/focei to nlme
lin_cmt concentrations from a linear compartment model
dynmodel Fit a non-population dynamic model
model nlmixr model block
nlmixrBounds Extract the Nlmixr bound information from a function.
gauss.quad Sets nodes and weigts of Gauss-Hermite quadrature
gnlmm Fit a generalized nonlinear mixed-effect model
configsaem Configure an SAEM model
ini nlmixr ini block handling
nlmixr nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrPrint Print x using the message facility
nlmixrAugPred Augmented Prediction for nlmixr fit
constructLinCmt Construct RxODE linCmt function
nlmixrSim Simulate a nlmixr solved system
nlmixrUI.saem.bres Get initial estimate for bres SAEM.
nlmixrUI.saem.ares Get initial estimate for ares SAEM.
nlmixrBounds.focei.upper.lower Get upper/lower/names for THETAs
saem.cleanup Cleanup saem_fit environment by removing dll after the object is no logner used by R.
residuals.nlmixrFitData Extract residuals from the FOCEI fit
nlmixrUI.saem.init.omega SAEM's init$omega
saemControl Control Options for SAEM
plot.nlmixrFitData Plot a nlmixr data object
nlmixrUI.saem.init Get saem initilization list
plot.dyn.mcmc Plot of a non-population dynamic model fit using mcmc
saem.fit Fit an SAEM model
getOMEGA Calculate gnlmm variance-covariance matrix of random effects
nlmixrUI.saem.fit Generate saem.fit user function.
nlmixrBounds.eta.names Get ETA names
nlmixrUI Prepares the UI function and returns a list.
nlmixrUI.dynmodelfun Return dynmodel variable translation function
nlmixrData Convert/Format the data appropriately for nlmixr
nlmixrLogo Messages the nlmixr logo...
nlme_lin_cmpt Fit nlme-based linear compartment mixed-effect model using closed form solution
nlmixrPred Predict a nlmixr solved system
nlmixrUI.nlmefun Create the nlme parameter transform function from the UI object.
nlme_ode Fit nlme-based mixed-effect model using ODE implementation
nlmixr_fit Fit a nlmixr model
nmxInclude Get a list of directories for inclusion
nlmixrfindLhs Find the assignments in R expression
nlmixrUI.rxode.pred Return RxODE model with predictions appended
nlmixrUI.saem.distribution Get SAEM distribution
nlmixrUI.nlme.specs Create the nlme specs list for nlmixr nlme solving
nlmixrEval_ Create a gradient function based on gill numerical differences
nlmixrUI.nlme.var Get the variance for the nlme fit process based on UI
nlmixrHess Calculate Hessian
nlmixrUI.saem.eta.trans Get the eta->eta.trans for SAEM
nlmixrUI.saem.fixed Get parameters that are fixed for SAEM
print.dyn.ID Print a non-population dynamic model fit object
ofv Return the objective function
print.dyn.mcmc Summary of a non-population dynamic model fit using mcmc
summary.dyn.ID Summary of a non-population dynamic model fit
nlme_gof GOF plots for nlme-based mixed-effect models
nlmixrUI.saem.model Generate SAEM model list
lincmt Parameters for a linear compartment model for SAEM
nlmeModList Access the model list information for nlmixr's nlme user functions
nlmixrForget Clear memoise cache for nlmixr
nlmixrUI.saem.model.omega Get the SAEM model Omega
summary.dyn.mcmc Summary of a non-population dynamic model fit using mcmc
nmDocx Create a run summary word document
nmLst Create a large output based on a nlmixr fit
nmDataConvert Convert data to RxODE format (depreciated)
plot.dyn.ID Plot of a non-population dynamic model fit
nlmixrUI.theta.pars Get the Parameter function with THETA/ETAs defined
nlmixrUI.saem.theta.name Get THETA names for nlmixr's SAEM
rats Pregnant Rat Diet Experiment
pheno_sd Single Dose Phenobarbitol PK/PD
nmsimplex Nelder-Mead of simplex search
pump Pump failure example dataset
print.saemFit Print an SAEM model fit summary
nlmixrUI.focei.fixed Get parameters that are fixed
nlmixrGill83 Get the optimal forward difference interval by Gill83 method
reexports Objects exported from other packages
theo_sd Multiple dose Theophiline PK data
theo_md Multiple dose Theophiline PK data
nlmixrUI.saem.res.mod Get the SAEM model$res.mod code
prediction Prediction after a gnlmm fit
print.nlmixrUI Print UI function
print.gnlmm.fit Print a gnlmm fit
traceplot Produce trace-plot for fit if applicable
plot.saemFit Plot an SAEM model fit
nlmixrUI.saem.res.name Get error names for SAEM
nlmixrUI.focei.inits Get the FOCEi initializations
setOfv Set Objective function type for a nlmixr object
sqrtm Return the square root of general square matrix A
vpc Vpc function for nlmixr
nlmixrVersion Dispaly nlmixr's version
summary.saemFit Print an SAEM model fit summary
vpc_nlmixr_nlme Visual predictive check (VPC) for nlmixr nlme objects
tableControl Output table/data.frame options
nlmixrUI.saem.log.eta Get model$log.eta for SAEM
nlmixrValidate Validate nlmixr
nlmixrUI.saem.init.theta Generate SAEM initial estimates for THETA.
vpc_saemFit VPC for nlmixr saemFit objects
warfarin Warfarin PK/PD data
vpc_ui VPC based on ui model
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Vignettes of nlmixr

Name
logo.png
running_nlmixr.Rmd
theo_inf.txt
theo_sd.dat
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