nlmixr v1.1.1-2

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by Wenping Wang View Source

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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Details

Type	Package
License	GPL (>= 2)
NeedsCompilation	yes
LinkingTo	dparser(>= 0.1.8), RxODE(>= 0.9.1-3), RcppEigen (>= 0.3.3.3.0), lbfgsb3c, Rcpp, BH, StanHeaders(>= 2.18.0)
URL	https://github.com/nlmixrdevelopment/nlmixr
LazyData	true
VignetteBuilder	knitr
RoxygenNote	6.1.1
Biarch	true
Packaged	2019-08-28 11:35:02 UTC; annie
Repository	CRAN
Date/Publication	2019-08-29 12:10:03 UTC

linkingto	BH , RcppEigen (>= 0.3.3.3.0) , StanHeaders (>= 2.18.0)
imports	brew , cli , crayon , digest , dparser , fastGHQuad , flextable , generics , ggplot2 , huxtable , lattice , lbfgs , magrittr , Matrix , memoise , methods , minqa , n1qn1 , nlme , parallel , R.utils , Rcpp (>= 0.12.3) , RcppArmadillo (>= 0.5.600.2.0) , rex , RxODE (>= 0.9.1-0) , stringr , sys , tidyr , vpc (>= 1.0.0) , yaml
suggests	broom.mixed , data.table , devtools , dotwhisker , dplyr , drake (>= 7.5.2) , expm , gridExtra , knitr , lbfgsb3c , madness , matrixcalc , nloptr , officer , pkgdown , reshape2 , rmarkdown , Rvmmin , testthat , ucminf , xpose
depends	R (>= 3.5)
Contributors	Katharine Mullen, Dirk Eddelbuettel, Hadley Wickham, Emmanuelle Comets, Audrey Lavenu, Marc Lavielle, David Ardia, Bill Denney, Matthew Fidler, Richard Hooijmaijers, Yuan Xiong, Rik Schoemaker, Justin Wilkins, Mirjam Trame, Teun Post, Robert Leary, Johannes Pfeifer, Robert B. Schnabel, Elizabeth Eskow