nlmixr v1.0.0-7

Monthly downloads

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
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
No Results!

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
No Results!

Last month downloads

Details

Type	Package
License	GPL (>= 2)
NeedsCompilation	yes
LinkingTo	dparser(>= 0.1.8), Rcpp (>= 0.12.3), RcppEigen (>= 0.3.3.3.0), StanHeaders, BH
URL	https://github.com/nlmixrdevelopment/nlmixr
LazyData	true
VignetteBuilder	knitr
RoxygenNote	6.1.0
Packaged	2018-09-22 12:09:18 UTC; annie
Repository	CRAN
Date/Publication	2018-09-23 14:00:03 UTC

linkingto	BH , RcppEigen (>= 0.3.3.3.0) , StanHeaders
imports	brew , cli , crayon , dparser , fastGHQuad , ggplot2 , lattice , lbfgs , magrittr , Matrix , memoise , methods , minqa , n1qn1 , nlme , numDeriv , parallel , PreciseSums , R.utils , Rcpp (>= 0.12.3) , RcppArmadillo (>= 0.5.600.2.0) , rex , RxODE (>= 0.8.0-4) , tidyr , vpc (>= 1.0.0)
suggests	data.table , devtools , dplyr , expm , knitr , lbfgsb3 , madness , matrixcalc , nloptr , reshape2 , rmarkdown , testthat , ucminf
depends	R (>= 3.2)
Contributors	Katharine Mullen, Dirk Eddelbuettel, Hadley Wickham, David Ardia, Matthew Fidler, Yuan Xiong, Rik Schoemaker, Justin Wilkins, Mirjam Trame, Teun Post, Robert Leary