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nlmixr (version 1.1.0-8)

Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics

Description

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 ). Differential equation solving is by compiled C code provided in the 'RxODE' package (Wang, Hallow, and James 2015 ).

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Install

install.packages('nlmixr')

Monthly Downloads

78

Version

1.1.0-8

License

GPL (>= 2)

Issues

69

Pull Requests

1

Stars

119

Forks

45

Maintainer

Wenping Wang

Last Published

May 31st, 2019

Functions in nlmixr (1.1.0-8)

coxBox

Cox Box transformation
constructLinCmt

Construct RxODE linCmt function
as.nlme

Return composite nlme/focei to nlme
addCwres

Add CWRES
instant.stan.extension

instant.stan.extension.
invgaussian

Inverse Guassian absorption model
nlmixr

nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrAugPred

Augmented Prediction for nlmixr fit
nlmixrUI.focei.fixed

Get parameters that are fixed
nlmixrUI.focei.inits

Get the FOCEi initializations
nlmixrUI.saem.ares

Get initial estimate for ares SAEM.
addNpde

NPDE calculation for nlmixr
nlmixrUI.saem.bres

Get initial estimate for bres SAEM.
nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.
nlmixrUI.saem.log.eta

Get model$log.eta for SAEM
nlmixrValidate

Validate nlmixr
nlmixrVersion

Dispaly nlmixr's version
plot.saemFit

Plot an SAEM model fit
prediction

Prediction after a gnlmm fit
calc.COV

Covariance matrix by Fisher Information Matrix via linearization
rats

Pregnant Rat Diet Experiment
calcCov

Calculate gnlmm variance-covariance matrix of fixed effects
.nmGetData

This gets the parsed data in the lower-level manner that nlmixr expects.
dynmodel

Fit a non-population dynamic model
reexports

Objects exported from other packages
lin_cmt

concentrations from a linear compartment model
lincmt

Parameters for a linear compartment model for SAEM
nlme_gof

GOF plots for nlme-based mixed-effect models
nlmeModList

Access the model list information for nlmixr's nlme user functions
Bolus_1CPT

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs
cholSE

Generalized Cholesky Matrix Decomposition
Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination
nlmixrData

Convert/Format the data appropriately for nlmixr
VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme
Bolus_2CPT

2 Compartment Model
configsaem

Configure an SAEM model
nlmixrUI.saem.fit

Generate saem.fit user function.
Bolus_2CPTMM

2 Compartment Model with Michelis Menton Clearance
Wang2007

Simulated Data Set for comparing objective functions
bootdata

Bootstrap data
foceiFit

FOCEi fit
gnlmm

Fit a generalized nonlinear mixed-effect model
as.saem

Return composite saem/focei to saem
foceiFitCpp_

Fit/Evaulate FOCEi
nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM
calc.2LL

Log-likelihood using Gaussian Quadrature
asHux.nlmixrFitCore

Change a nlmixr fit object to a huxtable
focei.theta

Get the FOCEi theta specification for the model
vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects
ini

nlmixr ini block handling
dynmodel.mcmc

Fit a non-population dynamic model using mcmc
focei.eta

Get the FOCEi theta or eta specification for model.
vpc_saemFit

VPC for nlmixr saemFit objects
nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM
foceiControl

Control Options for FOCEi
metabolite

Parent/Metabolite dataset
frwd_selection

Forward covariate selection for nlme-base non-linear mixed effect models
gen_saem_user_fn

Generate an SAEM model
getOMEGA

Calculate gnlmm variance-covariance matrix of random effects
nlmixrBounds

Extract the Nlmixr bound information from a function.
nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined
gauss.quad

Sets nodes and weigts of Gauss-Hermite quadrature
vpc_ui

VPC based on ui model
nlme_lin_cmpt

Fit nlme-based linear compartment mixed-effect model using closed form solution
warfarin

Warfarin PK/PD data
nlme_ode

Fit nlme-based mixed-effect model using ODE implementation
nlmixrBounds.eta.names

Get ETA names
nlmixrPred

Predict a nlmixr solved system
model

nlmixr model block
nlmixr_fit

Fit a nlmixr model
nlmixrSim

Simulate a nlmixr solved system
nlmixrfindLhs

Find the assignments in R expression
nlmixrPrint

Print x using the message facility
nlmixrUI

Prepares the UI function and returns a list.
print.gnlmm.fit

Print a gnlmm fit
nlmixrUI.saem.distribution

Get SAEM distribution
nlmixrForget

Clear memoise cache for nlmixr
nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM
nlmixrLogo

Messages the nlmixr logo...
nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving
nlmixrUI.saem.model

Generate SAEM model list
nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI
print.nlmixrUI

Print UI function
nlmixrUI.saem.model.omega

Get the SAEM model Omega
nmLst

Create a large output based on a nlmixr fit
nmsimplex

Nelder-Mead of simplex search
plot.dyn.mcmc

Plot of a non-population dynamic model fit using mcmc
nlmixrUI.saem.init

Get saem initilization list
residuals.nlmixrFitData

Extract residuals from the FOCEI fit
nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.
saem.cleanup

Cleanup saem_fit environment by removing dll after the object is no logner used by R.
nlmixrUI.rxode.pred

Return RxODE model with predictions appended
plot.nlmixrFitData

Plot a nlmixr data object
nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code
theo_md

Multiple dose Theophiline PK data
setOfv

Set Objective function type for a nlmixr object
theo_sd

Multiple dose Theophiline PK data
nlmixrUI.saem.res.name

Get error names for SAEM
nmDataConvert

Convert data to RxODE format (depreciated)
sqrtm

Return the square root of general square matrix A
nlmixrUI.saem.init.omega

SAEM's init$omega
summary.dyn.ID

Summary of a non-population dynamic model fit
nmDocx

Create a run summary word document
nmxInclude

Get a list of directories for inclusion
summary.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc
ofv

Return the objective function
print.dyn.ID

Print a non-population dynamic model fit object
print.dyn.mcmc

Summary of a non-population dynamic model fit using mcmc
pheno_sd

Single Dose Phenobarbitol PK/PD
plot.dyn.ID

Plot of a non-population dynamic model fit
print.saemFit

Print an SAEM model fit summary
traceplot

Produce trace-plot for fit if applicable
pump

Pump failure example dataset
vpc

Vpc function for nlmixr
yeoJohnson

Yeo-Johnson Transformation
saem.fit

Fit an SAEM model
saemControl

Control Options for SAEM
summary.saemFit

Print an SAEM model fit summary
tableControl

Output table/data.frame options
Oral_1CPT

Oral_1CPT -- 1 Compartment Model with Oral Absorption 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