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nlmixr (version 1.1.1-1)

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

124

Version

1.1.1-1

License

GPL (>= 2)

Issues

69

Pull Requests

1

Stars

119

Forks

45

Maintainer

Wenping Wang

Last Published

August 23rd, 2019

Functions in nlmixr (1.1.1-1)

Wang2007

Simulated Data Set for comparing objective functions
addNpde

NPDE calculation for nlmixr
Bolus_2CPTMM

2 Compartment Model with Michelis Menton Clearance
Bolus_1CPT

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
addCwres

Add CWRES
VarCorr.nlmixrNlme

Return VarCorr for nlmixr nlme
Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination
Bolus_2CPT

2 Compartment Model
Infusion_1CPT

Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
calcCov

Calculate gnlmm variance-covariance matrix of fixed effects
as.saem

Return composite saem/focei to saem
calc.2LL

Log-likelihood using Gaussian Quadrature
calc.COV

Covariance matrix by Fisher Information Matrix via linearization
Oral_1CPT

Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016
focei.theta

Get the FOCEi theta specification for the model
focei.eta

Get the FOCEi theta or eta specification for model.
dynmodel

Fit a non-population dynamic model
dynmodel.mcmc

Fit a non-population dynamic model using mcmc
cholSE

Generalized Cholesky Matrix Decomposition
.nmGetData

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

Control Options for FOCEi
as.focei

Convert fit to FOCEi style fit
as.nlme

Return composite nlme/focei to nlme
frwd_selection

Forward covariate selection for nlme-base non-linear mixed effect models
asHux.nlmixrFitCore

Change a nlmixr fit object to a huxtable
bootdata

Bootstrap data
boxCox

Cox Box, Yeo Johnson and inverse transformation
foceiFit

FOCEi fit
lin_cmt

concentrations from a linear compartment model
model

nlmixr model block
nlmixrBounds.focei.upper.lower

Get upper/lower/names for THETAs
nlmixrUI.focei.fixed

Get parameters that are fixed
nlmixrForget

Clear memoise cache for nlmixr
metabolite

Parent/Metabolite dataset
nlmixrData

Convert/Format the data appropriately for nlmixr
instant.stan.extension

instant.stan.extension.
nlmixrUI.focei.inits

Get the FOCEi initializations
invgaussian

Inverse Guassian absorption model
nlmixrUI.saem.fit

Generate saem.fit user function.
gauss.quad

Sets nodes and weigts of Gauss-Hermite quadrature
getOMEGA

Calculate gnlmm variance-covariance matrix of random effects
nlmixrBounds.eta.names

Get ETA names
constructLinCmt

Construct RxODE linCmt function
gen_saem_user_fn

Generate an SAEM model
nlmixrBounds

Extract the Nlmixr bound information from a function.
nlmixrUI.saem.ares

Get initial estimate for ares SAEM.
configsaem

Configure an SAEM model
nlmixrUI.saem.fixed

Get parameters that are fixed for SAEM
nlmixrUI.saem.bres

Get initial estimate for bres SAEM.
nlme_lin_cmpt

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

Fit/Evaulate FOCEi
nmDocx

Create a run summary word document
nmDataConvert

Convert data to RxODE format (depreciated)
residuals.nlmixrFitData

Extract residuals from the FOCEI fit
nlmeModList

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

GOF plots for nlme-based mixed-effect models
lincmt

Parameters for a linear compartment model for SAEM
nlmixrHess

Calculate Hessian
nlmixrEval_

Create a gradient function based on gill numerical differences
nlmixrUI.nlmefun

Create the nlme parameter transform function from the UI object.
gnlmm

Fit a generalized nonlinear mixed-effect model
nlmixrGill83

Get the optimal forward difference interval by Gill83 method
nlmixrUI.saem.model

Generate SAEM model list
saem.cleanup

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

Get SAEM distribution
nlmixrUI.saem.eta.trans

Get the eta->eta.trans for SAEM
nlmixrUI.saem.res.mod

Get the SAEM model$res.mod code
nlmixrUI.saem.model.omega

Get the SAEM model Omega
nlmixrUI.theta.pars

Get the Parameter function with THETA/ETAs defined
nlmixrUI.saem.theta.name

Get THETA names for nlmixr's SAEM
nmLst

Create a large output based on a nlmixr fit
nlmixr

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

nlmixr ini block handling
saem.fit

Fit an SAEM model
nlmixrUI.rxode.pred

Return RxODE model with predictions appended
nlmixrAugPred

Augmented Prediction for nlmixr fit
nlmixrUI.saem.res.name

Get error names for SAEM
nmsimplex

Nelder-Mead of simplex search
print.dyn.ID

Print a non-population dynamic model fit object
saemControl

Control Options for SAEM
nlmixrPrint

Print x using the message facility
nlmixrSim

Simulate a nlmixr solved system
nlmixrUI.dynmodelfun

Return dynmodel variable translation function
nlmixrUI

Prepares the UI function and returns a list.
nlmixr_fit

Fit a nlmixr model
nlmixrfindLhs

Find the assignments in R expression
nlmixrUI.saem.init

Get saem initilization list
nlmixrUI.saem.init.omega

SAEM's init$omega
prediction

Prediction after a gnlmm fit
plot.saemFit

Plot an SAEM model fit
vpc_saemFit

VPC for nlmixr saemFit objects
vpc_nlmixr_nlme

Visual predictive check (VPC) for nlmixr nlme objects
pump

Pump failure example dataset
print.saemFit

Print an SAEM model fit summary
pheno_sd

Single Dose Phenobarbitol PK/PD
plot.dyn.mcmc

Plot of a non-population dynamic model fit using mcmc
plot.dyn.ID

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

Print a gnlmm fit
print.nlmixrUI

Print UI function
plot.nlmixrFitData

Plot a nlmixr data object
nlmixrUI.nlme.specs

Create the nlme specs list for nlmixr nlme solving
nlmixrLogo

Messages the nlmixr logo...
nlme_ode

Fit nlme-based mixed-effect model using ODE implementation
nlmixrPred

Predict a nlmixr solved system
nlmixrUI.nlme.var

Get the variance for the nlme fit process based on UI
nlmixrUI.saem.init.theta

Generate SAEM initial estimates for THETA.
summary.saemFit

Print an SAEM model fit summary
tableControl

Output table/data.frame options
setOfv

Set Objective function type for a nlmixr object
sqrtm

Return the square root of general square matrix A
nlmixrValidate

Validate nlmixr
nlmixrUI.saem.log.eta

Get model$log.eta for SAEM
theo_md

Multiple dose Theophiline PK data
print.dyn.mcmc

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

Warfarin PK/PD data
vpc_ui

VPC based on ui model
theo_sd

Multiple dose Theophiline PK data
nlmixrVersion

Dispaly nlmixr's version
nmxInclude

Get a list of directories for inclusion
rats

Pregnant Rat Diet Experiment
ofv

Return the objective function
reexports

Objects exported from other packages
summary.dyn.mcmc

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

Produce trace-plot for fit if applicable
summary.dyn.ID

Summary of a non-population dynamic model fit
vpc

Vpc function for nlmixr