Interfacing nlmixr models

nlmixr

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

Adding residuals & covariance to fit object

addCwres()

Add CWRES

addNpde()

NPDE calculation for nlmixr

reexports

Objects exported from other packages

Model diagnostics

vpc()

Vpc function for nlmixr

traceplot()

Produce trace-plot for fit if applicable

Datasets

Bolus_1CPTMM

1 Compartment Model w/ Michelis Menton Elimination

Bolus_1CPT

Bolus_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016

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

Oral_1CPT

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

Wang2007

Simulated Data Set for comparing objective functions

pump

Pump failure example dataset

rats

Pregnant Rat Diet Experiment

Options for fitting and output

nmDocx() nmSave()

Create a run summary word document

saemControl()

Control Options for SAEM

foceiControl()

Control Options for FOCEi

reexports

Objects exported from other packages

tableControl()

Output table/data.frame options

Low level estimation routines

gnlmm() gnlmm2()

Fit a generalized nonlinear mixed-effect model

foceiFit() focei.fit()

FOCEi fit

saem.fit() saem()

Fit an SAEM model

dynmodel()

Fit a non-population dynamic model

dynmodel.mcmc()

Fit a non-population dynamic model using mcmc

nlme_lin_cmpt() nlmeLinCmpt() nlmeLinCmt()

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

nlme_ode() nlmeOde()

Fit nlme-based mixed-effect model using ODE implementation

Unit tests and validation functions

nlmixrValidate() nmTest()

Validate nlmixr

Internal functions

as.focei()

Convert fit to FOCEi style fit

bootdata()

Bootstrap data

calc.2LL()

Log-likelihood using Gaussian Quadrature

calc.COV()

Covariance matrix by Fisher Information Matrix via linearization

calcCov()

Calculate gnlmm variance-covariance matrix of fixed effects

cholSE()

Generalized Cholesky Matrix Decomposition

configsaem()

Configure an SAEM model

coxBox()

Cox Box transformation

focei.eta()

Get the FOCEi theta or eta specification for model.

focei.theta()

Get the FOCEi theta specification for the model

frwd_selection()

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

gauss.quad()

Sets nodes and weigts of Gauss-Hermite quadrature

gen_saem_user_fn()

Generate an SAEM model

getOMEGA()

Calculate gnlmm variance-covariance matrix of random effects

ini()

nlmixr ini block handling

instant.stan.extension()

instant.stan.extension.

invgaussian

Inverse Guassian absorption model

lin_cmt()

concentrations from a linear compartment model

lincmt()

Parameters for a linear compartment model for SAEM

metabolite

Parent/Metabolite dataset

model()

nlmixr model block

nlme_gof()

GOF plots for nlme-based mixed-effect models

nlmixr

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

nlmixrAugPred() augPred(<nlmixrFitData>)

Augmented Prediction for nlmixr fit

nlmixrBounds.eta.names()

Get ETA names

nlmixrBounds.focei.upper.lower()

Get upper/lower/names for THETAs

nlmixrLogo()

Messages the nlmixr logo...

nlmixrPred() predict(<nlmixrFitData>)

Predict a nlmixr solved system

nlmixrSim() rxSolve(<nlmixrFitData>) simulate(<nlmixrFitData>) solve(<nlmixrFitData>)

Simulate a nlmixr solved system

nlmixrUI.focei.fixed()

Get parameters that are fixed

nlmixrUI.focei.inits()

Get the FOCEi initializations

nlmixrUI.nlme.specs()

Create the nlme specs list for nlmixr nlme solving

nlmixrUI.rxode.pred()

Return RxODE model with predictions appended

nlmixrUI.saem.ares()

Get initial estimate for ares SAEM.

nlmixrUI.saem.bres()

Get initial estimate for bres SAEM.

nlmixrUI.saem.distribution()

Get SAEM distribution

nlmixrUI.saem.eta.trans()

Get the eta->eta.trans for SAEM

nlmixrUI.saem.fit()

Generate saem.fit user function.

nlmixrUI.saem.fixed()

Get parameters that are fixed for SAEM

nlmixrUI.saem.init()

Get saem initilization list

nlmixrUI.saem.init.omega()

SAEM's init$omega

nlmixrUI.saem.init.theta()

Generate SAEM initial estimates for THETA.

nlmixrUI.saem.log.eta()

Get model$log.eta for SAEM

nlmixrUI.saem.model()

Generate SAEM model list

nlmixrUI.saem.model.omega()

Get the SAEM model Omega

nlmixrUI.saem.res.mod()

Get the SAEM model$res.mod code

nlmixrUI.saem.res.name()

Get error names for SAEM

nlmixrUI.saem.theta.name()

Get THETA names for nlmixr's SAEM

nlmixrUI.theta.pars()

Get the Parameter function with THETA/ETAs defined

nlmixrVersion()

Dispaly nlmixr's version

nlmixr_fit()

Fit a nlmixr model

nmsimplex()

Nelder-Mead of simplex search

ofv()

Return the objective function

plot(<dyn.ID>)

Plot of a non-population dynamic model fit

plot(<dyn.mcmc>)

Plot of a non-population dynamic model fit using mcmc

plot(<nlmixrFitData>)

Plot a nlmixr data object

plot(<saemFit>)

Plot an SAEM model fit

prediction()

Prediction after a gnlmm fit

print(<dyn.ID>)

Print a non-population dynamic model fit object

print(<dyn.mcmc>)

Summary of a non-population dynamic model fit using mcmc

print(<gnlmm.fit>)

Print a gnlmm fit

print(<nlmixrUI>)

Print UI function

print(<saemFit>)

Print an SAEM model fit summary

residuals(<nlmixrFitData>)

Extract residuals from the FOCEI fit

saem(<cleanup>)

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

setOfv()

Set Objective function type for a nlmixr object

sqrtm()

Return the square root of general square matrix A

summary(<dyn.ID>)

Summary of a non-population dynamic model fit

summary(<dyn.mcmc>)

Summary of a non-population dynamic model fit using mcmc

summary(<saemFit>)

Print an SAEM model fit summary

theo_md

Multiple dose Theophiline PK data

theo_sd

Multiple dose Theophiline PK data

vpc_nlmixr_nlme() vpcNlmixrNlme() vpc(<nlmixrNlme>)

Visual predictive check (VPC) for nlmixr nlme objects

vpc_saemFit() vpc(<saemFit>)

VPC for nlmixr saemFit objects

vpc_ui() vpc(<nlmixrFitData>) vpc(<nlmixrVpc>) vpc(<ui>)

VPC based on ui model

yeoJohnson()

Yeo-Johnson Transformation