nlmixr v1.1.0-8

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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
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
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Vignettes of nlmixr

Name
logo.png
running_nlmixr.Rmd
theo_inf.txt
theo_sd.dat
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