nlmixr v1.1.0-9

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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
VarCorr.nlmixrNlme Return VarCorr for nlmixr nlme
Bolus_2CPT 2 Compartment Model
addNpde NPDE calculation for nlmixr
Oral_1CPT Oral_1CPT -- 1 Compartment Model with Oral Absorption Simulated Data from ACOP 2016
calcCov Calculate gnlmm variance-covariance matrix of fixed effects
calc.COV Covariance matrix by Fisher Information Matrix via linearization
asHux.nlmixrFitCore Change a nlmixr fit object to a huxtable
as.saem Return composite saem/focei to saem
bootdata Bootstrap data
.nmGetData This gets the parsed data in the lower-level manner that nlmixr expects.
dynmodel Fit a non-population dynamic model
calc.2LL Log-likelihood using Gaussian Quadrature
foceiFitCpp_ Fit/Evaulate FOCEi
foceiFit FOCEi fit
lincmt Parameters for a linear compartment model for SAEM
lin_cmt concentrations from a linear compartment model
as.nlme Return composite nlme/focei to nlme
dynmodel.mcmc Fit a non-population dynamic model using mcmc
as.focei Convert fit to FOCEi style fit
focei.eta Get the FOCEi theta or eta specification for model.
coxBox Cox Box transformation
cholSE Generalized Cholesky Matrix Decomposition
constructLinCmt Construct RxODE linCmt function
instant.stan.extension instant.stan.extension.
configsaem Configure an SAEM model
nlmeModList Access the model list information for nlmixr's nlme user functions
focei.theta Get the FOCEi theta specification for the model
nlmixrUI.focei.fixed Get parameters that are fixed
nlmixrUI.focei.inits Get the FOCEi initializations
nlme_gof GOF plots for nlme-based mixed-effect models
invgaussian Inverse Guassian absorption model
nlmixrUI.saem.ares Get initial estimate for ares SAEM.
nlmixrUI.saem.theta.name Get THETA names for nlmixr's SAEM
nlmixrValidate Validate nlmixr
nlmixrUI.saem.bres Get initial estimate for bres SAEM.
nlmixrUI.theta.pars Get the Parameter function with THETA/ETAs defined
foceiControl Control Options for FOCEi
frwd_selection Forward covariate selection for nlme-base non-linear mixed effect models
gauss.quad Sets nodes and weigts of Gauss-Hermite quadrature
gnlmm Fit a generalized nonlinear mixed-effect model
ini nlmixr ini block handling
nlmixr nlmixr fits population PK and PKPD non-linear mixed effects models.
nlmixrVersion Dispaly nlmixr's version
plot.dyn.mcmc Plot of a non-population dynamic model fit using mcmc
plot.nlmixrFitData Plot a nlmixr data object
nlmixrBounds Extract the Nlmixr bound information from a function.
nlmixrBounds.eta.names Get ETA names
nlmixrPred Predict a nlmixr solved system
gen_saem_user_fn Generate an SAEM model
getOMEGA Calculate gnlmm variance-covariance matrix of random effects
nlmixrAugPred Augmented Prediction for nlmixr fit
nlmixrBounds.focei.upper.lower Get upper/lower/names for THETAs
nlmixrUI.saem.fit Generate saem.fit user function.
nlmixrUI.saem.fixed Get parameters that are fixed for SAEM
print.saemFit Print an SAEM model fit summary
nlmixrUI.nlme.specs Create the nlme specs list for nlmixr nlme solving
metabolite Parent/Metabolite dataset
nlmixrPrint Print x using the message facility
pump Pump failure example dataset
nlmixrData Convert/Format the data appropriately for nlmixr
nlmixrUI.saem.model Generate SAEM model list
model nlmixr model block
nlmixrUI.saem.model.omega Get the SAEM model Omega
nlmixrUI.saem.init Get saem initilization list
ofv Return the objective function
nmxInclude Get a list of directories for inclusion
nlmixrUI.nlme.var Get the variance for the nlme fit process based on UI
print.gnlmm.fit Print a gnlmm fit
nlmixrUI.saem.init.omega SAEM's init$omega
traceplot Produce trace-plot for fit if applicable
vpc Vpc function for nlmixr
nlmixrfindLhs Find the assignments in R expression
plot.saemFit Plot an SAEM model fit
nlmixr_fit Fit a nlmixr model
print.nlmixrUI Print UI function
setOfv Set Objective function type for a nlmixr object
nlme_lin_cmpt Fit nlme-based linear compartment mixed-effect model using closed form solution
nlmixrForget Clear memoise cache for nlmixr
nlmixrLogo Messages the nlmixr logo...
nlmixrUI.nlmefun Create the nlme parameter transform function from the UI object.
nlme_ode Fit nlme-based mixed-effect model using ODE implementation
nmLst Create a large output based on a nlmixr fit
nlmixrUI.saem.log.eta Get model$log.eta for SAEM
nlmixrUI.rxode.pred Return RxODE model with predictions appended
sqrtm Return the square root of general square matrix A
nlmixrUI.saem.init.theta Generate SAEM initial estimates for THETA.
prediction Prediction after a gnlmm fit
summary.dyn.mcmc Summary of a non-population dynamic model fit using mcmc
summary.dyn.ID Summary of a non-population dynamic model fit
print.dyn.ID Print a non-population dynamic model fit object
nmsimplex Nelder-Mead of simplex search
nlmixrSim Simulate a nlmixr solved system
nlmixrUI Prepares the UI function and returns a list.
nlmixrUI.saem.res.name Get error names for SAEM
nmDataConvert Convert data to RxODE format (depreciated)
nlmixrUI.saem.distribution Get SAEM distribution
nlmixrUI.saem.res.mod Get the SAEM model$res.mod code
vpc_nlmixr_nlme Visual predictive check (VPC) for nlmixr nlme objects
nlmixrUI.saem.eta.trans Get the eta->eta.trans for SAEM
saem.cleanup Cleanup saem_fit environment by removing dll after the object is no logner used by R.
residuals.nlmixrFitData Extract residuals from the FOCEI fit
print.dyn.mcmc Summary of a non-population dynamic model fit using mcmc
nmDocx Create a run summary word document
rats Pregnant Rat Diet Experiment
theo_md Multiple dose Theophiline PK data
reexports Objects exported from other packages
warfarin Warfarin PK/PD data
theo_sd Multiple dose Theophiline PK data
vpc_ui VPC based on ui model
yeoJohnson Yeo-Johnson Transformation
vpc_saemFit VPC for nlmixr saemFit objects
pheno_sd Single Dose Phenobarbitol PK/PD
saemControl Control Options for SAEM
plot.dyn.ID Plot of a non-population dynamic model fit
saem.fit Fit an SAEM model
tableControl Output table/data.frame options
summary.saemFit Print an SAEM model fit summary
Wang2007 Simulated Data Set for comparing objective functions
Infusion_1CPT Infusion_1CPT -- 1 Compartment Model Simulated Data from ACOP 2016
addCwres Add CWRES
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
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Vignettes of nlmixr

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