nlmixr v1.1.1-1

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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
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
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Vignettes of nlmixr

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