Man pages for nlmixr
Nonlinear Mixed Effects Models in Population PK/PD

addCovariateAdd covariate expression to a function string
addCovMultipleAdd multiple covariates to a given model, sequentially or all...
addCovVarAdding covariate to a given variable in an nlmixr model...
addCwresAdd CWRES
addNpdeNPDE calculation for nlmixr
addTableAdd table information to nlmixr fit object without tables
as.dynmodelConvert fit to classic dynmodel object
as.foceiConvert fit to FOCEi style fit
as.focei.dynmodelOutput nlmixr format for dynmodel
as.nlmeReturn composite nlme/focei to nlme
as.saemReturn composite saem/focei to saem
backwardSearchBackward covariate search
Bolus_1CPTBolus_1CPT - 1 Compartment Model Simulated Data from ACOP...
Bolus_1CPTMM1 Compartment Model w/ Michaelis-Menten Elimination
Bolus_2CPT2 Compartment Model
Bolus_2CPTMM2 Compartment Model with Michaelis-Menten Clearance
bootdataBootstrap data
bootplotProduce trace-plot for fit if applicable
bootstrapFitBootstrap nlmixr fit
boxCoxCox Box, Yeo Johnson and inverse transformation
calc.2LLLog-likelihood using Gaussian Quadrature
calcCovCalculate gnlmm variance-covariance matrix of fixed effects
calc.COVCovariance matrix by Fisher Information Matrix via...
cholSEGeneralized Cholesky Matrix Decomposition
configsaemConfigure an SAEM model
covarSearchAutoStepwise Covariate Model-selection (SCM) method
dot-nmGetDataThis gets the parsed data in the lower-level manner that...
dynmodelFit a non-population dynamic model
dynmodelControlControl Options for dynmodel
dynmodel.mcmcFit a non-population dynamic model using mcmc
foceiControlControl Options for FOCEi
focei.etaGet the FOCEi theta or eta specification for model.
foceiFitFOCEi fit
foceiFitCpp_Fit/Evaulate FOCEi
focei.thetaGet the FOCEi theta specification for the model
forwardSearchForward covariate search
frwd_selectionForward covariate selection for nlme-base non-linear mixed...
gauss.quadSets nodes and weights of Gauss-Hermite quadrature
gen_saem_user_fnGenerate an SAEM model
getOMEGACalculate gnlmm variance-covariance matrix of random effects
gnlmmFit a generalized nonlinear mixed-effect model
gofPlot of a non-population dynamic model fit
Infusion_1CPTInfusion_1CPT - 1 Compartment Model Simulated Data from ACOP...
ininlmixr ini block handling
initializeCovarsInitializing covariates before estimation
invgaussianInverse Guassian absorption model
lin_cmtconcentrations from a linear compartment model
makeDummiesCreate categorical covariates
makeHockeyStickCreating Hockey-stick covariates
metaboliteParent/Metabolite dataset
modelnlmixr model block
nlme_gofGOF plots for nlme-based mixed-effect models
nlme_lin_cmptFit nlme-based linear compartment mixed-effect model using...
nlmeModListAccess the model list information for nlmixr's nlme user...
nlme_odeFit nlme-based mixed-effect model using ODE implementation
nlmixrnlmixr fits population PK and PKPD non-linear mixed effects...
nlmixrAugPredAugmented Prediction for nlmixr fit
nlmixrBoundsExtract the nlmixr bound information from a function.
nlmixrBounds.eta.namesGet ETA names
nlmixrBounds.focei.upper.lowerGet upper/lower/names for THETAs
nlmixrBoundsParserFunctions to assist with setting initial conditions and...
nlmixrDataConvert/Format the data appropriately for nlmixr
nlmixrDynmodelConvertConverting nlmixr objects to dynmodel objects
nlmixrEstGeneric for nlmixr estimation methods
nlmixrfindLhsFind the assignments in R expression
nlmixr_fitFit a nlmixr model
nlmixrGill83Get the optimal forward difference interval by Gill83 method
nlmixrGradFunCreate a gradient function based on gill numerical...
nlmixrHessCalculate Hessian
nlmixrLogoMessages the nlmixr logo...
nlmixrPosthocGet a posthoc estimate of x
nlmixrPredPredict a nlmixr solved system
nlmixrPrintPrint x using the message facility
nlmixrSimSimulate a nlmixr solved system
nlmixrTestnlmixTest function for testing
nlmixrUIPrepares the UI function and returns a list.
nlmixrUI.dynmodelfunReturn dynmodel variable translation function
nlmixrUI.dynmodelfun2Return dynmodel variable translation function
nlmixrUI.focei.fixedGet parameters that are fixed
nlmixrUI.focei.initsGet the FOCEi initializations
nlmixrUI.nlmefunCreate the nlme parameter transform function from the UI...
nlmixrUI.nlme.specsCreate the nlme specs list for nlmixr nlme solving
nlmixrUI.nlme.varGet the variance for the nlme fit process based on UI
nlmixrUI.rxode.predReturn RxODE model with predictions appended
nlmixrUI.saem.aresGet initial estimate for ares SAEM.
nlmixrUI.saem.bresGet initial estimate for bres SAEM.
nlmixrUI.saem.cresGet initial estimate for bres SAEM.
nlmixrUI.saem.distributionGet SAEM distribution
nlmixrUI.saem.eta.transGet the eta->eta.trans for SAEM
nlmixrUI.saem.fitGenerate user function.
nlmixrUI.saem.fixedGet parameters that are fixed for SAEM
nlmixrUI.saem.initGet saem initilization list
nlmixrUI.saem.init.omegaSAEM's init$omega
nlmixrUI.saem.init.thetaGenerate SAEM initial estimates for THETA.
nlmixrUI.saem.log.etaGet model$log.eta for SAEM
nlmixrUI.saem.modelGenerate SAEM model list
nlmixrUI.saem.model.omegaGet the SAEM model Omega
nlmixrUI.saem.res.modGet the SAEM model$res.mod code
nlmixrUI.saem.res.nameGet error names for SAEM
nlmixrUI.saem.rx1Return RxODE model with predictions appended
nlmixrUI.saem.theta.nameGet THETA names for nlmixr's SAEM
nlmixrUI.theta.parsGet the Parameter function with THETA/ETAs defined
nlmixrValidateValidate nlmixr
nlmixrVersionDisplay nlmixr's version
nmDataConvertConvert data to RxODE format (depreciated)
nmDocxCreate a run summary word document
nmLstCreate a large output based on a nlmixr fit
nmsimplexNelder-Mead simplex search
ofvReturn the objective function
Oral_1CPTOral_1CPT - 1 Compartment Model with Oral Absorption...
performNormPerform normalization of the covariate
pheno_sdSingle Dose Phenobarbitol PK/PD
plot.dyn.mcmcPlot of a non-population dynamic model fit using mcmc
plot.nlmixrFitDataPlot a nlmixr data object
plot.saemFitPlot an SAEM model fit
preCondInvCalculate the inverse preconditioning matrix
preconditionFitLinearly re-parameterize the model to be less sensitive to...
predictionPrediction after a gnlmm fit
print.dyn.IDPrint a non-population dynamic model fit object
print.dyn.mcmcPrint summary of a non-population dynamic model fit using...
print.gnlmm.fitPrint a gnlmm fit
print.nlmixrUIPrint UI function
print.saemFitPrint an SAEM model fit summary
pumpPump failure example dataset
ratsPregnant Rat Diet Experiment
reexportsObjects exported from other packages
removeCovariateRemove covariate expression from a function string
removeCovMultipleRemoving multiple covariates
removeCovVarRemove covariate from function string
residuals.nlmixrFitDataExtract residuals from the FOCEI fit
saemControlControl Options for SAEM
saem.fitFit an SAEM model
setCovSet the covariance type based on prior calculated covariances
setOfvSet/get Objective function type for a nlmixr object
sqrtmReturn the square root of general square matrix A
summary.dyn.IDSummary of a non-population dynamic model fit
summary.saemFitPrint an SAEM model fit summary
tableControlOutput table/data.frame options
theo_mdMultiple dose theophylline PK data
theo_sdMultiple dose theophylline PK data
traceplotProduce trace-plot for fit if applicable
VarCorr.nlmixrNlmeReturn VarCorr for nlmixr nlme
vpcVpc function for nlmixr
vpc_nlmixr_nlmeVisual predictive check (VPC) for nlmixr nlme objects
vpc_saemFitVPC for nlmixr saemFit objects
vpc_uiVPC based on ui model
Wang2007Simulated Data Set for comparing objective functions
warfarinWarfarin PK/PD data
nlmixr documentation built on March 27, 2022, 5:05 p.m.