R: Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions

# Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions

## Documentation for package ‘nlmixr2extra’ version 5.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

.nlmixrFormulaDataPrep | Perform any required data modifications for the nlmixrFormula interface
.nlmixrFormulaExpandStartParam | Expand parameters to include their covariate representations, if applicable.
.nlmixrFormulaExpandStartParamSingle | Expand parameters to include their covariate representations, if applicable.
.nlmixrFormulaParser | Parse the formula to extract the dependent variable, predictor, and random effects
.nlmixrFormulaParserRanef | Parse the random effects part of a formula
.nlmixrFormulaSetupIniFixed | Setup the ini() part of the model for fixed effects
.nlmixrFormulaSetupIniRandom | Setup the ini() part of the model for fixed effects
.renameOrOverwrite | Rename a column in a dataset
aaaNlmixr2ExtraCRAN | This function is to set the number of threads to 2
adaptivelassoCoefficients | Return Adaptive lasso coefficients after finding optimal t
addAllEtas | Add Individual Random Effects and Fix them to Small Value
addCatCovariates | Make dummy variable cols and updated covarsVec
addCovariate | Add Covariate to Model Fit (Generic)
addCovariate.default | Add Covariate to Model Fit (Generic)
addCovariate.nlmixr2FitCore | Add Covariate to Model Fit (Generic)
addCovariate.nlmixr2Linearize | Add Covariate to Model Fit (Generic)
addCovariate.rxUi | Add Covariate to Model Fit (Generic)
addData2Rx | Add Data to RxUi model
addorremoveCovariate | Add covariate
adjustedlassoCoefficients | Return Adjusted adaptive lasso coefficients after finding optimal t
bootplot | Produce delta objective function for boostrap
bootplot.nlmixr2FitCore | Produce delta objective function for boostrap
bootstrapFit | Bootstrap nlmixr2 fit
buildcovInfo | Build covInfo list from varsVec and covarsVec
buildupatedUI | Build updated from the covariate and variable vector list
covarSearchAuto | Stepwise Covariate Model-selection (SCM) method
extractEqHelper.if | Generate LaTeX for if blocks
fixedControl | Control options for fixed-value likelihood profiling
foldgen | Stratified cross-validation fold generator function, inspired from the caret
horseshoeSummardf | Create Horseshoe summary posterior estimates
iivSearch | Automated Inter-Individual Variability Search
iivSearch.default | Automated Inter-Individual Variability Search
iivSearch.nlmixr2Linearize | Automated Inter-Individual Variability Search
isLinearizeMatch | Check Linearization Match
knit_print.nlmixr2FitCore | Extract the equations from an nlmixr2/rxode2 model to produce a 'LaTeX' equation.
knit_print.rxUi | Extract the equations from an nlmixr2/rxode2 model to produce a 'LaTeX' equation.
lassoCoefficients | Return Final lasso coefficients after finding optimal t
lassoSummardf | Create Lasso summary posterior estimates
linearize | Perform linearization of a model fitted using FOCEI
linearizePlot | Plot Original Versus Linear Models iObj and Etas
linModGen | Generate a Linearization Model From Previous Fit
llpControl | Control options for log-likelihood profiling
nlmixrFormula | A simple formula-based interface for nlmixr2
normalizedData | Function to return data of normalized covariates
optimUnisampling | Sample from uniform distribution by optim
preconditionFit | Linearly re-parameterize the model to be less sensitive to rounding errors
print.linIIVSearch | Print Summary Table For Linearized IIV Search
profile.nlmixr2FitCore | Perform likelihood profiling on nlmixr2 focei fits
profileFixed | Estimate the objective function values for a model while fixing defined parameter values
profileFixedSingle | Estimate the objective function values for a model while fixing defined parameter values
profileLlp | Profile confidence intervals with log-likelihood profiling
profileNlmixr2FitCoreRet | Give the output data.frame for a single model for profile.nlmixr2FitCore
regularmodel | Regular lasso model
rerunTopN | Rerun Top N Original Models From A Search
rerunTopN.linIIVSearch | Rerun Top N Original Models From A Search
resSearch | Exhaustively Search for Residual Error Model
theoFitOde | Example single dose Theophylline ODE model