Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
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Documentation for package ‘nlmixr2extra’ version 5.1.0
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 |