Man pages for nlmixr2est
Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
| aaaCranNlmixrThreads | This function is to set the number of threads to 2 |
| addCwres | Add CWRES |
| addNpde | NPDE calculation for nlmixr2 |
| addTable | Add table information to nlmixr2 fit object without tables |
| agqControl | Control options for the agq estimation method |
| assertNlmixrFit | Assert that this is a nlmixr2 fit object |
| assertNlmixrFitData | Assert that this is a nlmixr2 fit data object |
| bobyqaControl | Control for bobyqa estimation method in nlmixr2 |
| boxCox | Cox Box, Yeo Johnson and inverse transformation |
| cholSE | Generalized Cholesky Matrix Decomposition |
| dot-absorbIterPrintControl | Wrap scalar or list arguments into an iterPrintControl object |
| dot-addPkgNlmixr2 | Adds a package to the nlmixr2's $sessioninfo inside the fit |
| dot-agq | Get the adaptive Gauss-Hermite quadrature points and weights |
| dot-augPredIpredModel | Augment Prediction for Ipred Model |
| dot-collectWarn | Collect warnings and just warn once. |
| dot-deparseDifferent | Identify Differences Between Standard and New Objects but... |
| dot-deparseFinal | Deparse finalize a control or related object into a language... |
| dot-downgradeEtas | This downgrades the UI for any of the zero etas in the model |
| dot-foceiPreProcessData | This function process the data for use in focei |
| dot-iniS3 | Initialize S3 methods |
| dot-loadSymengine | Load a model into a symengine environment |
| dot-nlmAdjustCov | Adjust covariance matrix based on scaling parameters |
| dot-nlmeGetNonMuRefNames | Get non mu referenced names from mu referenced theta |
| dot-nlmFamilyAdjustOutput | Adjust nlm and family output environment |
| dot-nlmFamilyControlGeneric | Shared control setup for the nlm-family estimation methods |
| dot-nlmFamilyFitGeneric | Shared fit driver for the nlm-family estimation methods |
| dot-nlmFinalizeList | Finalizes output list |
| dot-nlmFreeEnv | Frees nlm environment |
| dot-nlmixr0preProcessCovariatesPresent | Preprocess Covariates needed (or other data items) |
| dot-nlmixr0preProcessNpMuExpand | Preprocessing hook: mu-expand non-mu structural fixed-effect... |
| dot-nlmixr2estLastPredSimulationInfo | Get the least prediction simulation information for VPC |
| dot-nlmixr2FitUpdateParams | Update model to have final parameter estimates for piping and... |
| dot-nlmixr2objectNameAssign | Allows external methods (like those in nlmixr2) to assign... |
| dot-nlmixrNlmeFun | A surrogate function for nlme to call for ode solving |
| dot-nlmixrNlmFunC | A surrogate function for nlm to call for ode solving |
| dot-nlmixrNlminbFunC | A surrogate function for nlminb to call for ode solving |
| dot-nlmixrNlsData | Returns the data currently setup to run nls |
| dot-nlmixrNlsFun | A surrogate function for nls to call for ode solving |
| dot-nlmixrNlsFunVal | Internal nls functions for minpack.lm |
| dot-nlmixrOptimFunC | A surrogate function for optim to call for ode solving |
| dot-nlmixrPreprocessLiteralFix | This literally fixes parameters in the model |
| dot-nlmSetupEnv | Setup a nonlinear system for optimization |
| dot-preProcessDataUi | Preprocess the zero omegas |
| dot-preProcessLinCmtOde | Translate a mixed 'linCmt()'/ODE model to all-ODEs |
| dot-preProcessVaeNonMuTheta | VAE preprocessing hook: inject etas for non-mu-referenced... |
| dot-preProcessZeroOmega | Preprocess the zero omegas |
| dot-preProcessZeroTheta | Nudge exactly-zero theta initial estimates off zero (FOCEi... |
| dot-rxGetDVFTransform | Get the DV transformation |
| dot-saemDropMuRefFromModel | Drop mu referenced etas and covariates |
| dot-sensEtaOrTheta | Calculate d(state)/d(eta) or d(state)/d(theta) sensitivities |
| dot-uiApplyMu2 | This is an internal function for modifying the UI to apply... |
| dot-uiFinalizeMu2 | This is an internal function for replacing the ui with... |
| emviControl | Control for the variational inference methods emvi and fbvi... |
| fbviControl | Control for the fbvi (full-Bayes variational inference)... |
| foceControl | Control options for the foce estimation method |
| foceiControl | Control Options for FOCEi |
| foceiFitCpp_ | Fit/Evaluate FOCEi |
| foceiGradPooledDirect_ | Analytic outer gradient at a caller-supplied theta / eta /... |
| foceiGradPooledSetupLoad_ | Install the pooled analytic-gradient setup for a non-focei... |
| foceiLikLoad | Load a general FOCE-family likelihood into memory |
| foceiLikRun | Evaluate a loaded general FOCE-family likelihood at supplied... |
| foceiLikUnload | Unload the general FOCE-family likelihood from memory |
| focepControl | Control options for the focep (FOCE+) estimation method |
| foControl | Control options for the FO estimation method |
| foiControl | Control options foir the FOI estimation method |
| formatMinWidth | Format numeric values to minimize the printing width |
| getBaseSimModelFit | Method for getting simulation rxode2 classic models based on... |
| getValidNlmixrControl | Get valid nlmixr control object |
| iagqControl | Control options for the iagq estimation method |
| ifoceControl | Control options for the ifoce estimation method |
| ifoceiControl | Control options for the ifocei estimation method |
| ifocepControl | Control options for the ifocep (IRLS FOCE+) estimation method |
| ilaplaceControl | Control options for the ilaplace estimation method |
| impControl | Control for the imp (importance-sampling EM without MAP... |
| impmapControl | Control options for the impmap (importance-sampling EM)... |
| iterPrintControl | Control iteration-time print formatting |
| iterPrintParams | Iteration-print configuration parameters (documentation stub) |
| laplaceControl | Control options for the Laplace estimation method |
| lbfgsb3cControl | Control for lbfgsb3c estimation method in nlmixr2 |
| magqControl | Control options for the magq estimation method |
| mfoceControl | Control options for the mfoce estimation method |
| mfoceiControl | Control options for the mfocei estimation method |
| mfocepControl | Control options for the mfocep (mu-referenced FOCE+)... |
| mlaplaceControl | Control options for the mlaplace estimation method |
| n1qn1Control | Control for n1qn1 estimation method in nlmixr2 |
| newuoaControl | Control for newuoa estimation method in nlmixr2 |
| nlmControl | nlmixr2 defaults controls for nlm |
| nlmerSolveGrad | Per-subject prediction and Jacobian for mixed-effects engines |
| nlmGetParHist | Recover and finalize the resident nlm parameter history |
| nlminbControl | nlmixr2 nlminb defaults |
| nlmixr2 | nlmixr2 fits population PK and PKPD non-linear mixed effects... |
| nlmixr2AllEst | Show all the current estimation methods |
| nlmixr2AllEstType | Tagged list of the available nlmixr2 estimation methods |
| nlmixr2AugPredSolve | Augmented Prediction for nlmixr2 fit |
| nlmixr2CreateOutputFromUi | Create nlmixr output from the UI |
| nlmixr2Est | Generic for nlmixr2 estimation methods |
| nlmixr2fix | Try to fix a nlmixr2 fit |
| nlmixr2Gill83 | Get the optimal forward difference interval by Gill83 method |
| nlmixr2GradFun | Create a gradient function based on gill numerical... |
| nlmixr2Hess | Calculate Hessian |
| nlmixr2iovLogvarCv | Transform the estimated value to %CV for IOV |
| nlmixr2Keywords | A list and description of the fields in the nlmxir2 object |
| nlmixr2Logo | Messages the nlmixr2 logo... |
| nlmixr2NlmeControl | Control Values for nlme Fit with extra options for nlmixr |
| nlmixr2Print | Print x using the message facility |
| nlmixr2Validate | Validate nlmixr2 |
| nlmixr2Version | Display nlmixr2's version |
| nlmixrAddObjectiveFunctionDataFrame | Add objective function data frame to the current objective... |
| nlmixrAddTiming | Manually add time to a nlmixr2 object |
| nlmixrCbind | nlmixrCbind |
| nlmixrClone | Clone nlmixr environment |
| nlmixrUpdateObject | Update the nlmixr2 object with new fit information |
| nlmixrWithTiming | Time a part of a nlmixr operation and add to nlmixr object |
| nlsControl | nlmixr2 defaults controls for nls |
| nmGetDistributionSaemLines | This is a S3 method for getting the distribution lines for a... |
| nmNearPD | C++ implementation of Matrix's nearPD |
| nmObjGet | Get an item from a nlmixr core object |
| nmObjGetControl | Get control object from fit |
| nmObjGetData | Get an item from a nlmixr2FitData object |
| nmObjGetEstimationModel | Get the estimation model for a fit object depending on the... |
| nmObjGetFoceiControl | Method for getting focei compatible control object from... |
| nmObjGetIpredModel | Get the ipred model for a fit object depending on the object... |
| nmObjGetPredOnly | Get the pred-only model for a fit depending on the object... |
| nmObjGetRxSolve | Get an option for the estimation method |
| nmObjHandleControlObject | Handle the control object |
| nmObjHandleModelObject | Handle Model Object |
| nmObjUiSetCompressed | Set if the nlmixr2 object will return a compressed ui |
| nmsimplex | Nelder-Mead simplex search |
| nmSuppressMsg | Respect suppress messages for nlmixr2 C functions |
| npagControl | Control for the npag (nonparametric adaptive grid) method |
| npagCycle_ | Run the NPAG adaptive-grid cycle on a set-up inner problem |
| npbControl | Control for the npb (nonparametric Bayes) method |
| npBuildPsi | Build the nonparametric Psi (conditional-likelihood) matrix |
| npCondense_ | Condense support points (nonparametric engines) |
| npIpmBurke | Burke interior-point weight solver (nonparametric maximum... |
| npObjAtGamma_ | Diagnostic: NPAG objective at a fixed grid and residual... |
| npSobolGrid_ | Sobol initial grid over a box (nonparametric engines) |
| ofv | Return the objective function |
| optimControl | nlmixr2 optim defaults |
| postFinalObjectHooks | List all post-final-object processing hooks |
| postFinalObjectHooksAdd | Register a post-final-object hook run after estimation... |
| postFinalObjectHooksRm | Remove a post-final-object hook from nlmixr2est |
| posthocControl | Control options for the posthoc estimation method |
| predict.nlmixr2FitCore | Predict method for nlmixr2 fit core objects |
| preFinalParTableHooks | List all pre-final parameter table processing hooks |
| preFinalParTableHooksAdd | Register a pre-final parameter table hook run before final... |
| preFinalParTableHooksRm | Remove a pre-final parameter table hook from nlmixr2est |
| preProcessHooks | List all pre-processing hooks |
| preProcessHooksAdd | Register a pre-processing hook run before estimation begins |
| preProcessHooksRm | Remove a pre-processing hook from nlmixr2est |
| print.saemFit | Print an SAEM model fit summary |
| qrpemControl | Control for the qrpem (quasi-random parametric EM) estimation... |
| reexports | Objects exported from other packages |
| residuals.nlmixr2FitData | Extract residuals from the FOCEI fit |
| rmEta | Remove an eta from the model |
| rxGetDistributionFoceiLines | This is a S3 method for getting the distribution lines for a... |
| rxGetDistributionNlmeLines | This is a S3 method for getting the distribution lines for a... |
| rxGetDistributionNlsLines | This is a S3 method for getting the distribution lines for a... |
| rxode2stateOde | Get the ODE states of a model (rxode2 v3/v4 compatible) |
| rxUiGet.foceiHdEta2 | Second-order eta sensitivities of the prediction for the... |
| saemControl | Control Options for SAEM |
| setCov | Set the covariance type based on prior calculated covariances |
| setOfv | Set/get Objective function type for a nlmixr2 object |
| sqrtm | Return the square root of general square matrix A |
| summary.saemFit | Print an SAEM model fit summary |
| tableControl | Output table/data.frame options |
| uobyqaControl | Control for uobyqa estimation method in nlmixr2 |
| vaeControl | Control for vae (variational autoencoder) estimation method... |
| vaeCovariates | Covariates explored by the VAE covariate search |
| vpcNameDataCmts | Name the data and compartments |
| vpcSim | VPC simulation |
| vpcSimExpand | Expand a VPC simulation |
