Package: nlmixr2est 3.0.2
Matthew Fidler
nlmixr2est: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
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 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Authors:
nlmixr2est_3.0.2.tar.gz
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nlmixr2est.pdf |nlmixr2est.html✨
nlmixr2est/json (API)
NEWS
| # Install 'nlmixr2est' in R: |
| install.packages('nlmixr2est', repos = c('https://nlmixr2.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nlmixr2/nlmixr2est/issues
Pkgdown:https://nlmixr2.github.io
- nlmixr2Keywords - A list and description of the fields in the nlmxir2 object
Last updated 30 days agofrom:fc1a5e8344. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 23 2024 |
| R-4.5-win-x86_64 | OK | Dec 23 2024 |
| R-4.5-linux-x86_64 | OK | Dec 23 2024 |
| R-4.4-win-x86_64 | OK | Dec 23 2024 |
| R-4.4-mac-x86_64 | OK | Dec 23 2024 |
| R-4.4-mac-aarch64 | OK | Dec 23 2024 |
| R-4.3-win-x86_64 | OK | Dec 23 2024 |
| R-4.3-mac-x86_64 | OK | Dec 23 2024 |
| R-4.3-mac-aarch64 | OK | Dec 23 2024 |
Exports:.addPkgNlmixr2.deparseDifferent.deparseFinal.foceiPreProcessData.nlmFinalizeList.nlmFreeEnv.nlmixr2estLastPredSimulationInfo.nlmixr2objectNameAssign.nlmixrNlmeFun.nlmixrNlmFunC.nlmixrNlminbFunC.nlmixrNlminbGradC.nlmixrNlminbHessC.nlmixrNlsData.nlmixrNlsFun.nlmixrNlsFunGrad.nlmixrNlsFunVal.nlmixrNlsFunValGrad.nlmixrOptimFunC.nlmixrOptimGradC.nlmixrPreprocessLiteralFix.nlmSetupEnv.preProcessDataUi.preProcessZeroOmega.rxGetDVFTransform.saemDropMuRefFromModel.uiApplyMu2.uiFinalizeMu2%>%ACFadd.dosingadd.samplingaddCwresaddNpdeaddTableas.rxUiassertNlmixrFitassertNlmixrFitDataaugPredbobyqaControlboxCoxcholSEeteventTableexpitfixed.effectsfixeffoceiControlfoceiFitCpp_geom_amtgeom_censgetBaseSimModelFitgetDatagetOfvTypegetValidNlmixrControlgetValidNlmixrCtlgetVarCovgroupedDataiBoxCoxiniiYeoJohnsonlbfgsb3cControllogitlotrimodeln1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2AugPredSolvenlmixr2CreateOutputFromUinlmixr2Estnlmixr2Eval_nlmixr2Gill83nlmixr2Grad_nlmixr2GradFunnlmixr2Hessnlmixr2Logonlmixr2NlmeControlnlmixr2ParHist_nlmixr2Printnlmixr2Unscaled_nlmixr2Validatenlmixr2VersionnlmixrAddObjectiveFunctionDataFramenlmixrAddTimingnlmixrCbindnlmixrClonenlmixrUpdateObjectnlmixrWithTimingnlsControlnmGetDistributionSaemLinesnmNearPDnmObjGetnmObjGetControlnmObjGetDatanmObjGetEstimationModelnmObjGetFoceiControlnmObjGetIpredModelnmObjGetPredOnlynmObjGetRxSolvenmObjHandleControlObjectnmObjUiSetCompressednmsimplexnmSuppressMsgnmTestofvoptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmpreProcessHookspreProcessHooksAddpreProcessHooksRmprobitprobitInvrandom.effectsranefreStructrxCatrxCleanrxControlrxGetDistributionFoceiLinesrxGetDistributionNlmeLinesrxGetDistributionNlsLinesrxInitrxLhsrxModelVarsrxModelVarsS3rxodeRxODErxode2rxParamrxParamsrxSolverxStaterxUiDeparsesaemControlsetCovsetOfvsqrtmstat_amtstat_censtableControluobyqaControlvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcNameDataCmtsvpcSimvpcSimExpandyeoJohnson
Dependencies:backportsBHcachemcheckmateclicolorspacecpp11cpp11armadillocrayondata.tabledigestdparserevaluatefansifarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelazyevallbfgsb3clifecyclelotrimagrittrMASSMatrixmemoisemgcvminqamunselln1qn1nlmenlmixr2datanumDerivpillarpkgconfigPreciseSumsqsR6RApiSerializeRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llscalessitmoStanHeadersstringfishsymenginesystibbleutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Augment Prediction for Ipred Model | .augPredIpredModel |
| This literally fixes parameters in the model | .nlmixrPreprocessLiteralFix |
| Preprocess the zero omegas | .preProcessDataUi |
| Preprocess the zero omegas | .preProcessZeroOmega |
| Add CWRES | addCwres |
| NPDE calculation for nlmixr2 | addNpde |
| Add table information to nlmixr2 fit object without tables | addTable |
| Assert that this is a nlmixr2 fit object | assertNlmixrFit |
| Assert that this is a nlmixr2 fit data object | assertNlmixrFitData |
| Control for bobyqa estimation method in nlmixr2 | bobyqaControl |
| Cox Box, Yeo Johnson and inverse transformation | boxCox iBoxCox iYeoJohnson yeoJohnson |
| Generalized Cholesky Matrix Decomposition | cholSE |
| Control Options for FOCEi | foceiControl |
| Get valid nlmixr control object | getValidNlmixrControl getValidNlmixrCtl getValidNlmixrCtl.bobyqa getValidNlmixrCtl.default getValidNlmixrCtl.fo getValidNlmixrCtl.foce getValidNlmixrCtl.focei getValidNlmixrCtl.foi getValidNlmixrCtl.lbfgsb3c getValidNlmixrCtl.n1qn1 getValidNlmixrCtl.newuoa getValidNlmixrCtl.nlm getValidNlmixrCtl.nlme getValidNlmixrCtl.nlminb getValidNlmixrCtl.nls getValidNlmixrCtl.optim getValidNlmixrCtl.posthoc getValidNlmixrCtl.predict getValidNlmixrCtl.rxSolve getValidNlmixrCtl.saem getValidNlmixrCtl.simulate getValidNlmixrCtl.simulation getValidNlmixrCtl.tableControl getValidNlmixrCtl.uobyqa |
| Control for lbfgsb3c estimation method in nlmixr2 | lbfgsb3cControl |
| Control for n1qn1 estimation method in nlmixr2 | n1qn1Control |
| Control for newuoa estimation method in nlmixr2 | newuoaControl |
| nlmixr2 defaults controls for nlm | nlmControl |
| nlmixr2 nlminb defaults | nlminbControl |
| nlmixr2 fits population PK and PKPD non-linear mixed effects models. | nlmixr nlmixr2 nlmixr2.function nlmixr2.nlmixr2FitCore nlmixr2.nlmixr2FitData nlmixr2.rxUi |
| Show all the current estimation methods | nlmixr2AllEst |
| Augmented Prediction for nlmixr2 fit | augPred.nlmixr2FitData nlmixr2AugPredSolve |
| Create nlmixr output from the UI | nlmixr2CreateOutputFromUi |
| Generic for nlmixr2 estimation methods | nlmixr2Est nlmixr2Est.bobyqa nlmixr2Est.default nlmixr2Est.fo nlmixr2Est.foce nlmixr2Est.focei nlmixr2Est.foi nlmixr2Est.lbfgsb3c nlmixr2Est.n1qn1 nlmixr2Est.newuoa nlmixr2Est.nlm nlmixr2Est.nlme nlmixr2Est.nlminb nlmixr2Est.nls nlmixr2Est.optim nlmixr2Est.output nlmixr2Est.posthoc nlmixr2Est.predict nlmixr2Est.rxSolve nlmixr2Est.saem nlmixr2Est.simulate nlmixr2Est.simulation nlmixr2Est.uobyqa |
| Get the optimal forward difference interval by Gill83 method | nlmixr2Gill83 |
| Calculate Hessian | nlmixr2Hess |
| A list and description of the fields in the nlmxir2 object | nlmixr2Keywords |
| Messages the nlmixr2 logo... | nlmixr2Logo |
| Control Values for nlme Fit with extra options for nlmixr | nlmeControl nlmixr2NlmeControl |
| Validate nlmixr2 | nlmixr2Validate nmTest |
| Display nlmixr2's version | nlmixr2Version |
| Add objective function data frame to the current objective function | nlmixrAddObjectiveFunctionDataFrame |
| Manually add time to a nlmixr2 object | nlmixrAddTiming |
| nlmixrCbind | nlmixrCbind |
| Clone nlmixr environment | nlmixrClone |
| Time a part of a nlmixr operation and add to nlmixr object | nlmixrWithTiming |
| nlmixr2 defaults controls for nls | nlsControl |
| C++ implementation of Matrix's nearPD | nmNearPD |
| Get control object from fit | nmObjGetControl nmObjGetControl.bobyqa nmObjGetControl.default nmObjGetControl.fo nmObjGetControl.foce nmObjGetControl.focei nmObjGetControl.foi nmObjGetControl.lbfgsb3c nmObjGetControl.n1qn1 nmObjGetControl.newuoa nmObjGetControl.nlm nmObjGetControl.nlme nmObjGetControl.nlminb nmObjGetControl.nls nmObjGetControl.optim nmObjGetControl.posthoc nmObjGetControl.saem nmObjGetControl.uobyqa |
| Get the estimation model for a fit object depending on the object type | nmObjGetEstimationModel |
| Method for getting focei compatible control object from nlmixr object | nmObjGetFoceiControl nmObjGetFoceiControl.default nmObjGetFoceiControl.nlme nmObjGetFoceiControl.saem |
| Get the ipred model for a fit object depending on the object type | nmObjGetEstimationModel.default nmObjGetEstimationModel.saem nmObjGetIpredModel nmObjGetIpredModel.default nmObjGetIpredModel.saem |
| Get the pred-only model for a fit depending on the object type | nmObjGetPredOnly nmObjGetPredOnly.default nmObjGetPredOnly.saem |
| Handle the control object | nmObjHandleControlObject nmObjHandleControlObject.bobyqaControl nmObjHandleControlObject.default nmObjHandleControlObject.foceiControl nmObjHandleControlObject.lbfgsb3cControl nmObjHandleControlObject.n1qn1Control nmObjHandleControlObject.newuoaControl nmObjHandleControlObject.nlmControl nmObjHandleControlObject.nlmeControl nmObjHandleControlObject.nlminbControl nmObjHandleControlObject.nlsControl nmObjHandleControlObject.optimControl nmObjHandleControlObject.saemControl nmObjHandleControlObject.uobyqaControl |
| Handle Model Object | nmObjHandleModelObject nmObjHandleModelObject.default nmObjHandleModelObject.foceiModelList nmObjHandleModelObject.saemModelList |
| Set if the nlmixr2 object will return a compressed ui | nmObjUiSetCompressed |
| Nelder-Mead simplex search | nmsimplex |
| Return the objective function | ofv |
| nlmixr2 optim defaults | optimControl |
| Print an SAEM model fit summary | print.saemFit |
| Extract residuals from the FOCEI fit | residuals.nlmixr2FitData |
| Control Options for SAEM | saemControl |
| Set the covariance type based on prior calculated covariances | setCov |
| Set/get Objective function type for a nlmixr2 object | getOfvType setOfv |
| Return the square root of general square matrix A | sqrtm |
| Print an SAEM model fit summary | summary.saemFit |
| Output table/data.frame options | tableControl |
| Control for uobyqa estimation method in nlmixr2 | uobyqaControl |
| VPC simulation | vpcSim |
