Package: nlmixr2est 6.0.1
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_6.0.1.tar.gz
nlmixr2est_6.0.1.zip(r-4.7)nlmixr2est_6.0.1.zip(r-4.6)nlmixr2est_6.0.1.zip(r-4.5)
nlmixr2est_6.0.1.tgz(r-4.6-x86_64)nlmixr2est_6.0.1.tgz(r-4.6-arm64)nlmixr2est_6.0.1.tgz(r-4.5-x86_64)nlmixr2est_6.0.1.tgz(r-4.5-arm64)
nlmixr2est_6.0.1.tar.gz(r-4.6-arm64)nlmixr2est_6.0.1.tar.gz(r-4.6-x86_64)
nlmixr2est_6.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://nlmixr2.github.io
- nlmixr2Keywords - A list and description of the fields in the nlmxir2 object
Last updated from:6646e1c8f3. Checks:2 FAIL, 8 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | FAIL | 172 | ||
| linux-devel-x86_64 | FAIL | 172 | ||
| source / vignettes | OK | 378 | ||
| linux-release-arm64 | OK | 419 | ||
| linux-release-x86_64 | OK | 433 | ||
| macos-release-arm64 | OK | 335 | ||
| macos-release-x86_64 | OK | 533 | ||
| macos-oldrel-arm64 | OK | 278 | ||
| macos-oldrel-x86_64 | OK | 641 | ||
| windows-devel | ERROR | 456 | ||
| windows-release | ERROR | 416 | ||
| windows-oldrel | ERROR | 546 | ||
| wasm-release | OK | 263 |
Exports:.addPkgNlmixr2.agq.collectWarn.deparseDifferent.deparseFinal.downgradeEtas.foceiPreProcessData.iniS3.nlmAdjustCov.nlmFamilyAdjustOutput.nlmFinalizeList.nlmFreeEnv.nlmixr0preProcessCovariatesPresent.nlmixr2estLastPredSimulationInfo.nlmixr2FitUpdateParams.nlmixr2objectNameAssign.nlmixrNlmeFun.nlmixrNlmFunC.nlmixrNlminbFunC.nlmixrNlminbGradC.nlmixrNlminbHessC.nlmixrNlsData.nlmixrNlsFun.nlmixrNlsFunGrad.nlmixrNlsFunVal.nlmixrNlsFunValGrad.nlmixrOptimFunC.nlmixrOptimGradC.nlmixrPreprocessLiteralFix.nlmSetupEnv.preProcessDataUi.preProcessZeroOmega.rxGetDVFTransform.saemDropMuRefFromModel.uiApplyMu2.uiApplyMu2hook.uiFinalizeMu2aaaCranNlmixrThreadsACFadd.dosingadd.samplingaddCwresaddNpdeaddTableagqControlas.rxUiassertNlmixrFitassertNlmixrFitDataaugPredbobyqaControlboxCoxcholSEeteventTableexpitfixed.effectsfixeffoceControlfoceiControlfoceiFitCpp_foControlfoiControlgeom_amtgeom_censgetBaseSimModelFitgetDatagetOfvTypegetValidNlmixrControlgetValidNlmixrCtlgetVarCovgroupedDataiBoxCoxiniiYeoJohnsonlaplaceControllbfgsb3cControllogitlotrimodeln1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2AugPredSolvenlmixr2CreateOutputFromUinlmixr2Estnlmixr2Eval_nlmixr2fixnlmixr2Gill83nlmixr2Grad_nlmixr2GradFunnlmixr2Hessnlmixr2iovLogsdCvnlmixr2iovLogsdSdnlmixr2iovLogvarCvnlmixr2iovLogvarSdnlmixr2iovSdCvnlmixr2iovSdSdnlmixr2iovVarCvnlmixr2iovVarSdnlmixr2Logonlmixr2NlmeControlnlmixr2ParHist_nlmixr2Printnlmixr2Unscaled_nlmixr2Validatenlmixr2VersionnlmixrAddObjectiveFunctionDataFramenlmixrAddTimingnlmixrCbindnlmixrClonenlmixrUpdateObjectnlmixrWithTimingnlsControlnmGetDistributionSaemLinesnmNearPDnmObjGetnmObjGetControlnmObjGetDatanmObjGetEstimationModelnmObjGetFoceiControlnmObjGetIpredModelnmObjGetPredOnlynmObjGetRxSolvenmObjHandleControlObjectnmObjUiSetCompressednmsimplexnmSuppressMsgnmTestofvoptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmpostFinalObjectHookspostFinalObjectHooksAddpostFinalObjectHooksRmposthocControlpreFinalParTableHookspreFinalParTableHooksAddpreFinalParTableHooksRmpreProcessHookspreProcessHooksAddpreProcessHooksRmprobitprobitInvrandom.effectsranefreStructrmEtarxCatrxCleanrxControlrxGetDistributionFoceiLinesrxGetDistributionNlmeLinesrxGetDistributionNlsLinesrxInitrxLhsrxModelVarsrxModelVarsS3rxodeRxODErxode2rxParamrxParamsrxSolverxStaterxUiDeparsesaemControlsetCovsetOfvsqrtmstat_amtstat_censtableControluobyqaControlvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcNameDataCmtsvpcSimvpcSimExpandyeoJohnson
Dependencies:armadillo4rbackportsBHcachemcheckmateclicpp11cpp4rcrayondata.tabledescdigestdparserevaluatefarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelbfgsb3clifecyclelotriMatrixmemoiseminqan1qn1nlmenlmixr2datanumDerivPreciseSumsqs2R6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llS7scalessitmoStanHeadersstringfishsymenginesysvctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Augment Prediction for Ipred Model | .augPredIpredModel |
| Preprocess Covariates needed (or other data items) | .nlmixr0preProcessCovariatesPresent |
| This literally fixes parameters in the model | .nlmixrPreprocessLiteralFix |
| Preprocess the zero omegas | .preProcessDataUi |
| Preprocess the zero omegas | .preProcessZeroOmega |
| This function is to set the number of threads to 2 | aaaCranNlmixrThreads |
| Add CWRES | addCwres |
| NPDE calculation for nlmixr2 | addNpde |
| Add table information to nlmixr2 fit object without tables | addTable |
| Control options for the agq estimation method | agqControl |
| 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 the foce estimation method | foceControl |
| Control Options for FOCEi | foceiControl |
| Control options for the FO estimation method | foControl |
| Control options foir the FOI estimation method | foiControl |
| Get valid nlmixr control object | getValidNlmixrControl getValidNlmixrCtl getValidNlmixrCtl.agq getValidNlmixrCtl.bobyqa getValidNlmixrCtl.default getValidNlmixrCtl.fo getValidNlmixrCtl.foce getValidNlmixrCtl.focei getValidNlmixrCtl.foi getValidNlmixrCtl.laplace 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 options for the Laplace estimation method | laplaceControl |
| 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.agq nlmixr2Est.bobyqa nlmixr2Est.default nlmixr2Est.fo nlmixr2Est.foce nlmixr2Est.focei nlmixr2Est.foi nlmixr2Est.laplace 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 |
| Try to fix a nlmixr2 fit | nlmixr2fix |
| 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.agq nmObjGetControl.bobyqa nmObjGetControl.default nmObjGetControl.fo nmObjGetControl.foce nmObjGetControl.focei nmObjGetControl.foi nmObjGetControl.laplace 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.agq nmObjGetFoceiControl.default nmObjGetFoceiControl.foce nmObjGetFoceiControl.laplace nmObjGetFoceiControl.nlme nmObjGetFoceiControl.posthoc 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.agqControl nmObjHandleControlObject.bobyqaControl nmObjHandleControlObject.default nmObjHandleControlObject.foceControl nmObjHandleControlObject.foceiControl nmObjHandleControlObject.foControl nmObjHandleControlObject.foiControl nmObjHandleControlObject.laplaceControl nmObjHandleControlObject.lbfgsb3cControl nmObjHandleControlObject.n1qn1Control nmObjHandleControlObject.newuoaControl nmObjHandleControlObject.nlmControl nmObjHandleControlObject.nlmeControl nmObjHandleControlObject.nlminbControl nmObjHandleControlObject.nlsControl nmObjHandleControlObject.optimControl nmObjHandleControlObject.posthocControl 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 |
| Control options for the posthoc estimation method | posthocControl |
| Predict method for nlmixr2 fit core objects | predict.nlmixr2FitCore |
| Print an SAEM model fit summary | print.saemFit |
| Extract residuals from the FOCEI fit | residuals.nlmixr2FitData |
| Remove an eta from the model | rmEta |
| 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 |
