Package: nlmixr2est 7.0.1
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_7.0.1.tar.gz
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nlmixr2est_7.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nlmixr2est/json (API)
| # 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:c487d22b29. Checks:4 ERROR, 7 OK, 2 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | ERROR | 413 | ||
| linux-devel-x86_64 | ERROR | 470 | ||
| source / vignettes | OK | 435 | ||
| linux-release-arm64 | ERROR | 408 | ||
| linux-release-x86_64 | ERROR | 491 | ||
| macos-release-arm64 | OK | 329 | ||
| macos-release-x86_64 | OK | 478 | ||
| macos-oldrel-arm64 | OK | 289 | ||
| macos-oldrel-x86_64 | OK | 534 | ||
| windows-devel-x86_64 | FAIL | 871 | ||
| windows-release-x86_64 | OK | 737 | ||
| windows-oldrel-x86_64 | OK | 1025 | ||
| wasm-release | FAIL | 285 |
Exports:.absorbIterPrintControl.addPkgNlmixr2.agq.collectWarn.deparseDifferent.deparseFinal.downgradeEtas.foceiPreProcessData.iniS3.loadSymengine.nlmAdjustCov.nlmeGetNonMuRefNames.nlmFamilyAdjustOutput.nlmFamilyControlGeneric.nlmFamilyFitGeneric.nlmFinalizeList.nlmFreeEnv.nlmixr0preProcessCovariatesPresent.nlmixr0preProcessNpMuExpand.nlmixr2estLastPredSimulationInfo.nlmixr2FitUpdateParams.nlmixr2objectNameAssign.nlmixrNlmeFun.nlmixrNlmFunC.nlmixrNlminbFunC.nlmixrNlminbGradC.nlmixrNlminbHessC.nlmixrNlsData.nlmixrNlsFun.nlmixrNlsFunGrad.nlmixrNlsFunVal.nlmixrNlsFunValGrad.nlmixrOptimFunC.nlmixrOptimGradC.nlmixrPreprocessLiteralFix.nlmSetupEnv.preProcessDataUi.preProcessLinCmtOde.preProcessVaeNonMuTheta.preProcessZeroOmega.preProcessZeroTheta.rxGetDVFTransform.saemDropMuRefFromModel.sensEtaOrTheta.uiApplyMu2.uiApplyMu2hook.uiFinalizeMu2aaaCranNlmixrThreadsACFadd.dosingadd.samplingaddCwresaddNpdeaddTableadviControlagqControlas.rxUiassertNlmixrFitassertNlmixrFitDataaugPredbobyqaControlboxCoxcholSEeteventTableexpitfixed.effectsfixeffoceControlfoceiControlfoceiFitCpp_foceiLikLoadfoceiLikRunfoceiLikUnloadfocepControlfoControlfoiControlformatMinWidthgeom_amtgeom_censgetBaseSimModelFitgetDatagetOfvTypegetValidNlmixrControlgetValidNlmixrCtlgetVarCovgroupedDataiagqControliBoxCoxifoceControlifoceiControlifocepControlilaplaceControlimpControlimpmapControliniiterPrintControliYeoJohnsonlaplaceControllbfgsb3cControllogitlotrimagqControlmfoceControlmfoceiControlmfocepControlmlaplaceControlmodeln1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlmerSolveGradnlmGetParHistnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2AllEstTypenlmixr2AugPredSolvenlmixr2CreateOutputFromUinlmixr2Estnlmixr2Eval_nlmixr2fixnlmixr2Gill83nlmixr2Grad_nlmixr2GradFunnlmixr2Hessnlmixr2iovLogsdCvnlmixr2iovLogsdSdnlmixr2iovLogvarCvnlmixr2iovLogvarSdnlmixr2iovSdCvnlmixr2iovSdSdnlmixr2iovVarCvnlmixr2iovVarSdnlmixr2Logonlmixr2NlmeControlnlmixr2ParHist_nlmixr2Printnlmixr2Unscaled_nlmixr2Validatenlmixr2VersionnlmixrAddObjectiveFunctionDataFramenlmixrAddTimingnlmixrCbindnlmixrClonenlmixrUpdateObjectnlmixrWithTimingnlsControlnmGetDistributionSaemLinesnmNearPDnmObjGetnmObjGetControlnmObjGetDatanmObjGetEstimationModelnmObjGetFoceiControlnmObjGetIpredModelnmObjGetPredOnlynmObjGetRxSolvenmObjHandleControlObjectnmObjUiSetCompressednmsimplexnmSuppressMsgnmTestnpagControlnpagCycle_npbControlnpBuildPsinpCondense_npIpmBurkenpObjAtGamma_npSobolGrid_ofvoptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmpostFinalObjectHookspostFinalObjectHooksAddpostFinalObjectHooksRmposthocControlpreFinalParTableHookspreFinalParTableHooksAddpreFinalParTableHooksRmpreProcessHookspreProcessHooksAddpreProcessHooksRmprobitprobitInvqrpemControlrandom.effectsranefreStructrmEtarxCatrxCleanrxControlrxGetDistributionFoceiLinesrxGetDistributionNlmeLinesrxGetDistributionNlsLinesrxInitrxLhsrxModelVarsrxModelVarsS3rxodeRxODErxode2rxode2stateOderxParamrxParamsrxSolverxStaterxUiDeparsesaemControlsetCovsetOfvsqrtmstat_amtstat_censtableControluobyqaControlvaeControlvaeCovariatesvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcNameDataCmtsvpcSimvpcSimExpandyeoJohnson
Dependencies:armadillo4rbackportsBHcachemcheckmateclicpp11cpp4rcrayondata.tabledigestdparserevaluatefarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelbfgsb3clifecyclelotriMatrixmemoiseminqamirain1qn1nanonextnlmenlmixr2datanumDerivPreciseSumsR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llS7scalessitmoStanHeaderssymenginesysvctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Augment Prediction for Ipred Model | .augPredIpredModel |
| Shared fit driver for the nlm-family estimation methods | .nlmFamilyFitGeneric |
| Preprocess Covariates needed (or other data items) | .nlmixr0preProcessCovariatesPresent |
| Preprocessing hook: mu-expand non-mu structural fixed-effect thetas for the nonparametric engines, before the rest of the pipeline builds on the ui. Doing it here (rather than mutating the ui mid-setup) keeps the injected pseudo-etas consistent through covariate/mu processing and model compilation. Off when control$muExpand is FALSE. | .nlmixr0preProcessNpMuExpand |
| This literally fixes parameters in the model | .nlmixrPreprocessLiteralFix |
| Preprocess the zero omegas | .preProcessDataUi |
| Translate a mixed `linCmt()`/ODE model to all-ODEs | .preProcessLinCmtOde |
| VAE preprocessing hook: inject etas for non-mu-referenced thetas per vaeControl(nonMuTheta=). | .preProcessVaeNonMuTheta |
| Preprocess the zero omegas | .preProcessZeroOmega |
| Nudge exactly-zero theta initial estimates off zero (FOCEi family) | .preProcessZeroTheta |
| 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 for advi (automatic differentiation variational inference) in nlmixr2 | adviControl |
| 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 |
| Load a general FOCE-family likelihood into memory | foceiLikLoad |
| Evaluate a loaded general FOCE-family likelihood at supplied etas | foceiLikRun |
| Unload the general FOCE-family likelihood from memory | foceiLikUnload |
| Control options for the focep (FOCE+) estimation method | focepControl |
| Control options for the FO estimation method | foControl |
| Control options foir the FOI estimation method | foiControl |
| Format numeric values to minimize the printing width | formatMinWidth |
| Get valid nlmixr control object | getValidNlmixrControl getValidNlmixrCtl getValidNlmixrCtl.advi getValidNlmixrCtl.agq getValidNlmixrCtl.agqf getValidNlmixrCtl.bfgs getValidNlmixrCtl.bobyqa getValidNlmixrCtl.brent getValidNlmixrCtl.cg getValidNlmixrCtl.default getValidNlmixrCtl.fo getValidNlmixrCtl.foce getValidNlmixrCtl.focef getValidNlmixrCtl.focei getValidNlmixrCtl.foceif getValidNlmixrCtl.focep getValidNlmixrCtl.focepf getValidNlmixrCtl.foi getValidNlmixrCtl.iagq getValidNlmixrCtl.iagqf getValidNlmixrCtl.ifoce getValidNlmixrCtl.ifocef getValidNlmixrCtl.ifocei getValidNlmixrCtl.ifoceif getValidNlmixrCtl.ifocep getValidNlmixrCtl.ifocepf getValidNlmixrCtl.ilaplace getValidNlmixrCtl.imp getValidNlmixrCtl.impmap getValidNlmixrCtl.inpag getValidNlmixrCtl.inpb getValidNlmixrCtl.laplace getValidNlmixrCtl.lbfgsb getValidNlmixrCtl.lbfgsb3c getValidNlmixrCtl.magq getValidNlmixrCtl.magqf getValidNlmixrCtl.mfoce getValidNlmixrCtl.mfocef getValidNlmixrCtl.mfocei getValidNlmixrCtl.mfoceif getValidNlmixrCtl.mfocep getValidNlmixrCtl.mfocepf getValidNlmixrCtl.mlaplace getValidNlmixrCtl.mnpag getValidNlmixrCtl.mnpb getValidNlmixrCtl.n1qn1 getValidNlmixrCtl.neldermead getValidNlmixrCtl.newuoa getValidNlmixrCtl.nlm getValidNlmixrCtl.nlme getValidNlmixrCtl.nlminb getValidNlmixrCtl.nls getValidNlmixrCtl.npag getValidNlmixrCtl.npb getValidNlmixrCtl.optim getValidNlmixrCtl.posthoc getValidNlmixrCtl.predict getValidNlmixrCtl.qrpem getValidNlmixrCtl.rxSolve getValidNlmixrCtl.saem getValidNlmixrCtl.sann getValidNlmixrCtl.simulate getValidNlmixrCtl.simulation getValidNlmixrCtl.tableControl getValidNlmixrCtl.uobyqa getValidNlmixrCtl.vae |
| Control options for the iagq estimation method | iagqControl |
| Control options for the ifoce estimation method | ifoceControl |
| Control options for the ifocei estimation method | ifoceiControl |
| Control options for the ifocep (IRLS FOCE+) estimation method | ifocepControl |
| Control options for the ilaplace estimation method | ilaplaceControl |
| Control for the imp (importance-sampling EM without MAP search) method | impControl |
| Control options for the impmap (importance-sampling EM) estimation method | impmapControl |
| Control iteration-time print formatting | iterPrintControl |
| Control options for the Laplace estimation method | laplaceControl |
| Control for lbfgsb3c estimation method in nlmixr2 | lbfgsb3cControl |
| Control options for the magq estimation method | magqControl |
| Control options for the mfoce estimation method | mfoceControl |
| Control options for the mfocei estimation method | mfoceiControl |
| Control options for the mfocep (mu-referenced FOCE+) estimation method | mfocepControl |
| Control options for the mlaplace estimation method | mlaplaceControl |
| 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 |
| Tagged list of the available nlmixr2 estimation methods | nlmixr2AllEstType |
| Augmented Prediction for nlmixr2 fit | augPred.nlmixr2FitData nlmixr2AugPredSolve |
| Create nlmixr output from the UI | nlmixr2CreateOutputFromUi |
| Generic for nlmixr2 estimation methods | nlmixr2Est nlmixr2Est.advi nlmixr2Est.agq nlmixr2Est.agqf nlmixr2Est.bfgs nlmixr2Est.bobyqa nlmixr2Est.brent nlmixr2Est.cg nlmixr2Est.default nlmixr2Est.fo nlmixr2Est.foce nlmixr2Est.focef nlmixr2Est.focei nlmixr2Est.foceif nlmixr2Est.focep nlmixr2Est.focepf nlmixr2Est.foi nlmixr2Est.iagq nlmixr2Est.iagqf nlmixr2Est.ifoce nlmixr2Est.ifocef nlmixr2Est.ifocei nlmixr2Est.ifoceif nlmixr2Est.ifocep nlmixr2Est.ifocepf nlmixr2Est.ilaplace nlmixr2Est.imp nlmixr2Est.impmap nlmixr2Est.inpag nlmixr2Est.inpb nlmixr2Est.laplace nlmixr2Est.lbfgsb nlmixr2Est.lbfgsb3c nlmixr2Est.magq nlmixr2Est.magqf nlmixr2Est.mfoce nlmixr2Est.mfocef nlmixr2Est.mfocei nlmixr2Est.mfoceif nlmixr2Est.mfocep nlmixr2Est.mfocepf nlmixr2Est.mlaplace nlmixr2Est.mnpag nlmixr2Est.mnpb nlmixr2Est.n1qn1 nlmixr2Est.neldermead nlmixr2Est.newuoa nlmixr2Est.nlm nlmixr2Est.nlme nlmixr2Est.nlminb nlmixr2Est.nls nlmixr2Est.npag nlmixr2Est.npb nlmixr2Est.optim nlmixr2Est.output nlmixr2Est.posthoc nlmixr2Est.predict nlmixr2Est.qrpem nlmixr2Est.rxSolve nlmixr2Est.saem nlmixr2Est.sann nlmixr2Est.simulate nlmixr2Est.simulation nlmixr2Est.uobyqa nlmixr2Est.vae |
| 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.advi nmObjGetControl.agq nmObjGetControl.bobyqa nmObjGetControl.default nmObjGetControl.fo nmObjGetControl.foce nmObjGetControl.focei nmObjGetControl.focep nmObjGetControl.foi nmObjGetControl.iagq nmObjGetControl.ifoce nmObjGetControl.ifocei nmObjGetControl.ifocep nmObjGetControl.ilaplace nmObjGetControl.imp nmObjGetControl.impmap nmObjGetControl.inpag nmObjGetControl.inpb nmObjGetControl.laplace nmObjGetControl.lbfgsb3c nmObjGetControl.magq nmObjGetControl.mfoce nmObjGetControl.mfocei nmObjGetControl.mfocep nmObjGetControl.mlaplace nmObjGetControl.mnpag nmObjGetControl.mnpb nmObjGetControl.n1qn1 nmObjGetControl.newuoa nmObjGetControl.nlm nmObjGetControl.nlme nmObjGetControl.nlminb nmObjGetControl.nls nmObjGetControl.npag nmObjGetControl.npb nmObjGetControl.optim nmObjGetControl.posthoc nmObjGetControl.qrpem nmObjGetControl.saem nmObjGetControl.uobyqa nmObjGetControl.vae |
| 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.focep nmObjGetFoceiControl.iagq nmObjGetFoceiControl.ifoce nmObjGetFoceiControl.ifocei nmObjGetFoceiControl.ifocep nmObjGetFoceiControl.ilaplace nmObjGetFoceiControl.imp nmObjGetFoceiControl.impmap nmObjGetFoceiControl.inpag nmObjGetFoceiControl.inpb nmObjGetFoceiControl.laplace nmObjGetFoceiControl.magq nmObjGetFoceiControl.mfoce nmObjGetFoceiControl.mfocei nmObjGetFoceiControl.mfocep nmObjGetFoceiControl.mlaplace nmObjGetFoceiControl.mnpag nmObjGetFoceiControl.mnpb nmObjGetFoceiControl.nlme nmObjGetFoceiControl.npag nmObjGetFoceiControl.npb nmObjGetFoceiControl.posthoc nmObjGetFoceiControl.qrpem 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.adviControl nmObjHandleControlObject.agqControl nmObjHandleControlObject.bobyqaControl nmObjHandleControlObject.default nmObjHandleControlObject.foceControl nmObjHandleControlObject.foceiControl nmObjHandleControlObject.focepControl nmObjHandleControlObject.foControl nmObjHandleControlObject.foiControl nmObjHandleControlObject.iagqControl nmObjHandleControlObject.ifoceControl nmObjHandleControlObject.ifoceiControl nmObjHandleControlObject.ifocepControl nmObjHandleControlObject.ilaplaceControl nmObjHandleControlObject.impmapControl nmObjHandleControlObject.laplaceControl nmObjHandleControlObject.lbfgsb3cControl nmObjHandleControlObject.magqControl nmObjHandleControlObject.mfoceControl nmObjHandleControlObject.mfoceiControl nmObjHandleControlObject.mfocepControl nmObjHandleControlObject.mlaplaceControl nmObjHandleControlObject.n1qn1Control nmObjHandleControlObject.newuoaControl nmObjHandleControlObject.nlmControl nmObjHandleControlObject.nlmeControl nmObjHandleControlObject.nlminbControl nmObjHandleControlObject.nlsControl nmObjHandleControlObject.optimControl nmObjHandleControlObject.posthocControl nmObjHandleControlObject.saemControl nmObjHandleControlObject.uobyqaControl nmObjHandleControlObject.vaeControl |
| 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 |
| Control for the npag (nonparametric adaptive grid) method | npagControl |
| Control for the npb (nonparametric Bayes) method | npbControl |
| 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 |
| Control for the qrpem (quasi-random parametric EM) estimation method | qrpemControl |
| 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 |
| Control for vae (variational autoencoder) estimation method in nlmixr2 | vaeControl |
| Covariates explored by the VAE covariate search | vaeCovariates |
| VPC simulation | vpcSim |
