Package: nlmixr2est 6.1.0

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:Matthew Fidler [aut, cre], Wenping Wang [aut], Audrey Lavenu [ctb], Ben Goodrich [ctb], David Ardia [cph], Dirk Eddelbuettel [cph], Elizabeth Eskow [ctb], Emmanuelle Comets [ctb], Hadley Wickham [ctb], Hajar Besbassi [ctb], Johannes Pfeifer [ctb], Justin Wilkins [aut], Katharine Mullen [cph], Mahmoud Abdelwahab [ctb], Marc Lavielle [ctb], Mason McComb [ctb], Mirjam Trame [ctb], Richard Hooijmaijers [aut], Rik Schoemaker [aut], Robert B. Schnabel [ctb], Robert Leary [ctb], Teun Post [ctb], Vipul Mann [aut], Yuan Xiong [aut]

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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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • nlmixr2Keywords - A list and description of the fields in the nlmxir2 object

On CRAN:

Conda:

openblascppopenmp

9.20 score 13 stars 12 packages 55 scripts 2.4k downloads 213 exports 59 dependencies

Last updated from:182f8ae3cb. Checks:11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING428
linux-devel-x86_64WARNING516
source / vignettesOK423
linux-release-arm64WARNING408
linux-release-x86_64WARNING395
macos-release-arm64WARNING291
macos-release-x86_64WARNING837
macos-oldrel-arm64WARNING215
macos-oldrel-x86_64WARNING510
windows-develWARNING461
windows-releaseWARNING436
windows-oldrelWARNING479
wasm-releaseOK301

Exports:.absorbIterPrintControl.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_censgetBaseSimModelFitgetDatagetOfvTypegetValidNlmixrControlgetValidNlmixrCtlgetVarCovgroupedDataiBoxCoxiniirlsagqControlirlsfoceControlirlsfoceiControlirlslaplaceControliterPrintControliYeoJohnsonlaplaceControllbfgsb3cControllogitlotrimodelmuagqControlmufoceControlmufoceiControlmulaplaceControln1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlmerSolveGradnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2AugPredSolvenlmixr2CreateOutputFromUinlmixr2Estnlmixr2Eval_nlmixr2fixnlmixr2Gill83nlmixr2Grad_nlmixr2GradFunnlmixr2Hessnlmixr2iovLogsdCvnlmixr2iovLogsdSdnlmixr2iovLogvarCvnlmixr2iovLogvarSdnlmixr2iovSdCvnlmixr2iovSdSdnlmixr2iovVarCvnlmixr2iovVarSdnlmixr2Logonlmixr2NlmeControlnlmixr2ParHist_nlmixr2Printnlmixr2Unscaled_nlmixr2Validatenlmixr2VersionnlmixrAddObjectiveFunctionDataFramenlmixrAddTimingnlmixrCbindnlmixrClonenlmixrUpdateObjectnlmixrWithTimingnlsControlnmGetDistributionSaemLinesnmNearPDnmObjGetnmObjGetControlnmObjGetDatanmObjGetEstimationModelnmObjGetFoceiControlnmObjGetIpredModelnmObjGetPredOnlynmObjGetRxSolvenmObjHandleControlObjectnmObjUiSetCompressednmsimplexnmSuppressMsgnmTestofvoptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmpostFinalObjectHookspostFinalObjectHooksAddpostFinalObjectHooksRmposthocControlpreFinalParTableHookspreFinalParTableHooksAddpreFinalParTableHooksRmpreProcessHookspreProcessHooksAddpreProcessHooksRmprobitprobitInvrandom.effectsranefreStructrmEtarxCatrxCleanrxControlrxGetDistributionFoceiLinesrxGetDistributionNlmeLinesrxGetDistributionNlsLinesrxInitrxLhsrxModelVarsrxModelVarsS3rxodeRxODErxode2rxParamrxParamsrxSolverxStaterxUiDeparsesaemControlsetCovsetOfvsqrtmstat_amtstat_censtableControluobyqaControlvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcNameDataCmtsvpcSimvpcSimExpandyeoJohnson

Dependencies:armadillo4rbackportsBHcachemcheckmateclicpp11cpp4rcrayondata.tabledigestdparserevaluatefarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelbfgsb3clifecyclelotriMatrixmemoiseminqan1qn1nlmenlmixr2datanumDerivPreciseSumsqs2R6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llS7scalessitmoStanHeadersstringfishsundialrsymenginesysvctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
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 2aaaCranNlmixrThreads
Add CWRESaddCwres
NPDE calculation for nlmixr2addNpde
Add table information to nlmixr2 fit object without tablesaddTable
Control options for the agq estimation methodagqControl
Assert that this is a nlmixr2 fit objectassertNlmixrFit
Assert that this is a nlmixr2 fit data objectassertNlmixrFitData
Control for bobyqa estimation method in nlmixr2bobyqaControl
Cox Box, Yeo Johnson and inverse transformationboxCox iBoxCox iYeoJohnson yeoJohnson
Generalized Cholesky Matrix DecompositioncholSE
Control options for the foce estimation methodfoceControl
Control Options for FOCEifoceiControl
Control options for the FO estimation methodfoControl
Control options foir the FOI estimation methodfoiControl
Get valid nlmixr control objectgetValidNlmixrControl getValidNlmixrCtl getValidNlmixrCtl.agq getValidNlmixrCtl.bobyqa getValidNlmixrCtl.default getValidNlmixrCtl.fo getValidNlmixrCtl.foce getValidNlmixrCtl.focei getValidNlmixrCtl.foi getValidNlmixrCtl.irlsagq getValidNlmixrCtl.irlsfoce getValidNlmixrCtl.irlsfocei getValidNlmixrCtl.irlslaplace getValidNlmixrCtl.laplace getValidNlmixrCtl.lbfgsb3c getValidNlmixrCtl.muagq getValidNlmixrCtl.mufoce getValidNlmixrCtl.mufocei getValidNlmixrCtl.mulaplace 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 irlsagq estimation methodirlsagqControl
Control options for the irlsfoce estimation methodirlsfoceControl
Control options for the irlsfocei estimation methodirlsfoceiControl
Control options for the irlslaplace estimation methodirlslaplaceControl
Control iteration-time print formattingiterPrintControl
Control options for the Laplace estimation methodlaplaceControl
Control for lbfgsb3c estimation method in nlmixr2lbfgsb3cControl
Control options for the muagq estimation methodmuagqControl
Control options for the mufoce estimation methodmufoceControl
Control options for the mufocei estimation methodmufoceiControl
Control options for the mulaplace estimation methodmulaplaceControl
Control for n1qn1 estimation method in nlmixr2n1qn1Control
Control for newuoa estimation method in nlmixr2newuoaControl
nlmixr2 defaults controls for nlmnlmControl
nlmixr2 nlminb defaultsnlminbControl
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 methodsnlmixr2AllEst
Augmented Prediction for nlmixr2 fitaugPred.nlmixr2FitData nlmixr2AugPredSolve
Create nlmixr output from the UInlmixr2CreateOutputFromUi
Generic for nlmixr2 estimation methodsnlmixr2Est nlmixr2Est.agq nlmixr2Est.bobyqa nlmixr2Est.default nlmixr2Est.fo nlmixr2Est.foce nlmixr2Est.focei nlmixr2Est.foi nlmixr2Est.irlsagq nlmixr2Est.irlsfoce nlmixr2Est.irlsfocei nlmixr2Est.irlslaplace nlmixr2Est.laplace nlmixr2Est.lbfgsb3c nlmixr2Est.muagq nlmixr2Est.mufoce nlmixr2Est.mufocei nlmixr2Est.mulaplace 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 fitnlmixr2fix
Get the optimal forward difference interval by Gill83 methodnlmixr2Gill83
Calculate Hessiannlmixr2Hess
A list and description of the fields in the nlmxir2 objectnlmixr2Keywords
Messages the nlmixr2 logo...nlmixr2Logo
Control Values for nlme Fit with extra options for nlmixrnlmeControl nlmixr2NlmeControl
Validate nlmixr2nlmixr2Validate nmTest
Display nlmixr2's versionnlmixr2Version
Add objective function data frame to the current objective functionnlmixrAddObjectiveFunctionDataFrame
Manually add time to a nlmixr2 objectnlmixrAddTiming
nlmixrCbindnlmixrCbind
Clone nlmixr environmentnlmixrClone
Time a part of a nlmixr operation and add to nlmixr objectnlmixrWithTiming
nlmixr2 defaults controls for nlsnlsControl
C++ implementation of Matrix's nearPDnmNearPD
Get control object from fitnmObjGetControl nmObjGetControl.agq nmObjGetControl.bobyqa nmObjGetControl.default nmObjGetControl.fo nmObjGetControl.foce nmObjGetControl.focei nmObjGetControl.foi nmObjGetControl.irlsagq nmObjGetControl.irlsfoce nmObjGetControl.irlsfocei nmObjGetControl.irlslaplace nmObjGetControl.laplace nmObjGetControl.lbfgsb3c nmObjGetControl.muagq nmObjGetControl.mufoce nmObjGetControl.mufocei nmObjGetControl.mulaplace 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 typenmObjGetEstimationModel
Method for getting focei compatible control object from nlmixr objectnmObjGetFoceiControl nmObjGetFoceiControl.agq nmObjGetFoceiControl.default nmObjGetFoceiControl.foce nmObjGetFoceiControl.irlsagq nmObjGetFoceiControl.irlsfoce nmObjGetFoceiControl.irlsfocei nmObjGetFoceiControl.irlslaplace nmObjGetFoceiControl.laplace nmObjGetFoceiControl.muagq nmObjGetFoceiControl.mufoce nmObjGetFoceiControl.mufocei nmObjGetFoceiControl.mulaplace nmObjGetFoceiControl.nlme nmObjGetFoceiControl.posthoc nmObjGetFoceiControl.saem
Get the ipred model for a fit object depending on the object typenmObjGetEstimationModel.default nmObjGetEstimationModel.saem nmObjGetIpredModel nmObjGetIpredModel.default nmObjGetIpredModel.saem
Get the pred-only model for a fit depending on the object typenmObjGetPredOnly nmObjGetPredOnly.default nmObjGetPredOnly.saem
Handle the control objectnmObjHandleControlObject nmObjHandleControlObject.agqControl nmObjHandleControlObject.bobyqaControl nmObjHandleControlObject.default nmObjHandleControlObject.foceControl nmObjHandleControlObject.foceiControl nmObjHandleControlObject.foControl nmObjHandleControlObject.foiControl nmObjHandleControlObject.irlsagqControl nmObjHandleControlObject.irlsfoceControl nmObjHandleControlObject.irlsfoceiControl nmObjHandleControlObject.irlslaplaceControl nmObjHandleControlObject.laplaceControl nmObjHandleControlObject.lbfgsb3cControl nmObjHandleControlObject.muagqControl nmObjHandleControlObject.mufoceControl nmObjHandleControlObject.mufoceiControl nmObjHandleControlObject.mulaplaceControl nmObjHandleControlObject.n1qn1Control nmObjHandleControlObject.newuoaControl nmObjHandleControlObject.nlmControl nmObjHandleControlObject.nlmeControl nmObjHandleControlObject.nlminbControl nmObjHandleControlObject.nlsControl nmObjHandleControlObject.optimControl nmObjHandleControlObject.posthocControl nmObjHandleControlObject.saemControl nmObjHandleControlObject.uobyqaControl
Handle Model ObjectnmObjHandleModelObject nmObjHandleModelObject.default nmObjHandleModelObject.foceiModelList nmObjHandleModelObject.saemModelList
Set if the nlmixr2 object will return a compressed uinmObjUiSetCompressed
Nelder-Mead simplex searchnmsimplex
Return the objective functionofv
nlmixr2 optim defaultsoptimControl
Control options for the posthoc estimation methodposthocControl
Predict method for nlmixr2 fit core objectspredict.nlmixr2FitCore
Print an SAEM model fit summaryprint.saemFit
Extract residuals from the FOCEI fitresiduals.nlmixr2FitData
Remove an eta from the modelrmEta
Control Options for SAEMsaemControl
Set the covariance type based on prior calculated covariancessetCov
Set/get Objective function type for a nlmixr2 objectgetOfvType setOfv
Return the square root of general square matrix Asqrtm
Print an SAEM model fit summarysummary.saemFit
Output table/data.frame optionstableControl
Control for uobyqa estimation method in nlmixr2uobyqaControl
VPC simulationvpcSim