Package: nlmixr2est 3.0.1.9000

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

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nlmixr2est/json (API)
NEWS

# Install 'nlmixr2est' in R:
install.packages('nlmixr2est', repos = c('https://nlmixr2.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nlmixr2/nlmixr2est/issues

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:

8.13 score 7 stars 9 packages 22 scripts 2.1k downloads 165 exports 68 dependencies

Last updated 1 days agofrom:b2cc55ecac. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64OKNov 20 2024
R-4.5-linux-x86_64OKNov 20 2024
R-4.4-win-x86_64OKNov 20 2024
R-4.4-mac-x86_64OKNov 20 2024
R-4.4-mac-aarch64OKSep 18 2024
R-4.3-win-x86_64OKNov 20 2024
R-4.3-mac-x86_64OKNov 20 2024
R-4.3-mac-aarch64OKSep 18 2024

Exports:.addPkgNlmixr2.deparseDifferent.deparseFinal.foceiPreProcessData.nlmFinalizeList.nlmFreeEnv.nlmixr2estLastPredSimulationInfo.nlmixr2objectNameAssign.nlmixrNlmeFun.nlmixrNlmFunC.nlmixrNlminbFunC.nlmixrNlminbGradC.nlmixrNlminbHessC.nlmixrNlsData.nlmixrNlsFun.nlmixrNlsFunGrad.nlmixrNlsFunVal.nlmixrNlsFunValGrad.nlmixrOptimFunC.nlmixrOptimGradC.nlmSetupEnv.rxGetDVFTransform.saemDropMuRefFromModel.uiApplyMu2.uiFinalizeMu2%>%ACFadd.dosingadd.samplingaddCwresaddNpdeaddTableas.rxUiassertNlmixrFitassertNlmixrFitDataaugPredbobyqaControlboxCoxcholSEeteventTableexpitfixed.effectsfixeffoceiControlfoceiFitCpp_geom_amtgeom_censgetBaseSimModelFitgetDatagetOfvTypegetValidNlmixrControlgetValidNlmixrCtlgetVarCovgroupedDataiBoxCoxiniiYeoJohnsonlbfgsb3cControllogitlotrimodeln1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2AugPredSolvenlmixr2CreateOutputFromUinlmixr2Estnlmixr2Eval_nlmixr2Gill83nlmixr2Grad_nlmixr2GradFunnlmixr2Hessnlmixr2Logonlmixr2NlmeControlnlmixr2ParHist_nlmixr2Printnlmixr2Unscaled_nlmixr2Validatenlmixr2VersionnlmixrAddObjectiveFunctionDataFramenlmixrAddTimingnlmixrCbindnlmixrClonenlmixrUpdateObjectnlmixrWithTimingnlsControlnmGetDistributionSaemLinesnmNearPDnmObjGetnmObjGetControlnmObjGetDatanmObjGetEstimationModelnmObjGetFoceiControlnmObjGetIpredModelnmObjGetPredOnlynmObjGetRxSolvenmObjHandleControlObjectnmObjUiSetCompressednmsimplexnmSuppressMsgnmTestofvoptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmprobitprobitInvrandom.effectsranefreStructrxCatrxCleanrxControlrxGetDistributionFoceiLinesrxGetDistributionNlmeLinesrxGetDistributionNlsLinesrxInitrxLhsrxModelVarsrxModelVarsS3rxodeRxODErxode2rxParamrxParamsrxSolverxStaterxUiDeparsesaemControlsetCovsetOfvsqrtmstat_amtstat_censtableControluobyqaControlvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcNameDataCmtsvpcSimvpcSimExpandyeoJohnson

Dependencies:backportsBHcachemcheckmateclicolorspacecpp11cpp11armadillocrayondata.tabledigestdparserevaluatefansifarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelazyevallbfgsb3clifecyclelotrimagrittrMASSMatrixmemoisemgcvminqamunselln1qn1nlmenlmixr2datanumDerivpillarpkgconfigPreciseSumsqsR6RApiSerializeRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llscalessitmoStanHeadersstringfishsymenginesystibbleutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Augment Prediction for Ipred Model.augPredIpredModel
Add CWRESaddCwres
NPDE calculation for nlmixr2addNpde
Add table information to nlmixr2 fit object without tablesaddTable
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 FOCEifoceiControl
Get valid nlmixr control objectgetValidNlmixrControl 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 nlmixr2lbfgsb3cControl
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.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 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.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 typenmObjGetEstimationModel
Method for getting focei compatible control object from nlmixr objectnmObjGetFoceiControl nmObjGetFoceiControl.default nmObjGetFoceiControl.nlme 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.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 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
Print an SAEM model fit summaryprint.saemFit
Extract residuals from the FOCEI fitresiduals.nlmixr2FitData
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