Files in nlmixr2est

Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

configure

MD5

NEWS.md

NAMESPACE

DESCRIPTION

cleanup.win

configure.win

cleanup

R/RcppExports.R R/preProcessDataUi.R R/vae.R R/mfoce.R R/benchmarking.R R/nmObjHandle.R R/nlmixr2EstType.R R/rxPipeline.R R/laplace.R R/deparse.R R/preProcessLiteralFix.R R/lbfgsb3c.R R/npBox.R R/nlmixr2global.R R/emviControl.R R/assert.R R/nlmixrUpdateObject.R R/asFunction.R R/ifocep.R R/vaeOutput.R R/foceiCov.R R/aaaCranNlmixrThreads.R R/focei.R R/print.R R/fo.R R/covRecompute.R R/ifoce.R R/ifocei.R R/nmObjGet.R R/compat.R R/foceiGradAnalytic.R R/nlm.R R/complete.R R/rstudio.R R/optim.R R/preProcessLinCmtOde.R R/vaeCovSelectL0.R R/ofv.R R/sharedControl.R R/rxsolve.R R/newuoa.R R/mlaplace.R R/vi.R R/cloneNlmixr.R R/impmap.R R/iagq.R R/ini.R R/vaeGrad.R R/model.R R/coerce.R R/simulate.R R/nlminb.R R/viData.R R/impPsis.R R/foce.R R/vaeData.R R/saemControl.R R/nlmixrGrad.R R/posthoc.R R/reexports.R R/agq.R R/uobyqa.R R/foceiCovAnalytic.R R/splitModelRxUiGet.R R/vaeInner.R R/addCwres.R R/cov.R R/muRefLinear.R R/npb.R R/focep.R R/fitSim.R R/npCommon.R R/preProcessZeroOmega.R R/ilaplace.R R/update.R R/saemRxUiGetModel.R R/muRefControl.R R/mfocei.R R/nlmixrCbind.R R/bobyqa.R R/md5.R R/iterPrintControl.R R/saem.R R/preProcessZeroTheta.R R/imp.R R/vaeDecoder.R R/mix.R R/odeSwapVerify.R R/nlmixr2Keywords.R R/n1qn1.R R/foceiCovFdFull.R R/preProcessVaeNonMuTheta.R R/uninformativeEtas.R R/resid.R R/agqGen.R R/sessioninfo.R R/foi.R R/nlmixr2Est.R R/vaeFit.R R/foceiLik.R R/fbvi.R R/nmObjGetEtaMat.R R/magq.R R/nlmixr2output.R R/nlme.R R/mfocep.R R/nlmeRxUiGet.R R/iov.R R/hook.R R/build.R R/preProcessCovariatesPresent.R R/zzz.R R/npde.R R/saem_fit_aux.R R/nlmixr2_md5.R R/nlmixrAddObjectiveFunction.R R/impmapThetaSens.R R/foceiFast.R R/foceiControl.R R/vpc.R R/rxNamedModel.R R/npag.R R/nls.R R/saem_fit.R R/validate.R R/omegaBlock.R R/preProcessBoundedTransform.R R/npInner.R R/vaeCovShapes.R R/nlmixr2.R R/nlmShared.R R/mu2.R R/saemRxUiGet.R R/broom.R R/muRefClassify.R R/utils.R R/timing.R R/augPred.R R/npMuExpand.R R/pkpars.R R/qrpem.R R/sourceCppFunction.R

src/rxomp.h

src/neldermead.cpp

src/censEst.h

src/vaeEncoder.h

src/foceiGrad.h

src/odeSwap.h

src/utilc.c

src/npde.h

src/RcppExports.cpp

src/vaeEncoder.cpp

src/filterNormalLike.cpp

src/shi21.cpp

src/censResid.cpp

src/np.h

src/lbfgsR.c

src/inner.cpp

src/rxProtect.h

src/npde.cpp

src/imp.cpp

src/nlm.cpp

src/npCommon.cpp

src/npb.cpp

src/nearPD.h

src/imp.h

src/slice.cpp

src/ires.cpp

src/uninformativeEtas.cpp

src/cholse.cpp

src/init.c

src/odeSwap.cpp

src/nmMcmcRng.h

src/npCommon.h

src/res.cpp

src/resid.cpp

src/shi21.h

src/res.h

src/shrink.h

src/evaluate.h

src/rprintf.c

src/npag.cpp

src/merge3.c

src/ires.h

src/nearPD.cpp

src/Makevars.in

src/censResid.h

src/censEst.cpp

src/cwres.h

src/shrink.cpp

src/scale.h

src/rxcmp.cpp

src/expandNlme.cpp

src/foceiGrad.cpp

src/cwres.cpp

src/armahead.h

src/RcppExportMod.cpp

src/saem.cpp

src/utilc.h

src/inner.h

src/solveWarnHelper.h

inst/TODOs.txt

inst/reprex_fbio_eta_parallel.R

inst/quadrule.diff

inst/testfit_nlmixr3.rds

inst/revision.txt

inst/COPYRIGHT

inst/CITATION

inst/THANKS

inst/WORDLIST

inst/include/nlmixr2est.h

inst/include/generic_ode_interface_template.txt

inst/include/nlmixr2est_types.h

inst/include/nlmixr2est_RcppExports.h

inst/include/lin_cmt.hpp

inst/include/generic_ode_interface_template_cov.txt

inst/benchmarks/runtime-benchmarks.R inst/tools/workaround.R tests/testthat.R tests/testthat/test-focei-1.R tests/testthat/test-muRefClassify.R tests/testthat/test-nearPd.R tests/testthat/test-saem-funny-mu.R tests/testthat/test-np.R tests/testthat/test-fo-control.R tests/testthat/test-vae-iov.R tests/testthat/test-mu-parhist.R tests/testthat/test-single-subject.R tests/testthat/test-npag-bimodal.R tests/testthat/test-inpar-saem.R tests/testthat/test-focei-preprocess.R tests/testthat/test-indTolRelax-propagation.R tests/testthat/test-vpcSim.R tests/testthat/test-vae-hockey-fit.R

tests/testthat/out.focei.prop.rds

tests/testthat/test-mem-npde-empty.R tests/testthat/test-focei-wang2007-boxcox-half.R tests/testthat/test-npb-fit.R tests/testthat/test-imp-tprop.R tests/testthat/test-update-estimates.R tests/testthat/test-qrpem-slow.R tests/testthat/test-vae-covariate-estimate.R tests/testthat/test-lag.R tests/testthat/test-unary-mu.R tests/testthat/test-lincmt-ode.R tests/testthat/test-vae-elbo.R tests/testthat/test-focei-cens.R tests/testthat/test-cloneEnv-cycle.R tests/testthat/test-nmobj.R tests/testthat/test-saem-drop.R tests/testthat/test-focei-ll-fast-grad-fit.R tests/testthat/test-matexp.R tests/testthat/test-vi-repro.R tests/testthat/test-nlme.R tests/testthat/test-utils.R tests/testthat/test-issue-502.R tests/testthat/test-control-infer.R tests/testthat/test-vae-dataprep.R tests/testthat/test-vi-stan.R tests/testthat/test-vae-cov-groups.R tests/testthat/test-timing.R tests/testthat/test-saem-loglik.R tests/testthat/test-piping.R tests/testthat/test-nlme-cov.R

tests/testthat/test-restart.rds

tests/testthat/test-rxuideparse.R tests/testthat/test-vae-miqp.R tests/testthat/test-vae-encoder.R tests/testthat/test-ui-est-change.R tests/testthat/test-mu-family.R tests/testthat/test-vae-rvar.R tests/testthat/test-vae-train.R tests/testthat/test-saem-nearpd.R tests/testthat/test-focei-inner.R tests/testthat/test-nlmixr3-load.R tests/testthat/test-split.R

tests/testthat/testthat-problems.rds

tests/testthat/test-vpcSimExpand.R tests/testthat/test-focei-llik.R tests/testthat/test-review-batch2.R tests/testthat/test-vae-nonmutheta.R tests/testthat/test-tolFactor.R tests/testthat/test-cov-robust.R tests/testthat/test-saem-nonmutheta.R tests/testthat/test-zero-omega-restore.R tests/testthat/test-predict.R tests/testthat/test-focei-wang2007-lognormal.R tests/testthat/test-issue-503.R tests/testthat/test-vae-inner.R tests/testthat/test-dde-focei.R tests/testthat/test-00-reload-ll.R tests/testthat/test-subFinal.R tests/testthat/test-vi-inner.R tests/testthat/test-npag-psi.R tests/testthat/test-keep.R tests/testthat/test-vae-cov-shapes.R tests/testthat/helper-vae-resid.R tests/testthat/test-addCwres.R tests/testthat/test-mfocei.R tests/testthat/test-npag-fixed.R tests/testthat/test-vae-covariate-accessor.R tests/testthat/test-mu-timevarying.R tests/testthat/test-muRefLinear.R tests/testthat/test-splitbolus-interp.R tests/testthat/test-focei-theta-reset-bounds.R tests/testthat/test-cwres.R tests/testthat/test-coerce.R tests/testthat/test-nonmu.R tests/testthat/test-vae-residopt.R tests/testthat/test-cov-decouple-saimp.R tests/testthat/helper-zzz-fits.R tests/testthat/test-optim.R tests/testthat/test-focei-parallel.R tests/testthat/test-focei-eta-reset-path-dependence.R tests/testthat/test-etaMat.R tests/testthat/test-vae-l0learn.R tests/testthat/test-omega-offdiag.R tests/testthat/test-focei-foce-plus.R tests/testthat/test-rxsolve.R tests/testthat/test-saem-mix.R tests/testthat/test-vae-covariate-selection.R tests/testthat/test-augpred.R tests/testthat/test-warfarin.R tests/testthat/test-cov-focei.R tests/testthat/test-ar-est.R tests/testthat/test-broom.R tests/testthat/test-vae-nonmutheta-grad.R tests/testthat/test-saem-translate.R tests/testthat/test-issue-515.R tests/testthat/test-shi21-hbound.R tests/testthat/test-focei-cores-fresh-rx.R tests/testthat/test-agq-fast-grad.R tests/testthat/test-npag-error-models.R tests/testthat/test-model.R tests/testthat/helper-quiet.R tests/testthat/test-focei-zero-theta.R tests/testthat/test-fix-cov.R tests/testthat/test-npag-fit.R tests/testthat/test-iov-zero-eta.R tests/testthat/test-saem-cov-transpose.R tests/testthat/test-str-est.R tests/testthat/test-focei-mceta-empty-cube.R tests/testthat/test-issue-455.R tests/testthat/test-cov-condition.R tests/testthat/test-posthoc.R tests/testthat/test-cov-fdfull-install.R tests/testthat/test-npag-cycle.R tests/testthat/test-vae-fixbounds.R tests/testthat/test-bad-print.R tests/testthat/test-vi-control.R tests/testthat/test-vae-decoder.R tests/testthat/test-imp-psis.R tests/testthat/test-tad-in-models.R tests/testthat/test-mix.R tests/testthat/test-issue-579.R tests/testthat/test-nls.R tests/testthat/test-focei-wang2007-boxcox-lnorm.R tests/testthat/test-npde.R tests/testthat/test-saem-mix-regress.R tests/testthat/test-nlmsetup-fresh-rx.R tests/testthat/test-vi-neonatal.R tests/testthat/test-saem-theo_sd.R tests/testthat/test-vae-parhist.R tests/testthat/test-saem-cov-sa.R tests/testthat/test-focei-wang2007-yeojohnson.R tests/testthat/test-mu-plain.R tests/testthat/test-npag-muexpand.R tests/testthat/test-udf.R tests/testthat/test-focei-eta-only.R tests/testthat/test-focei-wang2007-bounded.R tests/testthat/test-vi-grad.R tests/testthat/test-cov-decouple.R tests/testthat/test-vae-ll-grad-fit.R tests/testthat/test-vi-dataprep.R

tests/testthat/test-saem-theo_sd.rds

tests/testthat/test-omega-boundary.R tests/testthat/test-table-cmt.R tests/testthat/test-vi-fullrank.R tests/testthat/test-iter-print-ofv-header.R tests/testthat/test-imp-parallel.R tests/testthat/test-vi-fullbayes.R tests/testthat/helper-models.R tests/testthat/test-uninformative-etas.R tests/testthat/test-vae-l0learn-fit.R tests/testthat/test-vae-errmodel.R tests/testthat/test-cov-analytic-defaults.R tests/testthat/test-focei-fast-methods.R tests/testthat/test-odeswap.R tests/testthat/test-benchmarking.R tests/testthat/test-focei-wang2007-boxcox.R tests/testthat/test-omega-block.R tests/testthat/helper-gradref.R tests/testthat/helper-wang2007.R tests/testthat/test-vae-covariate-table.R tests/testthat/test-focei-wang2007-combined.R tests/testthat/test-focei-ll-fast-grad.R tests/testthat/test-control.R tests/testthat/test-issue-641.R tests/testthat/test-npag-golden.R tests/testthat/test-simulation.R tests/testthat/test-vae-grad-fit.R tests/testthat/test-saem-no-pop.R

tests/testthat/datos_pac.rds

tests/testthat/test-npag-dispatch.R tests/testthat/test-fix-eta.R tests/testthat/test-nlm-cens.R tests/testthat/test-saem-aic.R tests/testthat/test-npag-grid.R tests/testthat/test-cov-mu.R tests/testthat/test-np-control-surface.R tests/testthat/test-rx-model-props.R tests/testthat/test-focei-wang2007-power.R tests/testthat/test-npag-ipm.R tests/testthat/test-bounded-transform.R tests/testthat/test-issue-470.R tests/testthat/test-imp-auto.R

tests/testthat/test-cwres-3.0.3.rds

tests/testthat/test-focei-fast-methods-fit.R tests/testthat/test-npag-mixture.R tests/testthat/test-saem-cov-analytic.R tests/testthat/test-agq-cov.R tests/testthat/test-est-type-list.R tests/testthat/test-impmap.R tests/testthat/test-print.R tests/testthat/test-qrpem.R tests/testthat/test-focei-wang2007-basic.R tests/testthat/test-saem-mu.R tests/testthat/test-vi-fit.R tests/testthat/test-mu-plain-fit.R tests/testthat/test-ini-ui.R tests/testthat/test-imp-xi-gamma.R tests/testthat/test-restart.R tests/testthat/test-saem-no-obs-subject.R tests/testthat/test-npag-general-lik.R tests/testthat/test-focei-zero-init-scale.R tests/testthat/test-focei-fast-grad.R tests/testthat/test-nlmixr2output.R tests/testthat/test-vae-neonatal.R tests/testthat/test-muRefResetOptOut.R tests/testthat/test-sens-fd.R tests/testthat/test-nlm.R tests/testthat/test-odeswap-fit.R tests/testthat/test-focei-shi21-bounds.R tests/testthat/test-data-assert.R tests/testthat/test-integerish-focei-print.R tests/testthat/test-iov.R tests/testthat/test-issue-429.R tests/testthat/test-nlme-control.R tests/testthat/test-foceiLik.R tests/testthat/test-vae-fit.R tests/testthat/test-vi-cores.R tests/testthat/test-cov-analytic.R tests/testthat/test-focei-char.R tests/testthat/test-manual-back-transform.R tests/testthat/test-vae-cov-control.R tests/testthat/test-issue-281.R tests/testthat/test-saem-resid-lambda.R tests/testthat/test-vi-focei-agreement.R tests/testthat/test-focei-warm.R tests/testthat/test-lincmt-ode-fit.R tests/testthat/test-parFixedDf.R tests/testthat/test-focei-family-control.R

tests/testthat/baselines/gradref-fit-fd-methods-ifocei.rds

tests/testthat/baselines/gradref-fit-fd-resfix-addFix-foceif.rds

tests/testthat/baselines/gradref-cov-lnorm-focei.rds

tests/testthat/baselines/gradref-agq-agqf-equivalence.rds

tests/testthat/baselines/gradref-fit-mu-plain-focei.rds

tests/testthat/baselines/gradref-cov-shared-eta.rds

tests/testthat/baselines/gradref-subfinal-multiple-endpoint.rds

tests/testthat/baselines/gradref-cov-nonmu-covariate-coef.rds

tests/testthat/baselines/gradref-agq-nAGQ2.rds

tests/testthat/baselines/gradref-cov-boxcox-foce-focep.rds

tests/testthat/baselines/vae-encoder-golden.rds

tests/testthat/baselines/gradref-cov-cens-m3-focei.rds

tests/testthat/baselines/gradref-fit-fd-resfix-combFix-ifoceif.rds

tests/testthat/baselines/gradref-modeled-dosing-f-lag.rds

tests/testthat/baselines/gradref-fit-fd-ll-pois.rds

tests/testthat/baselines/gradref-cov-covariate-etaless-param.rds

tests/testthat/baselines/gradref-lambda-boxcox-yeojohnson-yeojohnson-focei.rds

tests/testthat/baselines/gradref-subfinal-covariate.rds

tests/testthat/baselines/qrpem-baseline-ref.rds

tests/testthat/baselines/README.md

tests/testthat/baselines/gradref-cov-logitnorm-foce.rds

tests/testthat/baselines/gradref-cov-orphan-eta.rds

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tests/testthat/baselines/gradref-agq-nAGQ3.rds

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tests/testthat/fixtures/README.md

tests/testthat/fixtures/npag/pmetrics_reference.csv

tests/testthat/fixtures/npag/ipm/burke-golden.csv

data/nlmixr2Keywords.rda

man/nmObjUiSetCompressed.Rd man/optimControl.Rd man/dot-nlmixrNlsData.Rd man/rxGetDistributionNlsLines.Rd man/preFinalParTableHooksRm.Rd man/ofv.Rd man/saemControl.Rd man/npBuildPsi.Rd man/dot-rxGetDVFTransform.Rd man/npagControl.Rd man/emviControl.Rd man/dot-nlmixrNlsFun.Rd man/vaeCovariates.Rd man/nlmixr2AllEst.Rd man/bobyqaControl.Rd man/dot-nlmAdjustCov.Rd man/dot-downgradeEtas.Rd man/dot-nlmFamilyControlGeneric.Rd man/laplaceControl.Rd man/nlmixr2CreateOutputFromUi.Rd man/addTable.Rd man/dot-nlmixrNlmeFun.Rd man/nlmixrUpdateObject.Rd man/dot-nlmFinalizeList.Rd man/reexports.Rd man/foceiGradPooledSetupLoad_.Rd man/nlmixr2.Rd man/dot-sensEtaOrTheta.Rd man/nlmixrWithTiming.Rd man/impmapControl.Rd man/assertNlmixrFit.Rd man/dot-nlmixr2FitUpdateParams.Rd man/getValidNlmixrControl.Rd man/lbfgsb3cControl.Rd man/nlmixrAddTiming.Rd man/dot-nlmFreeEnv.Rd man/ilaplaceControl.Rd man/foceiFitCpp_.Rd man/getBaseSimModelFit.Rd man/nlmixr2Logo.Rd man/dot-nlmixrOptimFunC.Rd man/nmObjGet.Rd man/nmNearPD.Rd man/qrpemControl.Rd man/focepControl.Rd man/dot-nlmixrPreprocessLiteralFix.Rd man/rxode2stateOde.Rd man/npSobolGrid_.Rd man/aaaCranNlmixrThreads.Rd man/fbviControl.Rd man/ifoceiControl.Rd man/assertNlmixrFitData.Rd man/posthocControl.Rd man/nlmixr2Print.Rd man/magqControl.Rd man/npObjAtGamma_.Rd man/dot-nlmixrNlsFunVal.Rd man/nlmControl.Rd man/dot-augPredIpredModel.Rd man/nlmixr2fix.Rd man/preFinalParTableHooksAdd.Rd man/foceiControl.Rd man/print.saemFit.Rd man/foceiLikRun.Rd man/preProcessHooks.Rd man/postFinalObjectHooks.Rd man/formatMinWidth.Rd man/mlaplaceControl.Rd man/nlminbControl.Rd man/nlmerSolveGrad.Rd man/nmObjGetControl.Rd man/preFinalParTableHooks.Rd man/dot-deparseDifferent.Rd man/nmSuppressMsg.Rd man/rmEta.Rd man/iagqControl.Rd man/dot-nlmSetupEnv.Rd man/nmObjGetIpredModel.Rd man/summary.saemFit.Rd man/dot-deparseFinal.Rd man/dot-loadSymengine.Rd man/npbControl.Rd man/vpcSimExpand.Rd man/foceiLikLoad.Rd man/dot-nlmixrNlmFunC.Rd man/nlmixr2iovLogvarCv.Rd man/vaeControl.Rd man/cholSE.Rd man/addCwres.Rd man/nlmixr2Version.Rd man/dot-addPkgNlmixr2.Rd man/foceiGradPooledDirect_.Rd man/dot-nlmFamilyAdjustOutput.Rd man/nmObjHandleModelObject.Rd man/npCondense_.Rd man/residuals.nlmixr2FitData.Rd man/dot-preProcessLinCmtOde.Rd man/nlmixr2Hess.Rd man/nlmGetParHist.Rd man/dot-nlmixr0preProcessCovariatesPresent.Rd man/setOfv.Rd man/nlmixr2Gill83.Rd man/mfocepControl.Rd man/nlmixr2Est.Rd man/dot-iniS3.Rd man/dot-nlmixr2objectNameAssign.Rd man/n1qn1Control.Rd man/newuoaControl.Rd man/dot-preProcessDataUi.Rd man/dot-uiFinalizeMu2.Rd man/foiControl.Rd man/mfoceControl.Rd man/setCov.Rd man/rxGetDistributionNlmeLines.Rd man/dot-preProcessZeroOmega.Rd man/nlmixr2Keywords.Rd man/nmsimplex.Rd man/nmObjGetPredOnly.Rd man/nlmixr2NlmeControl.Rd man/postFinalObjectHooksAdd.Rd man/nlmixrAddObjectiveFunctionDataFrame.Rd man/iterPrintParams.Rd man/ifoceControl.Rd man/dot-collectWarn.Rd man/iterPrintControl.Rd man/rxUiGet.foceiHdEta2.Rd man/nlsControl.Rd man/uobyqaControl.Rd man/rxGetDistributionFoceiLines.Rd man/dot-nlmixrNlminbFunC.Rd man/dot-preProcessZeroTheta.Rd man/vpcNameDataCmts.Rd man/dot-absorbIterPrintControl.Rd man/dot-preProcessVaeNonMuTheta.Rd man/dot-nlmeGetNonMuRefNames.Rd man/nlmixrClone.Rd man/dot-agq.Rd man/nmObjGetFoceiControl.Rd man/dot-saemDropMuRefFromModel.Rd man/foceControl.Rd man/dot-nlmixr2estLastPredSimulationInfo.Rd man/postFinalObjectHooksRm.Rd man/preProcessHooksRm.Rd man/dot-foceiPreProcessData.Rd man/impControl.Rd man/addNpde.Rd man/dot-uiApplyMu2.Rd man/nmObjGetRxSolve.Rd man/nmGetDistributionSaemLines.Rd man/nmObjHandleControlObject.Rd man/boxCox.Rd man/nlmixr2GradFun.Rd man/tableControl.Rd man/nmObjGetEstimationModel.Rd man/npagCycle_.Rd man/preProcessHooksAdd.Rd man/vpcSim.Rd man/nlmixr2AugPredSolve.Rd man/foceiLikUnload.Rd man/foControl.Rd man/nlmixrCbind.Rd man/sqrtm.Rd man/ifocepControl.Rd man/dot-nlmixr0preProcessNpMuExpand.Rd man/nlmixr2AllEstType.Rd man/mfoceiControl.Rd man/nmObjGetData.Rd man/dot-nlmFamilyFitGeneric.Rd man/predict.nlmixr2FitCore.Rd man/nlmixr2Validate.Rd man/npIpmBurke.Rd man/agqControl.Rd man/rmdhunks/nlmixr2Keywords.Rmd

man/rmdhunks/figure/unnamed-chunk-2-1.png

man/figures/README-example-1.png

nlmixr2est documentation built on Aug. 5, 2026, 1:11 a.m.