Package: nlmixr2 3.0.1.9000

Matthew Fidler

nlmixr2: Nonlinear Mixed Effects Models in Population PK/PD

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 [ctb], Rik Schoemaker [ctb], Justin Wilkins [ctb], Wenping Wang [ctb], Mirjam Trame [ctb], Huijuan Xu [ctb], John Harrold [ctb], Bill Denney [ctb], Theodoros Papathanasiou [ctb], Teun Post [ctb], Richard Hooijmaijers [ctb]

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nlmixr2.pdf |nlmixr2.html✨
nlmixr2/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://nlmixr2.github.io

On CRAN:

8.38 score 44 stars 3 packages 106 scripts 1.4k downloads 97 exports 149 dependencies

Last updated 2 months agofrom:1b4efcf43a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-winOKDec 21 2024
R-4.5-linuxOKDec 21 2024
R-4.4-winOKDec 21 2024
R-4.4-macOKDec 21 2024
R-4.3-winOKDec 21 2024
R-4.3-macOKDec 21 2024

Exports:.nlmixrNlmeFun%>%ACFadd.dosingadd.samplingaddCwresaddNpdeaddTableaugPredbobyqaControlbootplotbootstrapFitetetExpandeventTableexpitfixed.effectsfixeffoceiControlgeom_amtgeom_censgetDatagetVarCovgroupedDatainiini<-lbfgsb3cControllogitlotrimodelmodel<-n1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2CheckInstallnlmixr2NlmeControlnlsControloptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmpreconditionFitprobitprobitInvprofileFixedprofileFixedSingleprofileLlprandom.effectsranefreStructrxCatrxCleanrxControlrxDerivedrxFunrxodeRxODErxode2rxParamrxParamsrxSetPipingAutorxSolvesaemControlsetOfvstat_amtstat_censtableControltraceplotuobyqaControlvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcCensvpcCensTadvpcPlotvpcPlotTadvpcSim

Dependencies:askpassassertthatbackportsbase64encBHbinombitbit64bitopsbootbslibcachemcellrangercheckmateclassclassIntclicliprclustercolorspacecommonmarkcpp11cpp11armadillocrayoncurldata.tableDerivDescToolsdigestdparserdplyre1071evaluateExactexpmfansifarverfastmapfontawesomeforcatsforeignFormulafsgenericsggplot2ggtextgldgluegridExtragridtextgtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrinlineisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevallbfgsb3clifecyclelmomlotrimagrittrmarkdownMASSMatrixmemoisemgcvmimeminpack.lmminqamunsellmvtnormn1qn1nlmenlmixr2datanlmixr2estnlmixr2extranlmixr2plotnnetnumDerivopensslpanderpillarpkgconfigpngPreciseSumsprettyunitsprogressproxypurrrqsR6RApiSerializerappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlreadrreadxlrematchrexrlangrmarkdownrootSolverpartrstudioapirxode2rxode2llsassscalessitmoStanHeadersstringfishstringistringrsurvivalsymenginesystibbletidyrtidyselecttinytextzdbutf8vctrsviridisviridisLitevpcvroomwithrxfunxgxrxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Add CWRESaddCwres
NPDE calculation for nlmixr2addNpde
Add table information to nlmixr2 fit object without tablesaddTable
Control for bobyqa estimation method in nlmixr2bobyqaControl
Produce delta objective function for boostrapbootplot
Bootstrap nlmixr2 fitbootstrapFit
Control Options for FOCEifoceiControl
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
Control Values for nlme Fit with extra options for nlmixrnlmeControl
nlmixr2 nlminb defaultsnlminbControl
nlmixr2 fits population PK and PKPD non-linear mixed effects models.nlmixr2
Check your nlmixr2 installation for potential issuesnlmixr2CheckInstall
nlmixr2 defaults controls for nlsnlsControl
nlmixr2 optim defaultsoptimControl
Linearly re-parameterize the model to be less sensitive to rounding errorspreconditionFit
Estimate the objective function values for a model while fixing defined parameter valuesprofileFixed
Estimate the objective function values for a model while fixing defined parameter valuesprofileFixedSingle
Profile confidence intervals with log-likelihood profilingprofileLlp
Control Options for SAEMsaemControl
Set/get Objective function type for a nlmixr2 objectsetOfv
Output table/data.frame optionstableControl
Produce trace-plot for fit if applicabletraceplot
Control for uobyqa estimation method in nlmixr2uobyqaControl
VPC based on ui modelvpcCens
VPC based on ui modelvpcCensTad
VPC based on ui modelvpcPlot
VPC based on ui modelvpcPlotTad
VPC simulationvpcSim