Package: nlmixr2lib 0.3.2.9000

Bill Denney

nlmixr2lib: A Model Library for 'nlmixr2'

A model library for 'nlmixr2'. The models include (and plan to include) pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. Where applicable, references for each model are included in the meta-data for each individual model. The package also includes model composition and modification functions to make model updates easier.

Authors:Richard Hooijmaijers [aut], Matthew Fidler [aut], Bill Denney [aut, cre], Kiranmayi Vedantham [aut]

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manual.pdf |manual.html✨
card.svg |card.png
nlmixr2lib/json (API)
NEWS

# Install 'nlmixr2lib' in R:
install.packages('nlmixr2lib', repos = c('https://nlmixr2.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nlmixr2/nlmixr2lib/issues

Pkgdown/docs site:https://nlmixr2.github.io

Datasets:
  • modeldb - Model library for nlmixr2

On CRAN:

Conda:

9.29 score 10 stars 520 scripts 265 downloads 68 exports 60 dependencies

Last updated from:d8a40f2649. Checks:1 FAIL, 8 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64FAIL145
source / vignettesOK288
linux-release-x86_64OK266
macos-release-arm64OK216
macos-oldrel-arm64OK230
windows-develOK385
windows-releaseOK356
windows-oldrelOK397
wasm-releaseOK162

Exports:addBaseline1expaddBaselineConstaddBaselineExpaddBaselineLinaddBioavailabilityaddCmtPropaddDepotaddDirectLinaddDirToModelDbaddDuraddEffectCmtLinaddEtaaddFileToModelDbaddIndirectaddIndirectLinaddIniaddLagaddLogEstimatesaddRateaddResErraddTransitaddWeibullAbsassertCompartmentExistsassertCompartmentNameassertParameterValueassertRxUiassertRxUiEstimatedResidualsassertRxUiMixedOnlyassertRxUiMuRefOnlyassertRxUiNormalassertRxUiPopulationOnlyassertRxUiPredictionassertRxUiRandomOnIdOnlyassertRxUiSingleEndpointassertRxUiTransformNormalassertVariableNameblankCombinebsvToCvcamelCombinecheckModelConventionscombinePaste2convertEmaxconvertEmaxHillconvertKinR0convertLogLinconvertMMconvertQuadcreateMarkovModelcreateMarkovModelDatasetcreateMarkovTransitionMatrixcvToBsvdefaultCombinedotCombineexpitfakeCclogitmodellibpkTransreadModelDbremoveDepotremoveLinesAndInisremoveTransitsearchReplacesearchReplaceHelpersetCombineTypesimMarkovsnakeCombineupdateOncologyXenograftSimeoni2004

Dependencies:armadillo4rbackportsBHcachemcheckmateclicpp11cpp4rcrayondata.tabledescdigestdparserevaluatefarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelbfgsb3clifecyclelotriMatrixmemoiseminqan1qn1nlmenlmixr2datanlmixr2estnumDerivPreciseSumsqs2R6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llS7scalessitmoStanHeadersstringfishsymenginesysvctrsviridisLitewithrxfunyaml

Canonical covariate columns

Rendered fromcovariate-columns.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-05-08
Started: 2026-05-08

Creating a model library

Rendered fromcreate-model-library.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-05-04
Started: 2022-09-16

List of models

Rendered fromlist-of-models.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-05-11
Started: 2023-04-22

Markov modeling

Rendered frommarkov.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-19
Started: 2026-01-26

PK_2cmt_mAb_Davda_2014

Rendered fromPK_2cmt_mAb_Davda_2014.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-19
Started: 2026-04-18

TMDD archetypes: full, QSS, and Michaelis-Menten approximations

Rendered fromtmdd_archetypes.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-19
Started: 2026-04-19

Readme and manuals

Help Manual

Help pageTopics
Add baseline that decays exponential with timeaddBaseline1exp
Add an estimated baseline constantaddBaselineConst
Add baseline that decays exponential with timeaddBaselineExp
Add an estimated baseline linear constantaddBaselineLin
Add a property to a compartmentaddBioavailability addCmtProp addDur addIni addLag addRate
To convert from infusion/intravenous administration to first-order oral absorptionaddDepot
Add direct linear effect with baseline=0addDirectLin
Add a directory to the modeldbaddDirToModelDb addFileToModelDb
Add effect compartmentaddEffectCmtLin
Add random effects to a modeladdEta
Add an indirect response model to a PK modeladdIndirect
Add linear indirect response modeladdIndirectLin
Add log estimates to a modeladdLogEstimates
Add residual error to a modeladdResErr
To add transit compartments to the modeladdTransit
Converts first order absorption model to Weibull absorption modeladdWeibullAbs
Check a model against nlmixr2lib conventionscheckModelConventions
Combine two strings using a naming conventioncombinePaste2
Convert linear effect to Emax effectconvertEmax
Convert linear effect to Emax-Hill effectconvertEmaxHill
Convert a kin/kout indirect response model to R0 and koutconvertKinR0
Converts a linear effect to a log-linear effectconvertLogLin
Convert models from linear elimination to Michaelis-Menten eliminationconvertMM
Convert linear elimination to quadratic eliminationconvertQuad
Create a Markov model for `nlmixr2`createMarkovModel
Create a Markov model dataset for use in estimating Markov modelscreateMarkovModelDataset createMarkovModelDataset.data.frame createMarkovModelDataset.default
Create the parts of a Markov model for transitioning from a single statecreateMarkovModelFromSingleState
Create a Markov transition matrix with probabilities of transitioning between every statecreateMarkovTransitionMatrix
Convert coefficient of variation (percent) to between-subject variancebsvToCv cvToBsv
Default combine stringsblankCombine camelCombine defaultCombine dotCombine snakeCombine
Fake blank Cc for creating PD only modelsfakeCc
Model library for nlmixr2modeldb
Get the model from the model librarymodellib
Change the transformation type for PK modelspkTrans
Read a model from the nlmixr2 model databasereadModelDb
To convert from first order oral absorption to IV/IntravenousremoveDepot
Removes lines and inis from a modelremoveLinesAndInis
To remove transit compartments from the modelremoveTransit
Search within a model to replace part of the modelsearchReplace searchReplaceHelper
Change the default combine type for the packagesetCombineType
Convert nlmixr2 simulations to Markov statessimMarkov
Simulate a Markov model broken down by IDsimMarkovId
Update an oncology xenograft model based on Simeoni 2004updateOncologyXenograftSimeoni2004