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]

nlmixr2lib_0.3.2.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nlmixr2lib/json (API)

# 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:

9.78 score 11 stars 1.3k scripts 361 downloads 72 exports 59 dependencies

Last updated from:f007f29cc4. Checks:7 OK, 2 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK533
source / vignettesOK334
linux-release-x86_64OK580
macos-release-arm64OK355
macos-oldrel-arm64OK312
windows-devel-x86_64FAIL637
windows-release-x86_64OK1315
windows-oldrel-x86_64OK1143
wasm-releaseFAIL158

Exports:addBaseline1expaddBaselineConstaddBaselineExpaddBaselineLinaddBioavailabilityaddCmtPropaddDepotaddDirectLinaddDirToModelDbaddDuraddEffectCmtLinaddEtaaddFileToModelDbaddIndirectaddIndirectLinaddIniaddLagaddLogEstimatesaddRateaddResErraddTransitaddWeibullAbsassertCompartmentExistsassertCompartmentNameassertParameterValueassertRxUiassertRxUiEstimatedResidualsassertRxUiMixedOnlyassertRxUiMuRefOnlyassertRxUiNormalassertRxUiPopulationOnlyassertRxUiPredictionassertRxUiRandomOnIdOnlyassertRxUiSingleEndpointassertRxUiTransformNormalassertVariableNameblankCombinebsvToCvcamelCombinecheckModelConventionscombinePaste2convertEmaxconvertEmaxHillconvertKinR0convertLogLinconvertMMconvertQuadcreateMarkovModelcreateMarkovModelDatasetcreateMarkovTransitionMatrixcvToBsvdefaultCombinedotCombineexpitfakeCclogitMann2022EquilibratemodellibncaComparisonTablencaParamLabelpkTransreadModelDbregister_lagStateremoveDepotremoveLinesAndInisremoveTransitsearchReplacesearchReplaceHelpersetCombineTypesimMarkovsnakeCombineupdateOncologyXenograftSimeoni2004

Dependencies:armadillo4rbackportsBHcachemcheckmateclicpp11cpp4rcrayondata.tabledigestdparserevaluatefarverfastmapggplot2gluegtablehighrinlineisobandknitrlabelinglatticelbfgsb3clifecyclelotriMatrixmemoiseminqamirain1qn1nanonextnlmenlmixr2datanlmixr2estnumDerivPreciseSumsR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrexrlangrxode2rxode2llS7scalessitmoStanHeaderssymenginesysvctrsviridisLitewithrxfunyaml

List of models
General | Specific Drugs | DDMoRe
Rendered fromlist-of-models.Rmdusingknitr::rmarkdown

Last update: 2026-06-28
Started: 2023-04-22

Canonical covariate columns
Rendered fromcovariate-columns.Rmdusingknitr::rmarkdown

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

Creating a model library
Model library conventions within nlmixr2lib | Compartment naming | Estimated parameter naming | Parameter naming | Multi-component clearance | Parent drug + metabolite parameters | Parameter transforms | Random effects | Covariate effects | Drug effects | Model files
Rendered fromcreate-model-library.Rmdusingknitr::rmarkdown

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

TMDD archetypes: full, QSS, and Michaelis-Menten approximations
Overview | Population and units | Source trace | Typical-value simulations | Single-dose profiles (100 mg SC) | Target and complex trajectories (1-cmt models) | Repeated SC dosing — drug-concentration difference across structures | Regime-convergence check | Assumptions and deviations
Rendered fromtmdd_archetypes.Rmdusingknitr::rmarkdown

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

Markov modeling
Create your dataset | Create your model | Fit the model | Simulate your data | Summarize the simulations
Rendered frommarkov.Rmdusingknitr::rmarkdown

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

PK_2cmt_mAb_Davda_2014
Model and source | Population | Source trace | Virtual cohort | Simulation | Replicate published figures | Figure 1 / 3 — typical IV vs SC profiles | VPC-style percentile bands | PKNCA validation | Comparison against published NCA | Assumptions and deviations
Rendered fromPK_2cmt_mAb_Davda_2014.Rmdusingknitr::rmarkdown

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

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
Pre-equilibrate the Mann 2022 respiratory-physiology statesMann2022Equilibrate
Model library for nlmixr2modeldb
Get the model from the model librarymodellib
Build a side-by-side NCA comparison table (simulated vs. reference)ncaComparisonTable
Map PKNCA parameter codes to friendly human-readable labelsncaParamLabel
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