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✨
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:

10.51 score 14 stars 4.0k scripts 637 downloads 82 exports 70 dependencies

Last updated from:f6c55c60f0. Checks:1 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
source / vignettes	OK	469

Exports:addBaseline1exp addBaselineConst addBaselineExp addBaselineLin addBioavailability addCmtProp addDepot addDirectLin addDirToModelDb addDur addEffectCmtLin addEta addFileToModelDb addIndirect addIndirectLin addIni addLag addLogEstimates addPeriph addRate addResErr addSecondAbsorption addTransit addWeibullAbs addZeroOrderAbs assertCompartmentExists assertCompartmentName assertParameterValue assertRxUi assertRxUiEstimatedResiduals assertRxUiMixedOnly assertRxUiMuRefOnly assertRxUiNormal assertRxUiPopulationOnly assertRxUiPrediction assertRxUiRandomOnIdOnly assertRxUiSingleEndpoint assertRxUiTransformNormal assertVariableName blankCombine bsvToCv camelCombine checkModelConventions checkNamingRegisters combinePaste2 convertAbsForceLongerDelay convertAbsSequential convertEmax convertEmaxHill convertKinR0 convertLogLin convertMM convertQuad createMarkovModel createMarkovModelDataset createMarkovTransitionMatrix cvToBsv defaultCombine dotCombine expit fakeCc logit Mann2022Equilibrate modellib ncaComparisonTable ncaParamLabel pkTrans Poels_2025_elranatamab_qsp_cauc_multiplier Poels_2025_elranatamab_qsp_events readModelDb register_lagState removeDepot removeLinesAndInis removePeriph removeTransit removeZeroOrderAbs searchReplace searchReplaceHelper setCombineType simMarkov snakeCombine updateOncologyXenograftSimeoni2004

Dependencies:armadillo4r backports BH cachem checkmate cli cpp11 cpp4r crayon data.table digest dparser evaluate farver fastmap ggplot2 glue gtable highr inline isoband knitr L0Learn labeling lattice lbfgsb3c lifecycle lotri magrittr MASS Matrix memoise minqa mirai n1qn1 nanonext nlme nlmixr2data nlmixr2est numDeriv plyr PreciseSums qs2 R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RcppTrust reshape2 rex rlang rxode2 rxode2lincmt rxode2ll S7 scales sitmo StanHeaders stringfish stringi stringr symengine sys vctrs viridisLite withr xfun yaml

List of models

General | Specific Drugs | DDMoRe

Rendered fromlist-of-models.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
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

Rendered fromcreate-model-library.Rmdusingknitr::rmarkdown

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

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

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

Rendered fromPK_2cmt_mAb_Davda_2014.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add baseline that decays exponential with time	addBaseline1exp
Add an estimated baseline constant	addBaselineConst
Add baseline that decays exponential with time	addBaselineExp
Add an estimated baseline linear constant	addBaselineLin
Add a property to a compartment	addBioavailability addCmtProp addDur addIni addLag addRate
To convert from infusion/intravenous administration to first-order oral absorption	addDepot
Add direct linear effect with baseline=0	addDirectLin
Add a directory to the modeldb	addDirToModelDb addFileToModelDb
Add effect compartment	addEffectCmtLin
Add random effects to a model	addEta
Add an indirect response model to a PK model	addIndirect
Add linear indirect response model	addIndirectLin
Add log estimates to a model	addLogEstimates
Add a peripheral compartment to a model	addPeriph
Add residual error to a model	addResErr
Add a second absorption path for double-absorption models	addSecondAbsorption
To add transit compartments to the model	addTransit
Converts first order absorption model to Weibull absorption model	addWeibullAbs
Convert a model to zero-order absorption (Monolix 'Tk0')	addZeroOrderAbs
Check a model against nlmixr2lib conventions	checkModelConventions
Check the naming registers for structural defects	checkNamingRegisters
Combine two strings using a naming convention	combinePaste2
Force the second absorption delay longer than the first	convertAbsForceLongerDelay
Convert double absorption to sequential delays	convertAbsSequential
Convert linear effect to Emax effect	convertEmax
Convert linear effect to Emax-Hill effect	convertEmaxHill
Convert a kin/kout indirect response model to R0 and kout	convertKinR0
Converts a linear effect to a log-linear effect	convertLogLin
Convert models from linear elimination to Michaelis-Menten elimination	convertMM
Convert linear elimination to quadratic elimination	convertQuad
Create a Markov model for `nlmixr2`	createMarkovModel
Create a Markov model dataset for use in estimating Markov models	createMarkovModelDataset createMarkovModelDataset.data.frame createMarkovModelDataset.default
Create the parts of a Markov model for transitioning from a single state	createMarkovModelFromSingleState
Create a Markov transition matrix with probabilities of transitioning between every state	createMarkovTransitionMatrix
Convert coefficient of variation (percent) to between-subject variance	bsvToCv cvToBsv
Default combine strings	blankCombine camelCombine defaultCombine dotCombine snakeCombine
Fake blank Cc for creating PD only models	fakeCc
Pre-equilibrate the Mann 2022 respiratory-physiology states	Mann2022Equilibrate
Model library for nlmixr2	modeldb
Get the model from the model library	modellib
Build a side-by-side NCA comparison table (simulated vs. reference)	ncaComparisonTable
Map PKNCA parameter codes to friendly human-readable labels	ncaParamLabel
Change the transformation type for PK models	pkTrans
Eq 37 cumulative-cytokine-exposure multiplier	Poels_2025_elranatamab_qsp_cauc_multiplier
Build an event table for the Poels 2025 elranatamab QSP model	Poels_2025_elranatamab_qsp_events
Read a model from the nlmixr2 model database	readModelDb
To convert from first order oral absorption to IV/Intravenous	removeDepot
Removes lines and inis from a model	removeLinesAndInis
Remove a peripheral compartment from a model	removePeriph
To remove transit compartments from the model	removeTransit
Remove zero-order absorption from a model	removeZeroOrderAbs
Search within a model to replace part of the model	searchReplace searchReplaceHelper
Change the default combine type for the package	setCombineType
Convert nlmixr2 simulations to Markov states	simMarkov
Simulate a Markov model broken down by ID	simMarkovId
Update an oncology xenograft model based on Simeoni 2004	updateOncologyXenograftSimeoni2004