Package: nlmixr2lib 0.3.0

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]

nlmixr2lib_0.3.0.tar.gz
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nlmixr2lib.pdf |nlmixr2lib.html✨
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:https://nlmixr2.github.io

Datasets:

modeldb - Model library for nlmixr2

On CRAN:

6.24 score 5 stars 9 scripts 294 downloads 61 exports 69 dependencies

Last updated 3 months agofrom:7f1eef6135. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 06 2024
R-4.5-win	OK	Dec 06 2024
R-4.5-linux	OK	Dec 06 2024
R-4.4-win	OK	Dec 06 2024
R-4.4-mac	OK	Dec 06 2024
R-4.3-win	OK	Dec 06 2024
R-4.3-mac	OK	Dec 06 2024

Exports:addBaseline1exp addBaselineConst addBaselineExp addBaselineLin addBioavailability addCmtProp addDepot addDirectLin addDirToModelDb addDur addEffectCmtLin addEta addFileToModelDb addIndirect addIndirectLin addIni addLag addLogEstimates addRate addResErr addTransit addWeibullAbs assertCompartmentExists assertCompartmentName assertParameterValue assertRxUi assertRxUiEstimatedResiduals assertRxUiMixedOnly assertRxUiMuRefOnly assertRxUiNormal assertRxUiPopulationOnly assertRxUiPrediction assertRxUiRandomOnIdOnly assertRxUiSingleEndpoint assertRxUiTransformNormal assertVariableName blankCombine camelCombine combinePaste2 convertEmax convertEmaxHill convertKinR0 convertLogLin convertMM convertQuad defaultCombine dotCombine expit fakeCc logit modellib pkTrans readModelDb removeDepot removeLinesAndInis removeTransit searchReplace searchReplaceHelper setCombineType snakeCombine updateOncologyXenograftSimeoni2004

Dependencies:backports BH cachem checkmate cli colorspace cpp11 cpp11armadillo crayon data.table digest dparser evaluate fansi farver fastmap ggplot2 glue gtable highr inline isoband knitr labeling lattice lazyeval lbfgsb3c lifecycle lotri magrittr MASS Matrix memoise mgcv minqa munsell n1qn1 nlme nlmixr2data nlmixr2est numDeriv pillar pkgconfig PreciseSums qs R6 RApiSerialize RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel rex rlang rxode2 rxode2ll scales sitmo StanHeaders stringfish symengine sys tibble utf8 vctrs viridisLite withr xfun yaml

Creating a model library

Rendered fromcreate-model-library.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-06-29
Started: 2022-09-16

List of models

Rendered fromlist-of-models.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2023-04-22
Started: 2023-04-22

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 residual error to a model	addResErr
To add transit compartments to the model	addTransit
Converts first order absorption model to Weibull absorption model	addWeibullAbs
Combine two strings using a naming convention	combinePaste2
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
Default combine strings	blankCombine camelCombine defaultCombine dotCombine snakeCombine
Fake blank Cc for creating PD only models	fakeCc
Model library for nlmixr2	modeldb
Get the model from the model library	modellib
Change the transformation type for PK models	pkTrans
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
To remove transit compartments from the model	removeTransit
Search within a model to replace part of the model	searchReplace searchReplaceHelper
Change the default combine type for the package	setCombineType
Update an oncology xenograft model based on Simeoni 2004	updateOncologyXenograftSimeoni2004