What is aggregate-data modelling? | The examplomycin dataset | Computing aggregate statistics | Model definition | Assembling the study specification | Fitting | Inspecting the fit | Diagnostic plots | Where to next
Package: admixr2 0.4.1
H. van de Beek
admixr2: Aggregate Data Modelling
Fit pharmacokinetic/pharmacodynamic (PK/PD) models to aggregate-level data (mean vector and covariance matrix per study) rather than individual-level data, for meta-analysis across studies. Integrates with the 'nlmixr2'/'rxode2' ecosystem via four estimation methods: a First-Order ('FO') analytical estimator, a Monte Carlo (MC) estimator, a Gauss-Hermite quadrature ('GH') estimator, and an Iterative Reweighting Monte Carlo ('IRMC') estimator. Methods are based on Välitalo (2021) <doi:10.1007/s10928-021-09760-1>; software described in van de Beek et al. (2025) <doi:10.1007/s10928-025-10011-w>.
Authors:
admixr2_0.4.1.tar.gz
admixr2_0.4.1.zip(r-4.7-x86_64)admixr2_0.4.1.zip(r-4.7-arm64)admixr2_0.4.1.zip(r-4.6-x86_64)admixr2_0.4.1.zip(r-4.6-arm64)admixr2_0.4.1.zip(r-4.5-x86_64)
admixr2_0.4.1.tgz(r-4.6-x86_64)admixr2_0.4.1.tgz(r-4.6-arm64)admixr2_0.4.1.tgz(r-4.5-x86_64)admixr2_0.4.1.tgz(r-4.5-arm64)
admixr2_0.4.1.tar.gz(r-4.7-arm64)admixr2_0.4.1.tar.gz(r-4.7-x86_64)admixr2_0.4.1.tar.gz(r-4.6-arm64)admixr2_0.4.1.tar.gz(r-4.6-x86_64)
admixr2_0.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
admixr2/json (API)
| # Install 'admixr2' in R: |
| install.packages('admixr2', repos = c('https://leidenpharmacology.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/leidenpharmacology/admixr2/issues
Pkgdown/docs site:https://leidenpharmacology.github.io
Datasets:
- examplomycin - Examplomycin dataset
meta-analysispharmacodynamicspharmacokineticspharmacometricscpp
Last updated from:ff6f098341. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 254 | ||
| linux-devel-x86_64 | OK | 260 | ||
| source / vignettes | OK | 405 | ||
| linux-release-arm64 | OK | 235 | ||
| linux-release-x86_64 | OK | 306 | ||
| macos-release-arm64 | OK | 198 | ||
| macos-release-x86_64 | OK | 447 | ||
| macos-oldrel-arm64 | OK | 163 | ||
| macos-oldrel-x86_64 | OK | 285 | ||
| windows-devel-arm64 | OK | 309 | ||
| windows-devel-x86_64 | OK | 260 | ||
| windows-release-arm64 | OK | 280 | ||
| windows-release-x86_64 | OK | 225 | ||
| windows-oldrel-x86_64 | OK | 218 | ||
| wasm-release | OK | 189 |
Exports:adfoControladghControladirmcControladmControladmDataadmStopWorkersdatagendatagenControl
Dependencies:armadillo4rbackportsBHcachemcheckmateclicpp11cpp4rcrayondata.tabledigestdparserevaluatefarverfastmapggplot2gluegtablehighrinlineisobandknitrL0Learnlabelinglatticelbfgsb3clifecyclelotrimagrittrMASSMatrixmemoiseminqamirain1qn1nanonextnlmenlmixr2datanlmixr2estnloptrnumDerivplyrPreciseSumsqs2R6randtoolboxRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rexrlangrngWELLrxode2rxode2llS7scalessitmoStanHeadersstringfishstringistringrsymenginesysvctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Control settings for the FO (First-Order) estimator | adfoControl |
| Control settings for the Gauss-Hermite (GH) quadrature estimator | adghControl |
| Control settings for the IRMC estimator | adirmcControl |
| Control settings for the ADM estimator | admControl |
| Dummy data frame for nlmixr2 dispatch | admData |
| Stop parallel workers | admStopWorkers |
| Generate aggregate study data from (possibly different) pharmacometric models | datagen |
| Control parameters for 'datagen()' | datagenControl |
| Examplomycin dataset | examplomycin |
| Fit an aggregate data model via First-Order (FO) approximation | nlmixr2Est.adfo |
| Fit an aggregate data model via Gauss-Hermite quadrature | nlmixr2Est.adgh |
| Fit an aggregate data model via Iterative Reweighting MC (adirmc estimator) | nlmixr2Est.adirmc |
| Fit an aggregate data model via Monte Carlo (admc estimator) | nlmixr2Est.admc |
| Diagnostic plots for an admixr2 fit | plot.admFit |
| Print method for admFit objects | print.admFit |