Package: rPBK 0.2.4
rPBK: Inference and Prediction of Generic Physiologically-Based Kinetic Models
Fit and simulate any kind of physiologically-based kinetic ('PBK') models whatever the number of compartments. Moreover, it allows to account for any link between pairs of compartments, as well as any link of each of the compartments with the external medium. Such generic PBK models have today applications in pharmacology (PBPK models) to describe drug effects, in toxicology and ecotoxicology (PBTK models) to describe chemical substance effects. In case of exposure to a parent compound (drug or chemical) the 'rPBK' package allows to consider metabolites, whatever their number and their phase (I, II, ...). Last but not least, package 'rPBK' can also be used for dynamic flux balance analysis (dFBA) to deal with metabolic networks. See also Charles et al. (2022) <doi:10.1101/2022.04.29.490045>.
Authors:
rPBK_0.2.4.tar.gz
rPBK_0.2.4.zip(r-4.5)rPBK_0.2.4.zip(r-4.4)rPBK_0.2.4.zip(r-4.3)
rPBK_0.2.4.tgz(r-4.4-x86_64)rPBK_0.2.4.tgz(r-4.4-arm64)rPBK_0.2.4.tgz(r-4.3-x86_64)rPBK_0.2.4.tgz(r-4.3-arm64)
rPBK_0.2.4.tar.gz(r-4.5-noble)rPBK_0.2.4.tar.gz(r-4.4-noble)
rPBK.pdf |rPBK.html✨
rPBK/json (API)
| # Install 'rPBK' in R: |
| install.packages('rPBK', repos = c('https://virgile-baudrot.r-universe.dev', 'https://cloud.r-project.org')) |
- dataCompartment4 - An example data set with 4 compartment
- dataMaleGammarusSingle - An example data set with 1 compartment
- fitPBK_C4 - An example of fitPBK object
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 months agofrom:ab7499848a. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 10 2024 |
| R-4.5-win-x86_64 | NOTE | Sep 10 2024 |
| R-4.5-linux-x86_64 | NOTE | Sep 10 2024 |
| R-4.4-win-x86_64 | NOTE | Sep 10 2024 |
| R-4.4-mac-x86_64 | NOTE | Sep 10 2024 |
| R-4.4-mac-aarch64 | NOTE | Sep 10 2024 |
| R-4.3-win-x86_64 | NOTE | Sep 10 2024 |
| R-4.3-mac-x86_64 | NOTE | Sep 10 2024 |
| R-4.3-mac-aarch64 | NOTE | Sep 10 2024 |
Exports:dataPBKexport_interpolatefitPBKnested_modelppc
Dependencies:abindbackportsBHcallrcheckmateclicolorspacedescdistributionalfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An example data set with 4 compartment | dataCompartment4 |
| An example data set with 1 compartment | dataMaleGammarusSingle |
| Create a list giving data and parameters to use in the model inference. | dataPBK dataPBK.data.frame nested_model nested_model.stanPBKdata |
| Compute 95 credible intervals | df_quant95_ |
| Interpolate function implemented in Stan only export for checking | export_interpolate |
| Bayesian inference of TK model with Stan | fitPBK fitPBK.stanPBKdata |
| An example of fitPBK object | fitPBK_C4 |
| Plotting method for 'fitPBK' objects | plot.fitPBK |
| Posterior predictive check plot | ppc ppc.fitPBK |
