Package: rbioacc 1.1-2

Virgile Baudrot

rbioacc: Inference and Prediction of ToxicoKinetic (TK) Models

The MOSAICbioacc application is a turnkey package providing bioaccumulation factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances. See Ratier et al. (2021) <doi:10.1101/2021.09.08.459421>.

Authors:Virgile Baudrot [aut, cre], Sandrine Charles [aut], Ophélia Gestin [ctb], Miléna Kaag [aut], Christelle Lopes [ctb], Gauthier Multari [ctb], Alain Pavé [ctb], Aude Ratier [aut], Aurélie Siberchicot [ctb]

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rbioacc.pdf |rbioacc.html✨
rbioacc/json (API)

# Install 'rbioacc' in R:
install.packages('rbioacc', repos = c('https://lbbe-software.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lbbe-software/rbioacc/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Chiro_Creuzot - Data on Chironomus with several exposure routes.
  • Chironomus_benzoapyrene - Data on Chironomus exposed to benzoapyrene
  • Exposure_Sialis_lutaria - Data on Sialis lutaria exposure time series
  • Gammarus_azoxistrobine_1d_Rosch2017 - Data on Gammarus exposed to azoxistrobine
  • Internal_Sialis_lutaria - Data on Sialis lutaria internal time series
  • Male_Gammarus_Merged - Male 'Gammarus fossarum' exposed to Hg spiked water. Three exposure concentrations were tested in triplicates. The duration of the accumulation phase is 4 days for 0.0000708021 and 0.000283208 mu g.m L^{-1} exposure concentrations, and 7 days for 0.000141604 mu g.m L^{-1} exposure concentration.
  • Male_Gammarus_Single - Bio-accumulation data set for _Gammarus fossarum_ exposed to Hg spiked water.
  • Male_Gammarus_seanine_growth - Male 'Gammarus pulex' exposed to seanine spiked water. A single exposure concentration was tested. The duration of the accumulation phase is 1.417 days. Three metabolites were quantified. The growth of organism was included.
  • Oncorhynchus_two - Data on Oncorhynchus exposition

On CRAN:

21 exports 1.39 score 81 dependencies 8 scripts 1.2k downloads

Last updated 12 months agofrom:e35af346b5. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-win-x86_64NOTEAug 27 2024
R-4.5-linux-x86_64NOTEAug 27 2024
R-4.4-win-x86_64NOTEAug 27 2024
R-4.4-mac-x86_64NOTEAug 27 2024
R-4.4-mac-aarch64NOTEAug 27 2024
R-4.3-win-x86_64NOTEAug 27 2024
R-4.3-mac-x86_64NOTEAug 27 2024
R-4.3-mac-aarch64NOTEAug 27 2024

Exports:bioacc_metriccorrMatrixcorrPlotdf_ppcdf_PriorPostequationsexposure_namesfitTKmcmcTracesmodelDatamodelData_odeplot_exposureplot_PriorPostppcpredict_manualpredict_stanpsrfquantile_tablereplace_t95waic

Dependencies:abindbackportsBHbitbit64broombroom.helperscallrcheckmateclicliprcolorspacecpp11crayondescdistributionaldplyrfansifarverforcatsgenericsGGallyggmcmcggplot2ggstatsgluegridExtragtablehavenhmsinlineisobandlabelinglabelledlatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpatchworkpillarpkgbuildpkgconfigplyrposteriorprettyunitsprocessxprogresspspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreadrrlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrzoo

Minimal Working Examples

Rendered fromMWE.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2023-09-19
Started: 2021-06-25

Tutorial

Rendered fromTutorial.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2022-01-03
Started: 2021-04-30

Readme and manuals

Help Manual

Help pageTopics
The 'rbioacc' package.rbioacc-package rbioacc
A simple implementation of to pivot_longer of tidyr.fonte
Return column matching "expw", "exps", "expf", "exppw" of a 'data.frame'.index_col_exposure
Return column matching "concX" of a 'data.frame' where X is metabolite.index_col_metabolite
Check if two vectors 'x' and y are equal after remove 'Inf'.is_equal_rmInf
Biaccumulation metricsbioacc_metric bioacc_metric.fitTK
Data on Chironomus with several exposure routes.Chiro_Creuzot
Data on Chironomus exposed to benzoapyreneChironomus_benzoapyrene
Correlations between parameters: colored matrixcorrMatrix
Correlations between parameters: pairs plotcorrPlot
PPC data.framedf_ppc df_ppc.fitTK ppc ppc.fitTK
Data frame of Posterior over Priordf_PriorPost df_PriorPost.fitTK
Equations of the mathematical model used for the fitequations
Retrieve exposure routes names from objectexposure_names
Data on Sialis lutaria exposure time seriesExposure_Sialis_lutaria
Posterior predictive checkfitTK fitTK.stanTKdataCST fitTK.stanTKdataVAR
Data on Gammarus exposed to azoxistrobineGammarus_azoxistrobine_1d_Rosch2017
Data on Sialis lutaria internal time seriesInternal_Sialis_lutaria
Male 'Gammarus fossarum' exposed to Hg spiked water. Three exposure concentrations were tested in triplicates. The duration of the accumulation phase is 4 days for 0.0000708021 and 0.000283208 mu g.m L^{-1} exposure concentrations, and 7 days for 0.000141604 mu g.m L^{-1} exposure concentration.Male_Gammarus_Merged
Male 'Gammarus pulex' exposed to seanine spiked water. A single exposure concentration was tested. The duration of the accumulation phase is 1.417 days. Three metabolites were quantified. The growth of organism was included.Male_Gammarus_seanine_growth
Bio-accumulation data set for _Gammarus fossarum_ exposed to Hg spiked water.Male_Gammarus_Single
Traces of MCMC iterationsmcmcTraces
Create a list giving data and parameters to use in the model inference.modelData modelData.data.frame
Create a list giving data and parameters to use in the model inference.modelData_ode
Data on Oncorhynchus expositionOncorhynchus_two
Plot exposure profileplot_exposure
Plot Posterior over Priorplot_PriorPost plot_PriorPost.df_PP plot_PriorPost.fitTK
Plot function for object of class 'bioaccMetric'plot.bioaccMetric
Plotting method for 'fitTK' objectsplot.fitTK
Plotting method for 'predictTK' objectsplot.predictTK plot.predictTKstan
Prediction function using 'fitTK' objectpredict.fitTK predict_manual predict_stan
Potential Scale Reduction Factors (PSRF) of the parameterspsrf
Quantiles of parametersquantile_table
Replace element of a vectorreplace_
Return the time at 95% depuration of the parent componentt95
Widely Applicable Information Criterion (WAIC)waic